kharchenkolab / dropest Goto Github PK
View Code? Open in Web Editor NEWPipeline for initial analysis of droplet-based single-cell RNA-seq data
License: GNU General Public License v3.0
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
License: GNU General Public License v3.0
I got below issues when trying to install the pipeline:
~/dropEst$ cmake . && make
-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- unit_test_framework
-- thread
-- system
-- log
-- iostreams
-- filesystem
-- chrono
-- date_time
-- atomic
-- log_setup
-- regex
-- Could NOT find BAMTOOLS (missing: BAMTOOLS_LIBRARY BAMTOOLS_INCLUDE_DIR)
-- Found R: /usr/lib/R
-- Configuring done
CMake Error: Unable to open check cache file for write. /home/dz33/dropEst/CMakeFiles/cmake.check_cache
The bamtools have bee installed in:
:~/dropEst$ which bamtools
/usr/bin/bamtools
Any suggestions? Thanks
Hello,
I am trying to do UMI error correction using the Bayesian correction method (I also want to note that the other correction methods used here: https://vpetukhov.github.io/dropEstAnalysis/umi_correction__umi_bmmc1.html work with no issues). When I run something similar to:
CorrectUmiSequenceErrors(method='Bayesian', return='reads',
collisions.info=collisions_info, umi.probabilities=umi_probs,
verbosity.level=2, mc.cores=30)
from the DropEstAnalysis site (https://vpetukhov.github.io/dropEstAnalysis/umi_correction__umi_bmmc1.html) I get the following error:
Error in $<-.data.frame
(*tmp*
, "IsMerged", value = logical(0)) :
replacement has 0 rows, data has 2
The actual code that I run (using my own DropSeq data which has UMI and cell BC quality tags) is:
corrected_reads$Bayesian <- holder$reads_per_umi_per_cell %>%
CorrectUmiSequenceErrors(method='Bayesian', return='reads',
collisions.info=collisions_info, umi.probabilities=umi_probs,
verbosity.level=2, mc.cores=NULL)
Walking through the various functions, I am able to get to the CorrectUmiSequenceErrorsBayesian function, which is where the error occurs.
This step works ok:
clf <- try(TrainNBClassifier(reads.per.umi.per.cb, adj.umi.num=adj.umi.num, quality.quants.num=quality.quants.num, mc.cores=mc.cores))
The error occurs here:
filt.genes <- plapply(reads.per.umi.per.cb, FilterUmisInGene, clf, correction.info$dp.matrices,
correction.info$neighb.prob.index, collisions.info, mc.cores=mc.cores)
If I look inside the FilterUmisInGene function:
I see that the error occurs in the 10th entry in my reads.per.umi.per.cb object which looks as follows:
holder$reads_per_umi_per_cell$reads_per_umi[[10]]
$CCCCCGCT
$CCCCCGCT[[1]]
[1] 1
$CCCCCGCT[[2]]
[1] 41 41 41 41 41 41 41 41
$CCCCCGCG
$CCCCCGCG[[1]]
[1] 1
$CCCCCGCG[[2]]
[1] 41 41 41 41 41 41 41 41
Within FilterUmisInGene, the error occurs in:
predictions <- PredictBayesian(classifier, classifier.df, cur.gene[not.filtered.umis], dp.matrices,
neighbours.prob.index, size.adj)
my classifier.df looks as follows (when I look here, I am guessing maybe this is where the problems arise, they are both one edit distance away from the other with the same quality and sam quality and error probs):
Base Target MinRpU MaxRpU Quality RealQualityProb ErrorQualityProb
1 CCCCCGCG CCCCCGCT 1 1 41 -0.6379865 -0.3912805
2 CCCCCGCT CCCCCGCG 1 1 41 -0.6379865 -0.3912805
classifier.dfs object is as follows:
$CCCCCGCG
MinRpUCS MaxRpU Target ErrorProb RealProb LargerNum
2 1 1 CCCCCGCG -0.3912805 -0.6379865 0
$CCCCCGCT
MinRpUCS MaxRpU Target ErrorProb RealProb LargerNum
1 1 1 CCCCCGCT -0.3912805 -0.6379865 0
err.prior.probs is as follows (where I assume the problems arise):
$CCCCCGCG
1 2
NA NA
$CCCCCGCT
1 2
NA NA
real.prior.probs is as follows:
$CCCCCGCG
[1] 0.999478247 0.000521753
$CCCCCGCT
[1] 0.9997391235 0.0002608765
When we put this into, there is a problem in the ErrorsNumMle function:
classifier.df$IsMerged <- mapply(function(e.p, r.p, df)
ErrorsNumMle(e.p, r.p, df$ErrorProb, df$RealProb, max.adj.num=classifier$MaxAdjacentUmisNum,
larger.num=df$LargerNum[1]) >= 1:nrow(df),
err.prior.probs, real.prior.probs, classifier.dfs, SIMPLIFY=F) %>% unlist()
The problem is at the end of the function:
return(which.max(log(prior.error.prob) + log(rev(prior.real.prob)) + error.part.prob + real.part.prob) - 1)
Because the prior.error.prob is NA NA this makes everything else inside NA NA and end up returning numeric(0)
Tldr: Do you have a suggested way to deal with UMIs which are a single edit distance away and have the same quality scores (which I assume results in the NA)? �Should I just return both (e.g. return(cur.gene[not.filtered.umis]) )?
If I have missed the mark here and there is another underlying issue, I would greatly appreciate any help you can offer.
The error occurs at 62%. GCC 7.1.0, boost 1.61.0. Any suggestions would be appreciated.
[ 60%] Building CXX object CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o
[ 62%] Linking CXX executable TestTools
/usr/bin/ld: warning: libboost_date_time.so.1.61.0, needed by /home/zhuqin/.local/lib/gcc/x86_64-pc-linux-gnu/7.1.0/../../../libboost_log.so, may conflict with libboost_date_time.so.5
/usr/bin/ld: warning: libboost_filesystem.so.1.61.0, needed by /home/zhuqin/.local/lib/gcc/x86_64-pc-linux-gnu/7.1.0/../../../libboost_log.so, may conflict with libboost_filesystem.so.5
/usr/bin/ld: warning: libboost_system.so.1.61.0, needed by /home/zhuqin/.local/lib/gcc/x86_64-pc-linux-gnu/7.1.0/../../../libboost_log.so, may conflict with libboost_system.so.5
/usr/bin/ld: warning: libboost_regex.so.1.61.0, needed by /home/zhuqin/.local/lib/gcc/x86_64-pc-linux-gnu/7.1.0/../../../libboost_log.so, may conflict with libboost_regex.so.5
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function _ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEmiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_.constprop.442': TestTools.cpp:(.text+0x27c): undefined reference to
boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function _ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEmiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_.constprop.441': TestTools.cpp:(.text+0x4ed): undefined reference to
boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testReadParams::test_method()': TestTools.cpp:(.text+0x29a7): undefined reference to
boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
TestTools.cpp:(.text+0x3105): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function
TestTools::testGeneMerge::test_method()':
TestTools.cpp:(.text+0x3ae9): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text+0x3d50): more undefined references to
boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' follow
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function boost::unit_test::make_test_case(boost::function<void ()()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long)': TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x22): undefined reference to
_ZN5boost9unit_test9ut_detail24normalize_test_case_nameB5cxx11ENS0_13basic_cstringIKcEE'
TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x61): undefined reference to boost::unit_test::test_case::test_case(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::function<void ()()> const&)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function
_Z41__static_initialization_and_destruction_0ii.constprop.437':
TestTools.cpp:(.text.startup+0x2b4): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::unit_test::decorator::collector&)' TestTools.cpp:(.text.startup+0x325): undefined reference to
boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x3ac): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' TestTools.cpp:(.text.startup+0x43c): undefined reference to
boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x4cc): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' TestTools.cpp:(.text.startup+0x55c): undefined reference to
boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text.startup+0x5ec): more undefined references to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' follow CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function
bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char [5]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char const*, char const (&) [5], char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA5_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA5_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO]+0xdb): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function
bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char [7]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char const*, char const (&) [7], char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA7_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA7_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO]+0xdb): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function
bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, unsigned int, int>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned int const&, char const*, int const&, char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEjiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEjiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH]+0xfa): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function
bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char [6]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char const*, char const (&) [6], char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA6_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA6_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO]+0xdb): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function
bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char [3]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char const*, char const (&) [3], char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA3_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA3_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO]+0xdb): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EEbT_RKNS_9unit_test12lazy_ostreamENSB_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSG_RKT1_SN_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EEbT_RKNS_9unit_test12lazy_ostreamENSB_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSG_RKT1_SN_]+0x11c): more undefined references to
boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' follow
collect2: error: ld returned 1 exit status
make[2]: *** [TestTools] Error 1
make[1]: *** [CMakeFiles/TestTools.dir/all] Error 2
make: *** [all] Error 2
Hello,
We have some ddSEQ data, and were interested in applying an open-source tool to generate counts from our reads. I'm assuming we would need a list of barcodes, but in theory could dropEST work for this type of droplet-based data? The library preps are organized like in the following link:
Hi, I am trying to apply your pipeline on my 10X Genomics data. When I run command for dropTaq. It didn't work for me. I don't have separate 3 files in my data as you explained in your pipeline. I am also attaching the files that I received from 10X.
I also tried to get help from dropTag but I received this error.
[sikh@login-0 dropEst]$ droptag -h
-bash: droptag: command not found
How I can fix this issue. Thanks in advance.
I am confused about the usage of dropEst about how merging data from different samples when I found that it accepts multiple bams as input.
Assume I generated two 10X libraries from two samples , I ran the cellranger then I got two bams.
The question is that should I input these two bams for dropEst if I want to analysis them as one matrix ?
Or I should merge these two matrices after dropEst and dropEstR filtered ?
Hi I am trying to compile dropEst but I am getting a strange ld error with 62%. By looking the code I can't tell any clue about what is going on. Can you help me ? Thanks!
cmake ..
-- The C compiler identification is GNU 5.5.0
-- The CXX compiler identification is GNU 5.5.0
-- Check for working C compiler: /ru-auth/local/home/linuxbrew/.linuxbrew/bin/cc
-- Check for working C compiler: /ru-auth/local/home/linuxbrew/.linuxbrew/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /ru-auth/local/home/linuxbrew/.linuxbrew/bin/c++
-- Check for working CXX compiler: /ru-auth/local/home/linuxbrew/.linuxbrew/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.67.0
-- Found the following Boost libraries:
-- filesystem
-- iostreams
-- log
-- system
-- thread
-- unit_test_framework
-- regex
-- date_time
-- log_setup
-- chrono
-- atomic
-- ** Boost Include: /ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/include
-- ** Boost Libraries: /ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib
-- ** Boost Link-Libs: /ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_filesystem-mt.so;/ru-auth/local/home/linuxbrew/.linuxb
rew/Cellar/boost/1.67.0_1/lib/libboost_iostreams-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_log-mt.so;/ru-auth/loc
al/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_system-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_
thread-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_unit_test_framework-mt.so;/ru-auth/local/home/linuxbrew/.linuxbr
ew/Cellar/boost/1.67.0_1/lib/libboost_regex-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_date_time-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_log_setup-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/[6$
ost_chrono-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_atomic-mt.so
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Found BAMTOOLS: /data_alpha/local/bioinformatic_tools/bamtools/bin/../lib/libbamtools.so
-- Found R: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so
-- Found R: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R
-- Configuring done
-- Generating done
-- Build files have been written to: /ru-auth/local/home/trezende/localPrograms/dropEst/build
make
Scanning dependencies of target DropTools
[ 1%] Building CXX object CMakeFiles/DropTools.dir/Tools/CollisionsAdjuster.cpp.o
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/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: warning: libreadline.so.6, needed by /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so,
not found (try using -rpath or -rpath-link)
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: warning: libicuuc.so.42, needed by /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so, no
t found (try using -rpath or -rpath-link)
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: warning: libicui18n.so.42, needed by /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so,
not found (try using -rpath or -rpath-link)
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_mark'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `read_history'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_attempted_
completion_over'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_completio$_append_character'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_getLocal
eByType_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_library_ve
rsion'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_open_4_2
'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_close_4_
2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_strcollI
ter_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_setStren
gth_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_attempted_
completion_function'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_completion
_matches'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_callback_h
andler_remove'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_point'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `u_getVersion_
4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_basic_word
_break_characters'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_line_buffe
r'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `uiter_setUTF8
_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `tilde_expand'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_end'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_readline_n
ame'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_free_line_
state'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_completer_
word_break_characters'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_callback_r
ead_char'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `clear_history
'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_callback_h
andler_install'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_setAttri
bute_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_sort_compl
etion_matches'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_cleanup_af
ter_signal'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `add_history'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `u_versionToSt
ring_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `history_trunc
ate_file'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_readline_s
tate'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `write_history
'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `uloc_setDefau
lt_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_done'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `stifle_histor
y'
collect2: error: ld returned 1 exit status
make[2]: *** [TestTools] Error 1
make[1]: *** [CMakeFiles/TestTools.dir/all] Error 2
make: *** [all] Error 2
I updated to the most recent version of dropEst package (0.8.0) and had successfully compiled it. When I am running the droptag with -s option, I get an extra ".params.gz" file, but not ".reads.gz" file. The documentation specifies I should use ".reads.gz" file for the -r option. Am I missing something?
Here is an example of cell names present in the generated count matrix: TGACAATACTTGATTAGAC
.
TGACAATACTT|GATTAGAC
where the last 8 letters come from barcode-2 with fixed length and the rest comes from barcode-1 with variable length. Is it correct?I am using indrop_v2 with two cell barcodes list. One for BC-1 and the other for BC-2.
Thanks.
Dear developers,
once installed dropReport.Rsc I manged to have the report in html but I cannot when I use -t option and providing the tagged rds file.
I got the following error:
label: unnamed-chunk-9 (with options)
List of 2
$ fig.width : num 5
$ fig.height: num 3
|................................... | 54%
ordinary text without R code
|..................................... | 57%
label: unnamed-chunk-10
Quitting from lines 95-97 (report.Rmd)
Error in total.reads.per.cell[merge.targets] :
invalid subscript type 'list'
Calls: ... eval -> ScorePipelineCells -> PrepareLqCellsDataPipeline
In addition: Warning messages:
1: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
2: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
3: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
4: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
5: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
6: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
7: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
8: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
9: Removed 1 rows containing missing values (geom_bar).
Execution halted
I am trying to run dropest on my .bam file generated from DropSeq and get the following error:
Start parsing of bams: 22:06:27.
Wrong quality length: 0, expected: 5
I am not sure what this is in reference to, is it something to do with my bam file? Any help would be much appreciated.
I used cmake/2.8.10.2 (cmake3 had a bug), boost 1.6.0 during compilation.
However, compiling fails at 90% (TestEstimation step) with the error below. Any ideas what might be going on?
CMakeFiles/TestEstimation.dir/Tests/TestEstimation.cpp.o:
In function
_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEliEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_.constprop.507': TestEstimation.cpp:(.text+0x448): undefined reference to
boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
...
collect2: error: ld returned 1 exit status
make[2]: *** [TestEstimation] Error 1
make[1]: *** [CMakeFiles/TestEstimation.dir/all] Error 2
make: *** [all] Error 2
I am afraid people will keep missing the barcode configs. It's commented out in the standard configs, so most will probably leave it that way (and the program will run, but the output will be worse).
Also, specifying "~/dropEst/data/barcodes/indrop_v3" doesnt' work for me .. I have to specify full path (i.e. /home/pkharchenko/dropEst/...).
Perhaps we should just have another tag and paste the whole barcode list there? Will make for an ugly xml file though.
After going through vignette , I wonder that should the UMI correction phased be done before or after QC ?
The reads_per_umi_per_cell
from dropEst is already filtered. If I perform some manual filter again and then rescued some cells not in the reads_per_umi_per_cell
, how can I get reads_per_umi_per_cell
for these rescued cells ?
Since the UMI count is the corrected count and the paper mention that
the proposed corrections can result in significantly higher expression profile correlation of cells belonging to the same cluster, compared to uncorrected molecular counts
I am wondering that do you have some specific gene examples in the specific known cell population ( CD4 in T cells for example) indicating that such correction is very important to accurate gene abundance quantification ?
Hello--I'm testing dropEst on a dataset generated with the 10X V1 chemistry (https://support.10xgenomics.com/single-cell-gene-expression/sequencing/doc/specifications-sequencing-requirements-for-single-cell-3). It seems that the V2 chemistry is the one that's specified in the 10x.xml file, and the necessary changes for V1 data aren't obvious to me.
Naively trying
barcode1_length: 0
barcode2_length: 14
umi_length: 10
r1_rc_length: 0
in the config.xml seems to stall at the reads per UMI per gene
estimation step. I'd appreciate any advice you might have!
when I type “cmake .. && make” ,errors show below, help....
-- Boost version: 1.60.0
-- Found the following Boost libraries:
-- filesystem
-- iostreams
-- log
-- system
-- thread
-- unit_test_framework
-- regex
-- date_time
-- log_setup
-- chrono
-- atomic
-- ** Boost Include: /usr/local/include
-- ** Boost Libraries: /usr/local/lib
-- ** Boost Link-Libs: /usr/local/lib/libboost_filesystem.so;/usr/local/lib/libboost_iostreams.a;/usr/local/lib/libboost_log.so;/usr/local/lib/libboost_system.so;/usr/local/lib/libboost_thread.so;/usr/local/lib/libboost_unit_test_framework.so;/usr/local/lib/libboost_regex.so;/usr/local/lib/libboost_date_time.so;/usr/local/lib/libboost_log_setup.so;/usr/local/lib/libboost_chrono.so;/usr/local/lib/libboost_atomic.so
-- Could not find libR shared library.
CMake Error at /usr/local/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find R (missing: R_LIBRARIES)
Call Stack (most recent call first):
/usr/local/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
CMake/FindR.cmake:136 (find_package_handle_standard_args)
CMake/deps.cmake:34 (find_package)
CMakeLists.txt:18 (include)
-- Configuring incomplete, errors occurred!
I have now these following files after running dropest pipeline..
https://github.com/VPetukhov/dropEstAnalysis
https://github.com/hms-dbmi/dropEst/tree/master/dropestr/vignettes
I am looking forward to.
Linker error on compilation of current code:
libEstimation.a(BamController.cpp.o): In function `Estimation::BamProcessing::BamController::parse_bam_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<c
har> > const&, std::shared_ptr<Estimation::BamProcessing::BamProcessorAbstract>&, std::shared_ptr<Estimation::BamProcessing::ReadParamsParser>&, bool) const':
BamController.cpp:(.text+0xb85): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
libEstimation.a(BamProcessorAbstract.cpp.o): In function `Estimation::BamProcessing::BamProcessorAbstract::save_alignment(BamTools::BamAlignment, std::__cxx11::basic_string<char, st
d::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::ch
ar_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
BamProcessorAbstract.cpp:(.text+0x474): undefined reference to `BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > c
onst&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
BamProcessorAbstract.cpp:(.text+0x4cf): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const
&, char*&, unsigned int const&, unsigned int&) const'
BamProcessorAbstract.cpp:(.text+0x526): undefined reference to `BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > c
onst&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
BamProcessorAbstract.cpp:(.text+0x57f): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const
&, char*&, unsigned int const&, unsigned int&) const'
BamProcessorAbstract.cpp:(.text+0x5d6): undefined reference to `BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > c
onst&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
BamProcessorAbstract.cpp:(.text+0x62f): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const
&, char*&, unsigned int const&, unsigned int&) const'
libEstimation.a(BamProcessorAbstract.cpp.o): In function `Estimation::BamProcessing::BamProcessorAbstract::update_bam(std::__cxx11::basic_string<char, std::char_traits<char>, std::a
llocator<char> > const&, BamTools::BamReader const&)':
BamProcessorAbstract.cpp:(.text+0xccb): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Bam
Tools::SamHeader const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)'
libEstimation.a(FilledBamParamsParser.cpp.o): In function `Estimation::BamProcessing::FilledBamParamsParser::get_read_params(BamTools::BamAlignment const&, Tools::ReadParameters&)':
FilledBamParamsParser.cpp:(.text+0xd2): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const
&, char*&, unsigned int const&, unsigned int&) const'
FilledBamParamsParser.cpp:(.text+0x1b2): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > cons
t&, char*&, unsigned int const&, unsigned int&) const'
libEstimation.a(ReadParamsParser.cpp.o): In function `Estimation::BamProcessing::ReadParamsParser::get_gene(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<c
har> > const&, BamTools::BamAlignment, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const':
ReadParamsParser.cpp:(.text+0xb70): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, c
har*&, unsigned int const&, unsigned int&) const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/dropest.dir/build.make:112: dropest] Error 1
make[1]: *** [CMakeFiles/Makefile2:218: CMakeFiles/dropest.dir/all] Error 2
make: *** [Makefile:95: all] Error 2
When running CorrectUmiSequenceErrors function, it occurs error
Estimating prior error probabilities...
Error in CorrectUmiSequenceErrorsBayesian(reads.per.umi.per.cb, adj.umi.num = adj.umi.num, :
Information about quality is required for UMI correction
It seems that format of reads_per_umi_per_cell is different from the example data "reads_per_umi_per_cell" in umi-correction vignette.
I tried to modify the format but failed to make the function work.
What can i do excluding run dropEst with "-u" ?
Hi,
I have run the pipeline and have gotten great data. However, I am a little but stuck trying to extract high quality cells from the filtered count matrix in R. I can see the cells qualified as high quality in dropreport, but cant seem to find cell rank in any of the rds files. Any advice on how to better extract high quality cells?
Best,
Dylan
It looks like the bzip website is currently down. Not sure if it's permanent, but for anyone else that is having the same issue I was able to install 1.0.6 with wget https://web.archive.org/web/20180624184835/http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
.
I loaded all the modules and install R packeges.
module load boost/1.54.0
module load bamtools/2.4.1
module load cmake/3.9.6
module load gcc/6.3.0
module load zlib/1.2.5
Firstly:
$ cmake . && make
......
CMake Error at CMake/deps.cmake:3 (message):
DropEst requires gcc version 4.8 or later
However, my gcc version is gcc/6.3.0. So I removed CMake/deps.cmake line "message(FATAL_ERROR "DropEst requires gcc version 4.8 or later")"
Then:
$ cmake . && make
......
[ 1%] Building CXX object CMakeFiles/DropTools.dir/Tools/CollisionsAdjuster.cpp.o
cc1plus: error: unrecognized command line option "-std=c++11"
make[2]: *** [CMakeFiles/DropTools.dir/Tools/CollisionsAdjuster.cpp.o] Error 1
make[1]: *** [CMakeFiles/DropTools.dir/all] Error 2
make: *** [all] Error 2
Does anyone meet the same problem? Thanks.
I am processing a fairly large bam file for use in velocyto, using dropEst with the -V option.
My issue is that the file is too big for my computer to process, so half the way through everything hangs and I cannot finish the processing (after a while the system hangs, then aborts the process before any output is written)...
I have tried subsampling the file using sambamba and I can run the whole thing with the smaller bam file, suggesting the issue is not in the file itself or in the way I use dropEst. My idea is therefore to split the bam file in smaller chunks, for example by splitting it by chromosome, then run dropEst on each of them then merge the output matrices in R.
Could you advise on whether this is a sensible thing to do, or whether there could be issues in proceeding in this way?
I am on Centos
I've installed boost and bamtools with linuxbrew
I've installed RInside package to a specific directory as it is said here https://www.r-bloggers.com/installing-r-packages/
Then I tried to compile dropEst and got the massage:
"CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testR::test_method()': TestTools.cpp:(.text+0x4df): undefined reference to
RInside::parseEval(std::string const&)'
TestTools.cpp:(.text+0x571): undefined reference to RInside::parseEval(std::string const&)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function
boost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring, boost::unit_test::basic_cstring, unsigned long)':
TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x26): undefined reference to boost::unit_test::ut_detail::normalize_test_case_name(boost::unit_test::basic_cstring<char const>)' libDropTools.a(Logs.cpp.o): In function
void boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator >::aligned_write<wchar_t>(wchar_t const*, long)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0xdc): undefined reference to boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::string&, unsigned long, std::locale const&)' Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x139): undefined reference to
boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::string&, unsigned long, std::locale const&)'
libDropTools.a(Logs.cpp.o): In function void boost::log::v2_mt_posix::type_dispatcher::callback_base::trampoline<boost::log::v2_mt_posix::binder1st<boost::log::v2_mt_posix::output_fun, boost::log::v2_mt_posix::expressions::aux::stream_ref<boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits<char>, std::allocator<char> > >&>, std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > >(void*, std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEESbIwSB_IwESaIwEEEEvPvRKT0_[_ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEESbIwSB_IwESaIwEEEEvPvRKT0_]+0xf9): undefined reference to
boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::string&, unsigned long, std::locale const&)'
libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE]+0xb8): undefined reference to
boost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)'
libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::try_consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE]+0xde): undefined reference to
boost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)'
libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE]+0xb8): undefined reference to
boost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)'
libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::try_consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE]+0xde): undefined reference to
boost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)'
libDropTools.a(UtilFunctions.cpp.o): In function Tools::init_r()': UtilFunctions.cpp:(.text+0x5f0): undefined reference to
RInside::parseEvalQ(std::string const&)'
/home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to
std::ios_base::failure[abi:cxx11]::what() const@GLIBCXX_3.4.21'
//home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __pthread_barrier_init@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_mutate(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::find_first_not_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::~failure()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_assign(std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/libquadmath.so.0: undefined reference to
__signgam@GLIBC_2.23'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to
std::__cxx11::collate const& std::use_facet<std::__cxx11::collate >(std::locale const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to
std::__cxx11::numpunct<wchar_t> const& std::use_facet<std::__cxx11::numpunct<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, char)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to typeinfo for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to
std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::basic_istream<char, std::char_traits<char> >& std::operator>><char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to
std::__cxx11::messages<wchar_t> const& std::use_facet<std::__cxx11::messages<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::append(char const*)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to
std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to
std::logic_error::logic_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to std::basic_istream<wchar_t, std::char_traits<wchar_t> >& std::getline<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >(std::basic_istream<wchar_t, std::char_traits<wchar_t> >&, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::compare(char const*) const@GLIBCXX_3.4.21'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::swap(std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&)@GLIBCXX_3.4.21'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::failure(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to
typeinfo for std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::failure(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::rfind(char, unsigned long) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::numpunct<char> const& std::use_facet<std::__cxx11::numpunct<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct(unsigned long, char)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::resize(unsigned long, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, wchar_t)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::invalid_argument::invalid_argument(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to
__socket@GLIBC_PRIVATE'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::logic_error::logic_error(std::logic_error const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_replace(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::collate<wchar_t> const& std::use_facet<std::__cxx11::collate<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::compare(unsigned long, unsigned long, char const*) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::out_of_range::out_of_range(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to
std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::resize(unsigned long, char)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::reserve(unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::push_back(char)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to
bool std::has_facet<std::__cxx11::messages<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
//home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __shm_directory@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_construct(unsigned long, wchar_t)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_istringstream()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::find_last_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to
std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()@GLIBCXX_3.4.21'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::compare(wchar_t const*) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to bool std::has_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to
std::ios_base::failure[abi:cxx11]::~failure()@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to
__libc_pread@GLIBC_PRIVATE'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::messages<char> const& std::use_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to
std::__cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::out_of_range::out_of_range(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::compare(std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&) const@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to
__pthread_barrier_wait@GLIBC_PRIVATE'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::_M_sync(char*, unsigned long, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find_first_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to
std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_append(wchar_t const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to
vtable for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::logic_error::logic_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::~basic_string()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to
std::overflow_error::overflow_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
//home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __recv@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_thread-mt.so: undefined reference to
std::basic_istream<char, std::char_traits >& std::getline<char, std::char_traits, std::allocator >(std::basic_istream<char, std::char_traits >&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >&, char)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::swap(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to
vtable for std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::basic_istream<wchar_t, std::char_traits<wchar_t> >& std::operator>><wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >(std::basic_istream<wchar_t, std::char_traits<wchar_t> >&, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to
std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::str() const@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
make[2]: *** [TestTools] Error 1
make[1]: *** [CMakeFiles/TestTools.dir/all] Error 2
make: *** [all] Error 2
"
hi,
I had errors with running make command:
Firstly, cmake was ran as below.
$ cmake -DCMAKE_INSTALL_PREFIX=~/local
-DCMAKE_C_COMPILER=~/local/bin/gcc
-DCMAKE_CXX_COMPILER=~/local/bin/g++
-DBOOST_ROOT=~/local/include
-DBOOST_LIBRARYDIR:PATH=~/src/boost_1_68_0/libs
-DR_EXECUTABLE=~/local/bin/R
-DR_ROOT=~/local/bin/R
-DR_LIB_DIRS=~/local/lib64/R/lib
-DR_LIBRARIES=~/local/lib64/R/lib/libR.so
-DBAMTOOLS_ROOT=~/local/include
-DRINSIDE_INCLUDE_DIR=~/local/lib64/R/library/RInside/include
-DRINSIDE_LIBRARY=~/local/lib64/R/library/RInside/lib/libRInside.a
-DR_CORE_LIBRARY=~/local/lib64/R/library
-DLIBR_CORE_LIBRARY=~/local/lib64/R/library
-DR_INCLUDE_DIRS=~/local/lib64/R/include
-DRCPP_INCLUDE_DIR=~/local/lib64/R/library/Rcpp/include
-DRCPP_EIGEN_INCLUDE_DIR=~/local/lib64/R/library/RcppEigen/include
-DR_MATRIX_PKG=~/local/lib64/R/library/Matrix ..
It completed without errors.
Then, I ran make command, and got below error.
[ 84%] Linking CXX executable TestTools
/usr/bin/ld: warning: libboost_date_time.so.1.68.0, needed by /lustre4/home/akimitsu-lab/local/bin/../lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../libboost_log.so, may conflict with libboost_date_time.so.5
/usr/bin/ld: warning: libboost_filesystem.so.1.68.0, needed by /lustre4/home/akimitsu-lab/local/bin/../lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../libboost_log.so, may conflict with libboost_filesystem.so.5
/usr/bin/ld: warning: libboost_system.so.1.68.0, needed by /lustre4/home/akimitsu-lab/local/bin/../lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../libboost_log.so, may conflict with libboost_system.so.5
/usr/bin/ld: warning: libboost_regex.so.1.68.0, needed by /lustre4/home/akimitsu-lab/local/bin/../lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../libboost_log.so, may conflict with libboost_regex.so.5
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEmiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_.constprop.548':
TestTools.cpp:(.text+0x1fe): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `TestTools::testEditDistance::test_method()':
TestTools.cpp:(.text+0xde6): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `TestTools::testReadParams::test_method()':
TestTools.cpp:(.text+0x2f40): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `TestTools::testRelativePaths::test_method()':
TestTools.cpp:(.text+0x3ce9): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
TestTools.cpp:(.text+0x3eb7): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text+0x46d0): more undefined references to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' follow
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `boost::unit_test::lazy_ostream_impl<boost::unit_test::lazy_ostream, boost::test_tools::tt_detail::print_helper_t<bool>, boost::test_tools::tt_detail::print_helper_t<bool> const&>::operator()(std::ostream&) const':
TestTools.cpp:(.text._ZNK5boost9unit_test17lazy_ostream_implINS0_12lazy_ostreamENS_10test_tools9tt_detail14print_helper_tIbEERKS6_EclERSo[_ZNK5boost9unit_test17lazy_ostream_implINS0_12lazy_ostreamENS_10test_tools9tt_detail14print_helper_tIbEERKS6_EclERSo]+0x29): undefined reference to `boost::test_tools::tt_detail::print_log_value<bool>::operator()(std::ostream&, bool)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `_ZN9TestTools14testReadParams11test_methodEv.cold.559':
TestTools.cpp:(.text.unlikely+0x63b): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `boost::unit_test::make_test_case(boost::function<void ()()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long)':
TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x25): undefined reference to `_ZN5boost9unit_test9ut_detail24normalize_test_case_nameB5cxx11ENS0_13basic_cstringIKcEE'
TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x72): undefined reference to `boost::unit_test::test_case::test_case(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::function<void ()()> const&)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `_Z41__static_initialization_and_destruction_0ii.constprop.538':
TestTools.cpp:(.text.startup+0x233): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::unit_test::decorator::collector&)'
TestTools.cpp:(.text.startup+0x2ba): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x361): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x409): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x4b1): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x559): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text.startup+0x601): more undefined references to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' follow
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char [5]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*, char const (&) [5], char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA5_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA5_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_]+0x120): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char [7]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*, char const (&) [7], char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA7_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA7_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_]+0x120): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, unsigned int, int>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned int const&, char const*, int const&, char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEjiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEjiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_]+0x11a): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char [6]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*, char const (&) [6], char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA6_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA6_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_]+0x120): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char [3]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*, char const (&) [3], char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA3_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA3_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_]+0x120): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EEbT_RKNS_9unit_test12lazy_ostreamENSB_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSG_RKT1_SN_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EEbT_RKNS_9unit_test12lazy_ostreamENSB_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSG_RKT1_SN_]+0x121): more undefined references to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' follow
collect2: error: ld returned 1 exit status
make[2]: *** [TestTools] error 1
make[1]: *** [CMakeFiles/TestTools.dir/all] error 2
make: *** [all] error 2
anyone helps?
Thanks!
I have successfully run dropEst (v0.8.3) on my .bam file generated by 10X cellranger (2.1.1)
the command is
dropest -f -w -u -V -G 20 -c /home/reprod/bin/dropEst/configs/10x.xml ./possorted_genome_bam.bam
Log file looks good with no serious problem.
dropest -f -w -u -V -G 20 -c /home/reprod/bin/dropEst/configs/10x.xml ./possorted_genome_bam.bam
Version: 0.8.3.
Run: 07/18/2018 21:19:30.
No merge selected.
Start parsing of bams: 21:19:30.
ERROR: can't find chromosome, id: -1
./possorted_genome_bam.bam: 4673842 total reads; 26.6% intergenic; 68.2% touch exon; 0% touch intron; 0% touch not annotated regions; can't parse 0.0305316% reads; 348073 CBs read
Bams parsed: 21:20:23.
13075 CBs with more than 20 genes
top CBs:
1531 CAGCGACCATGTCCTC
1504 ACAGCTAGTAAATGTG
1494 GACGTTAAGCCAGGAT
1448 GTTCGGGAGGGTTTCT
1422 CACACCTCAGCATGAG
1417 GAGGTGAGTTTGGGCC
1376 ACACCAATCTCTTATG
1357 CTAATGGAGAAGGACA
1353 TCAGGTATCTGTCTCG
Start merge: 21:20:23.
Merge initialized: 21:20:23.
Merge finished: 21:20:23.
Start UMI merge: 21:20:23.
13075 cells processed. Merged 58 UMIs from 58 cells.
UMI merge finished: 21:20:24.
13075 cells are considered as real.
13075 CBs with more than 20 genes, which have UMIs of the requested type.
top CBs:
1531 CAGCGACCATGTCCTC
1504 ACAGCTAGTAAATGTG
1494 GACGTTAAGCCAGGAT
1448 GTTCGGGAGGGTTTCT
1422 CACACCTCAGCATGAG
1417 GAGGTGAGTTTGGGCC
1376 ACACCAATCTCTTATG
1357 CTAATGGAGAAGGACA
1353 TCAGGTATCTGTCTCG
Done: 21:20:25.
20783 genes
top genes:
ENSG00000122304 42526
ENSG00000175646 21533
ENSG00000065978 9621
ENSG00000106013 7076
ENSG00000167468 7074
ENSG00000010318 6500
ENSG00000163467 6138
ENSG00000167526 6100
ENSG00000170315 5772
ENSG00000198804 5054
Compiling diagnostic stats:
Reads per chromosome per cell;
Fill exon results
Fill intron results
Fill intergenic results
Saturation info;
Mean reads per UMI;
Merge targets;
Completed.
Compiling raw count matrix: 21:20:29.
20783 genes, 13075 cells.
Done: 21:20:29.
Compiling filtered count matrix: 21:20:29.
20783 genes, 13075 cells.
Done: 21:20:30.
Writing R data to cell.counts.rds ...: 21:20:30.
Completed: 21:20:39.
Writing cell.counts.mtx ...
Completed.
Compiling intron/exon matrices: 21:20:40.
Exon
20783 genes, 13075 cells.
Intron
0 genes, 13075 cells.
Intron/exon spanning
0 genes, 13075 cells.
Done: 21:20:42.
Writing R data to cell.counts.matrices.rds ...: 21:20:42.
Completed: 21:20:43.
All done: 21:20:45.
However, command dropReport.Rsc ./cell.counts.rds
ran with error:
Quitting from lines 118-122 (report.Rmd)
Error: 'ds.mincount' is not an exported object from 'namespace:preseqR'
In addition: Warning messages:
1: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
2: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
3: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
4: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
5: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
6: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
7: In GetUmisDistributionOld(reads.per.umi.per.cb, smooth = smooth) :
UMIs distribution is empty
8: Removed 2 rows containing missing values (geom_bar).
9: In PredictKDE(clf, bc.df.pca, bandwidth.mult = kde.bandwidth.mult) :
Found 2 points with 0 density. Either it's outliers or you should increase bandwidth. Setting score for these points to 0.5.
Execution halted
Some results have been generated. One of them appears wrong.
So I guess it may be caused by the cell.counts.rds. It does not have reads_per_umi_per_cell.
This problem appeared in the older version #29 . And I tried to re-run dropEst but the cell.counts.rds but it had no change
Here is the fields in cell.counts.rds
d <- readRDS("./cell.counts.rds")
names(d)
[1] "cm" "cm_raw" "reads_per_chr_per_cells" "mean_reads_per_umi"
[5] "saturation_info" "merge_targets" "aligned_reads_per_cell" "aligned_umis_per_cell"
[9] "requested_umis_per_cb" "requested_reads_per_cb"
Hi @VPetukhov ,
I am trying to use DropEst with one of the 10x datasets from here.
I downloaded the BAM from the above link and used dropest -f
mode to generate the count matrix and the rds
file for the downstream UMI correction. Unfortunately I am noob in R and just copy pasting code from this tutorial. I have got a couple of question regarding the working of dropEst pipeline:
dropest
command do before generating the count matrix? I am guessing it simply count the tags from the BAM if I don't give either -m
or -M
?dropestr
R package following the above tutorial it seems to give good umi distribution till here. But once I try to use the functioncollisions_info <- FillCollisionsAdjustmentInfo(umi_probabilities, max_umi_per_gene, step=20, mc.cores=5, verbose=T)
the program give following error
> FillCollisionsAdjustmentInfo(umi_probabilities, max_umi_per_gene, step=20, mc.cores=5, verbose=T)
Error in FillCollisionsAdjustmentInfo(umi_probabilities, max_umi_per_gene, :
unused arguments (step = 20, mc.cores = 5, verbose = T)
So I removed step = 20, mc.cores = 5, verbose = T
but it has been 3 days now and the program won't finish.
What am I doing wrong? Thanks again for your help.
my config.xml
<config>
<!-- droptag -->
<TagsSearch>
<protocol>10x</protocol>
<BarcodesSearch>
<barcode1_length>8</barcode1_length>
<barcode2_length>16</barcode2_length>
<umi_length>10</umi_length>
<r1_rc_length>0</r1_rc_length>
</BarcodesSearch>
<Processing>
<min_align_length>10</min_align_length>
<reads_per_out_file>10000000</reads_per_out_file>
<poly_a_tail>AAAAAAAA</poly_a_tail>
</Processing>
</TagsSearch>
<!-- dropest -->
<Estimation>
<Merge>
<barcodes_file>/mnt/scratch5/avi/dropest_data/barcodes.tsv</barcodes_file>
<barcodes_type>const</barcodes_type>
<min_merge_fraction>0.2</min_merge_fraction>
<max_cb_merge_edit_distance>2</max_cb_merge_edit_distance>
<max_umi_merge_edit_distance>1</max_umi_merge_edit_distance>
<min_genes_after_merge>100</min_genes_after_merge>
<min_genes_before_merge>20</min_genes_before_merge>
</Merge>
<PreciseMerge>
<max_merge_prob>1e-5</max_merge_prob>
<max_real_merge_prob>1e-7</max_real_merge_prob>
</PreciseMerge>
</Estimation>
<BamTags> <!-- Optional. Tags, which are used to parse .bam file (-f option) or to print tagged .bam file (-b or -F options). Default values correspond to 10x protocol. -->
<cb>CB</cb> <!-- Cell barcode. Default: CB. -->
<cb_raw>CR</cb_raw> <!-- Cell barcode raw. Used only for bam output. Default: CR. -->
<umi>UB</umi> <!-- UMI. Default: UB. -->
<umi_raw>UR</umi_raw> <!-- UMI raw. Used only for bam output. Default: UR. -->
<gene>GX</gene> <!-- Gene id. Default: GX. -->
<cb_quality>CQ</cb_quality> <!-- Cell barcode quality. Default: CQ. -->
<umi_quality>UQ</umi_quality> <!-- UMI quality. Default: UQ. -->
</BamTags>
</config>
Can anyone tell me why I get this error when I run Dropest on a 10x aligned bam file? I have configured everything correctly, I assume.
After running dropEst the final output was empty. Can you help me ? This is the command I tried:
dropest -m -f -L eiEIBA -V -o run1 -g /home/trezende/cellranger/genes/genes.gtf -c /home/trezende/dropEst/c
onfigs/indrop_v3.xml IEL.bam LPL.bam MLN.bam
Version: 0.8.3.
Run: 09/14/2018 00:12:21.
Real CBs merge selected.
Start parsing of bams: 00:12:21.
WARNING: Can't find chromosome 'JH584301.1'
WARNING: Can't find chromosome 'GL456379.1'
WARNING: Can't find chromosome 'GL456393.1'
WARNING: Can't find chromosome 'GL456366.1'
WARNING: Can't find chromosome 'GL456367.1'
WARNING: Can't find chromosome 'GL456239.1'
WARNING: Can't find chromosome 'GL456213.1'
WARNING: Can't find chromosome 'GL456383.1'
WARNING: Can't find chromosome 'GL456378.1'
WARNING: Can't find chromosome 'GL456372.1'
WARNING: Can't find chromosome 'GL456370.1'
WARNING: Can't find chromosome 'GL456390.1'
WARNING: Can't find chromosome 'GL456392.1'
WARNING: Can't find chromosome 'GL456382.1'
WARNING: Can't find chromosome 'GL456396.1'
WARNING: Can't find chromosome 'GL456368.1'
ERROR: can't find chromosome, id: -1
IEL.bam: 70488019 total reads; 8.1% intergenic; 57.8% touch exon; 16.7% touch intron; 0.682% touch not annotated regions; can't parse
1.48036% reads; 183545 CBs read
WARNING: Can't find chromosome 'JH584301.1'
WARNING: Can't find chromosome 'JH584300.1'
WARNING: Can't find chromosome 'JH584302.1'
WARNING: Can't find chromosome 'GL456379.1'
WARNING: Can't find chromosome 'GL456366.1'
WARNING: Can't find chromosome 'GL456367.1'
WARNING: Can't find chromosome 'GL456239.1'
WARNING: Can't find chromosome 'GL456213.1'
WARNING: Can't find chromosome 'GL456383.1'
WARNING: Can't find chromosome 'GL456378.1'
WARNING: Can't find chromosome 'GL456372.1'
WARNING: Can't find chromosome 'GL456370.1'
WARNING: Can't find chromosome 'GL456390.1'
WARNING: Can't find chromosome 'GL456392.1'
WARNING: Can't find chromosome 'GL456382.1'
WARNING: Can't find chromosome 'GL456396.1'
ERROR: can't find chromosome, id: -1 [123/9987]
LPL.bam: 113802132 total reads; 8.32% intergenic; 55.7% touch exon; 18.2% touch intron; 0.671% touch not annotated regions; can't par
se 1.51082% reads; 320152 CBs read
WARNING: Can't find chromosome 'JH584301.1'
WARNING: Can't find chromosome 'GL456379.1'
WARNING: Can't find chromosome 'GL456366.1'
WARNING: Can't find chromosome 'GL456367.1'
WARNING: Can't find chromosome 'GL456213.1'
WARNING: Can't find chromosome 'GL456383.1'
WARNING: Can't find chromosome 'GL456378.1'
WARNING: Can't find chromosome 'GL456372.1'
WARNING: Can't find chromosome 'GL456370.1'
WARNING: Can't find chromosome 'GL456390.1'
WARNING: Can't find chromosome 'GL456392.1'
WARNING: Can't find chromosome 'GL456382.1'
WARNING: Can't find chromosome 'GL456368.1'
ERROR: can't find chromosome, id: -1
MLN.bam: 140551180 total reads; 8.57% intergenic; 54.9% touch exon; 18.4% touch intron; 0.703% touch not annotated regions; can't par
se 1.51098% reads; 399448 CBs read
Bams parsed: 00:59:37.
121907 CBs with more than 20 genes
top CBs:
4440 GTCTCGTGTATTCGTG-1
4303 TTTCCTCAGGCTAGCA-1
4195 TGAGAGGCAAACTGTC-1
4161 CCGTGGAGTCTCACCT-1
3866 CAGCTGGCACATTAGC-1
3843 ATCATCTAGAGACTTA-1
3839 GTCTTCGGTCGACTAT-1
3799 CACTCCATCCAGAAGG-1
3798 CTTCTCTCACATCCGG-1
Start merge: 00:59:53.
Merge initialized: 00:59:53.
Total 100000 tags processed
Total 0 cells merged
Total 121907 cells excluded
Merge finished: 01:01:00.
Merge UMIs with N's: 01:01:00.
0 cells processed. Merged 0 UMIs from 0 cells.
UMI merge finished: 01:01:00.
0 cells are considered as real.
0 CBs with more than 100 genes, which have UMIs of the requested type.
no valid CBs found
Done: 01:01:15.
The following run (log):
cat est_main.log
/home/cl266/dropEst/dropest -m -V -r drop/dlib27.FC04320.L001.params.gz drop/dlib27.FC04320.L002.params.gz drop/dlib27.FC04320.L003.params.gz drop/dlib27.FC04320.L004.params.gz -g drop.reference.wo.pseudo/mm10.with.compact.transgenes.filtered.20180315.gtf -o drop/dlib27.out/cell.counts.bcconfig.rds -c /home/cl266/dropEst/configs/indrop_v3_with_barcodes.xml drop/dlib27.out/Aligned.out.sorted.bam
Version: 0.8.3.
produces this immediate error:
Error in intToUtf8(8216) :
3 arguments passed to .Internal(intToUtf8) which requires 2
In addition: Warning message:
package "methods" in options("defaultPackages") was not found
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
there is no .Internal function 'sorted_fpass'
Fatal error: unable to initialize the JIT
I am wondering whether it had to do with updating the R to 3.5.1. I tried to do all package updates but produces the same error. Would there by a workaround?
hi,
I had some errors with boost :
cmake -DBAMTOOLS_ROOT=/BIGDATA1/cygene_sydu_1/local/usr/local -DBOOST_ROOT=/BIGDATA1/cygene_sydu_1/local ..
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
CMake Error at /BIGDATA1/app/cmake/3.10.1-gcc-4.8.5/share/cmake-3.10/Modules/FindBoost.cmake:1928 (message):
Unable to find the requested Boost libraries.
Boost version: 1.60.0
Boost include path: /BIGDATA1/cygene_sydu_1/local/include
Could not find the following Boost libraries:
boost_filesystem
boost_log
boost_system
boost_thread
boost_unit_test_framework
Some (but not all) of the required Boost libraries were found. You may
need to install these additional Boost libraries. Alternatively, set
BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT
to the location of Boost.
Call Stack (most recent call first):
CMake/deps.cmake:19 (find_package)
CMakeLists.txt:18 (include)
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found BAMTOOLS: /BIGDATA1/cygene_sydu_1/local/usr/local/bin/../lib64/libbamtools.a
-- Found R: /BIGDATA1/cygene_sydu_1/R/3.4/lib64/R/lib/libR.so
-- Found R: /BIGDATA1/cygene_sydu_1/R/3.4/lib64/R
-- Configuring incomplete, errors occurred!
See also "/BIGDATA1/cygene_sydu_1/software/dropEst-master/build/CMakeFiles/CMakeOutput.log".
See also "/BIGDATA1/cygene_sydu_1/software/dropEst-master/build/CMakeFiles/CMakeError.log".
I install boost followed by the user's guide like this :
./bootstrap.sh --with-libraries=filesystem,iostreams,log,system,thread,test
./b2 cxxflags="-std=c++11" include="$LOCAL_LIBS/include/" search="$LOCAL_LIBS/lib/" link=shared threading=multi install --prefix=$LOCAL_LIBS
anyone helps? Thanks!
Hello, I keep gettting this error when I'm compiling dropEst. Has anyone seen this error before, thank you!
libDropTools.a(UtilFunctions.cpp.o): In function Tools::init_r()':
UtilFunctions.cpp:(.text+0x747): undefined reference toRInside::instancePtr()'
UtilFunctions.cpp:(.text+0x797): undefined reference to RInside::parseEvalQ(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
UtilFunctions.cpp:(.text+0x7e0): undefined reference toRInside::RInside(int, char const* const*, bool, bool, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [droptag] Error 1
make[1]: *** [CMakeFiles/droptag.dir/all] Error 2
make: *** [all] Error 2
Dear developers,
I got this error at the end of the procedure and I don't know how to solve it:
./dropReport.Rsc SRR1784313.est.rds -o $HOME/report.html
processing file: report.Rmd
|.. | 3%
inline R code fragments
|.... | 6%
label: unnamed-chunk-1 (with options)
List of 1
$ include: logi FALSE
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> library
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'report.knit.md': Permission denied
Execution halted
PS: I am using the docker image for debyan.
Can you help me, please?
Long version of u/--merge-umi parameter is not recognised, short one works fine
Dear dropEst developer, I confronted an error to install dropEst at the step of
Linking CXX executable TestEstimation
.
It seems that the error may relate to the following error. But I am not sure how to fix this, any suggestions?
/usr/bin/ld: warning: liblzma.so.5, needed by /net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so, not found (try using -rpath or -rpath-link)```
[ 11%] Built target DropTools
[ 65%] Built target Estimation
[ 88%] Built target TagsSearch
Linking CXX executable TestEstimation
/usr/bin/ld: warning: libpcre.so.1, needed by /net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: liblzma.so.5, needed by /net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so, not found (try using -rpath or -rpath-link)
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_fullinfo'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_lzma_preset@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_alone_decoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_crc64@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_raw_encoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_config'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_code@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_stream_decoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_free'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_raw_decoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_free_study'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_assign_jit_stack'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_exec'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_version_string@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_maketables'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_stream_encoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_compile'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_study'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_version'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_end@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
collect2: error: ld returned 1 exit status
make[2]: *** [TestEstimation] Error 1
make[1]: *** [CMakeFiles/TestEstimation.dir/all] Error 2
make: *** [all] Error 2
Not really sure these are issues but might be useful for future reference.
[ 61%] Linking CXX executable TestTools
/usr/lib/R/lib/libR.so: undefined reference to `GOMP_parallel@GOMP_4.0'
Fixed this by editing line 7 of CMakeLists.txt to include '-fopenmp':
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -m64 -DBOOST_LOG_DYN_LINK -std=c++11 -Wno-attributes -Wno-deprecated -Wno-deprecated-declarations")
Also, when having previously installed the software GMAP/GSNAP it seems to add two files in /usr/local/include/ - except.h and assert.h which causes the below errors, until they are removed .
from /home/transcriptomics/software/dropEst/Tools/ReadParameters.cpp:1:
/usr/local/include/except.h:15:32: error: conflicting declaration ‘typedef struct Except_Frame_T* Except_Frame_T’
typedef struct Except_Frame_T *Except_Frame_T;
^
/usr/local/include/except.h:15:16: note: previous declaration as ‘struct Except_Frame_T’
typedef struct Except_Frame_T *Except_Frame_T;
^
/usr/local/include/except.h:17:18: error: field ‘prev’ has incomplete type ‘Except_Frame_T’
Except_Frame_T prev;
^
/usr/local/include/except.h:16:8: note: definition of ‘struct Except_Frame_T’ is not complete until the closing brace
struct Except_Frame_T {
^
CMakeFiles/DropTools.dir/build.make:62: recipe for target 'CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o' failed
make[2]: *** [CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o] Error 1
CMakeFiles/Makefile2:179: recipe for target 'CMakeFiles/DropTools.dir/all' failed
make[1]: *** [CMakeFiles/DropTools.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2
master@transcriptomics:/ho
and
/usr/local/include/assert.h:5:20: fatal error: except.h: No such file or directory
compilation terminated.
CMakeFiles/DropTools.dir/build.make:62: recipe for target 'CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o' failed
make[2]: *** [CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o] Error 1
CMakeFiles/Makefile2:179: recipe for target 'CMakeFiles/DropTools.dir/all' failed
make[1]: *** [CMakeFiles/DropTools.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2
Hello,
I have a BAM from cellranger 10x tool. I would like to use it for velocyto and therefore want to create input file using dropest.
Here is the command I use:
dropest -f -c 10x.xml 10x_001/001_possorted_genome_bam.bam
it runs successfully and created cell.counts.matrices.rds and cell.counts.rds files. The matrix only contains Exonic reads info and when I load the cell.counts.matrices.rds file for velocity it doesnt work as there is no data for intronic and intergenic.
Although I looked my BAM and found the reads for intronic and intergenic regions.
Any idea why dropest only selecting exonic reads?
Many thanks.
Hi,
Thank you for developing this excellent tool. I am trying to use dropTag to demultiplex fastq files generated by inDrop v1. The command line I am using is the following:
../dropEst/droptag -c ../dropEst/configs/indrop_v1_2.xml -l log.file.name -p 8 -S file_1.fastq.gz file_2.fastq.gz
Note that file_1.fastq.gz corresponds to the barcodes file and file_2.fatsq.gz corresponds to the gene reads file.
However, I am only getting a single tagged file called file_2.fastq.gz.tagged.1.fastq.gz instead of getting multiple demultiplexed files. Can I instead get two files for each cell, one corresponding to the demultiplexed barcode file, and the other to the demultiplexed gene reads file?
Thank you in advance!
Best,
Leon
Hi,
I'm trying DropEst in the 10X scRNAseq data (https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/neurons_900) for velocyto on Docker. But there is no result file after running.
My code is following:
dropest -V -f -g refdata-cellranger-mm10-1.2.0/genes/genes.gtf -c config_desc.xml neurons_900_possorted_genome_bam.bam
and standard output is following:
Version: 0.8.3.
Run: 07/13/2018 09:30:55.
config_desc.xml(43): expected =
Could you help me?
Hi,
In my lab, we sequenced for the first time some libraries by using the SeqWell protocol.
Then I ran the Dropseq pipeline to get my count matrix. But, I would like to have some statistics about the mapping, for example number of exonic, intronic and intergenic reads.
After the alignment step I got a unique bam file for all barcodes. Is there a way to run dropEst with this bam file to get these statistics per CB?
Thank you,
Elisabetta
my command is
/dropest -w -m -r sample8.params.gz sample7.params.gz sample6.params.gz sample5.params.gz sample4.params.gz sample3.params.gz sample2.params.gz sample1.params.gz -g /home/dushiyi/database/refdata-cellranger-GRCh38-1.2.0/genes/genes.gtf -c /cygene/work/02.dropEst/10x.test.xml ../02_alignment/Aligned.out.bam
while the output is :
../02_alignment/Aligned.out.bam: 400000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.489% touch not annotated regions; can't parse 0.0792053% reads; 7678441 CBs read
../02_alignment/Aligned.out.bam: 410000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.487% touch not annotated regions; can't parse 0.078822% reads; 7874334 CBs read
WARNING: Can't find chromosome 'KI270510.1'
../02_alignment/Aligned.out.bam: 420000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.485% touch not annotated regions; can't parse 0.0784669% reads; 8050887 CBs read
../02_alignment/Aligned.out.bam: 430000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.483% touch not annotated regions; can't parse 0.078086% reads; 8214251 CBs read
../02_alignment/Aligned.out.bam: 440000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.481% touch not annotated regions; can't parse 0.0777873% reads; 8365859 CBs read
std::bad_alloc
and the result is
$ cat cell.counts.mtx
%%MatrixMarket matrix coordinate pattern symmetric
0 0 0
what's wrong with me? The step1 dropTag
and step 2 alignment
are all correct.
When I run the code from the vignette for UMI correction,
I get the following error:
> CorrectUmiSequenceErrors(d, umi_probabilities, collisions_info,
+ method = "Bayesian",
+ mc.cores=NULL, verbosity.level=2)
Correcting UMI sequence errors.
Filling info about adjacent UMIs...0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Completed.
Completed.
Estimating prior error probabilities...Error in reads.per.umi.per.cb[[1]][[1]][[2]] : subscript out of bounds
Another error with classic method:
CorrectUmiSequenceErrors(d, umi_probabilities, collisions_info, correction_info, adjust.collisions=TRUE, quality.quants.num=10, mc.cores=NULL, verbosity.level=3, return='matrix', distribution.smooth=10, method='Classic', mult=1)
Correcting UMI sequence errors.
Error in FUN(X[[i]], ...) : Not compatible with STRSXP: [type=NULL].
When I looked into the code, essentially the d$reads_per_umi
does not have a training set. Maybe related to recent update of the code?
Also, this might be related, when I compare my UMI counts from a standard Indrops v3 run to that of from dropEst
, roughly I see double the number for the dropEst
(before UMI correction, which I cannot run). Is this a normal situation?
Thank you very much!
Hi,
I've been trying to build dropEst, but I keep running against these errors:
Scanning dependencies of target droptag
[ 34%] Building CXX object CMakeFiles/droptag.dir/droptag.cpp.o
[ 36%] Linking CXX executable droptag
libDropTools.a(Logs.cpp.o): In function `boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::consume(boost::log::v2_mt_posix::record_view const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE]+0x2ba): undefined reference to `boost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
libDropTools.a(Logs.cpp.o): In function `boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::consume(boost::log::v2_mt_posix::record_view const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE]+0x2ba): undefined reference to `boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char>::consume(boost::log::v2_mt_posix::record_view const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
libDropTools.a(Logs.cpp.o): In function `void boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits<char>, std::allocator<char> >::aligned_write<wchar_t>(wchar_t const*, long)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x77): undefined reference to `boost::log::v2_mt_posix::aux::code_convert(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::locale const&)'
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0xf1): undefined reference to `boost::log::v2_mt_posix::aux::code_convert(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::locale const&)'
libDropTools.a(Logs.cpp.o): In function `void boost::log::v2_mt_posix::type_dispatcher::callback_base::trampoline<boost::log::v2_mt_posix::binder1st<boost::log::v2_mt_posix::output_fun, boost::log::v2_mt_posix::expressions::aux::stream_ref<boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits<char>, std::allocator<char> > >&>, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > >(void*, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEENSt7__cxx1112basic_stringIwSB_IwESaIwEEEEEvPvRKT0_[_ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEENSt7__cxx1112basic_stringIwSB_IwESaIwEEEEEvPvRKT0_]+0x5e): undefined reference to `boost::log::v2_mt_posix::aux::code_convert(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::locale const&)'
libDropTools.a(Logs.cpp.o): In function `boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::try_consume(boost::log::v2_mt_posix::record_view const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE]+0x2d8): undefined reference to `boost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
libDropTools.a(Logs.cpp.o): In function `boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::try_consume(boost::log::v2_mt_posix::record_view const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE]+0x2d8): undefined reference to `boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char>::consume(boost::log::v2_mt_posix::record_view const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
collect2: error: ld returned 1 exit status
make[2]: *** [droptag] Error 1
make[1]: *** [CMakeFiles/droptag.dir/all] Error 2
make: *** [all] Error 2
This was my configuration output:
/share/pkg/cmake/3.10.0/install/bin/cmake \
> -DCMAKE_C_COMPILER=/share/pkg/gcc/7.2.0/install/bin/gcc \
> -DCMAKE_CXX_COMPILER=/share/pkg/gcc/7.2.0/install/bin/g++ \
> -D R_ROOT="/share/pkg/r/3.4.2/install/lib64/R" \
> -D BOOST_ROOT="/share/pkg/boost/1.57.0/install" \
> .
-- The C compiler identification is GNU 7.2.0
-- The CXX compiler identification is GNU 7.2.0
-- Check for working C compiler: /share/pkg/gcc/7.2.0/install/bin/gcc
-- Check for working C compiler: /share/pkg/gcc/7.2.0/install/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /share/pkg/gcc/7.2.0/install/bin/g++
-- Check for working CXX compiler: /share/pkg/gcc/7.2.0/install/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.57.0
-- Found the following Boost libraries:
-- filesystem
-- iostreams
-- log
-- system
-- thread
-- unit_test_framework
-- regex
-- log_setup
-- date_time
-- chrono
-- atomic
-- ** Boost Include: /share/pkg/boost/1.57.0/install/include
-- ** Boost Libraries: /share/pkg/boost/1.57.0/install/lib
-- ** Boost Link-Libs: /share/pkg/boost/1.57.0/install/lib/libboost_filesystem.so;/share/pkg/boost/1.57.0/install/lib/libboost_iostreams.so;/share/pkg/boost/1.57.0/install/lib/libboost_log.so;/share/pkg/boost/1.57.0/install/lib/libboost_system.so;/share/pkg/boost/1.57.0/install/lib/libboost_thread.so;/share/pkg/boost/1.57.0/install/lib/libboost_unit_test_framework.so;/share/pkg/boost/1.57.0/install/lib/libboost_regex.so;/share/pkg/boost/1.57.0/install/lib/libboost_log_setup.so;/share/pkg/boost/1.57.0/install/lib/libboost_date_time.so;/share/pkg/boost/1.57.0/install/lib/libboost_chrono.so;/share/pkg/boost/1.57.0/install/lib/libboost_atomic.so
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Found BAMTOOLS: /share/pkg/bamtools/2.4.0/install/bin/../lib/libbamtools.so
-- Found R: /share/pkg/r/3.4.2/install/lib64/R/lib/libR.so
-- Found R: /share/pkg/r/3.4.2/install/lib64/R
-- Configuring done
-- Generating done
-- Build files have been written to: /my/path/dropEst/dropEst
Any advice?
Hi,
after built the docker image I was not able to run it since I got following error:
docker run -ti --name dropest dropest /bin/bash
/bin/bash: /bin/bash: cannot execute binary file
I fix it by commenting this part in the Docker file:
#ENTRYPOINT ["/bin/bash"]
Best,
Luca
There is no way to to specify the output file name for the --bam-output parameter
I have got cellbarcode whitelist from 10X Genomics. I tried to link it via configuration xml file and tried running dropEst, but it did not accept the input. Cell barcodes look like following.
AAACCTGAGAAACCAT
AAACCTGAGAAACCGC
AAACCTGAGAAACCTA
AAACCTGAGAAACGAG
AAACCTGAGAAACGCC
.
.
.
I got following warning.
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACCAT'
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACCGC'
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACCTA'
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACGAG'
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACGCC'
I used configs/10x.xml file and changed my_fiile.txt>myfile</barcodes_file>.
I used to get the right dropReport using the dropReport.Rsc, but once I upgraded to v0.8.0, it keeps failing:
~/dropEst/dropReport.Rsc dlib1.out/cell.counts.bcconfig.rds -o dlib1.filtered.bcconfig.report.html
processing file: report.Rmd
|.. | 3%
inline R code fragments
|.... | 6%
label: unnamed-chunk-1 (with options)
List of 1
$ include: logi FALSE
|...... | 9%
ordinary text without R code
|....... | 11%
label: unnamed-chunk-2
|......... | 14%
ordinary text without R code
|........... | 17%
label: unnamed-chunk-3 (with options)
List of 3
$ fig.width : num 5.5
$ fig.height: num 3.5
$ warning : logi FALSE
|............. | 20%
ordinary text without R code
|............... | 23%
label: unnamed-chunk-4 (with options)
List of 2
$ fig.width : num 3.5
$ fig.height: num 3.5
Quitting from lines 55-56 (report.Rmd)
Error in GetUmisDistributionNew(reads.per.umi.per.cb) :
Not compatible with STRSXP: [type=NULL].
Calls: <Anonymous> ... GetUmisDistribution -> GetUmisDistributionNew -> .Call
In addition: Warning messages:
1: In grDevices::png(f) : unable to open connection to X11 display ''
2: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
3: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
4: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
5: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
6: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
7: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
8: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
9: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
Execution halted
The error in function appears to be coming from a Rcpp code so I couldn't get more useful information. I tried to install dropestr as well as dropest again without any improvement. (Compilation succeeds).
Hi,
I have updated from 0.8.0 version to 0.8.2, and ran dropEst and the cells.counts.rds does not seem to have a reads_per_umi_per_cell
any more. (Note that the cell.counts.bcconfig.rds
is just my way of naming convention of outputing the usual cell.counts.rds
file).
> d <- readRDS("cell.counts.bcconfig.rds");
> names(d)
[1] "cm" "cm_raw"
[3] "reads_per_chr_per_cells" "mean_reads_per_umi"
[5] "saturation_info" "merge_targets"
[7] "aligned_reads_per_cell" "aligned_umis_per_cell"
[9] "requested_umis_per_cb" "requested_reads_per_cb"
The following is the log after the dropEst
run:
/home/cl266/dropEst/dropest -m -V -r drop/dlib7.FC03835.L001.params.gz drop/dlib7.FC03835.L002.params.gz drop/dlib7.FC03835.L003.params.gz drop/dlib7.FC03835.L004.params.gz -g drop.reference.wo.pseudo/mm10.with.compact.transgenes.filtered.20180315.gtf -o drop/dlib7.out/cell.counts.bcconfig.rds -c /home/cl266/dropEst/configs/indrop_v3_with_barcodes.xml drop/dlib7.out/Aligned.out.sorted.bam
Version: 0.8.2.
Run: 05/11/2018 23:35:13.
Real CBs merge selected.
Start parsing of bams: 23:35:13.
Start loading read parameters
Start reading file: drop/dlib7.FC03835.L001.params.gz
Total 10000000 read records processed
Start reading file: drop/dlib7.FC03835.L002.params.gz
Total 20000000 read records processed
Total 30000000 read records processed
Start reading file: drop/dlib7.FC03835.L003.params.gz
Total 40000000 read records processed
Total 50000000 read records processed
Start reading file: drop/dlib7.FC03835.L004.params.gz
Total 60000000 read records processed
Total 70000000 read records processed
All read parameters were loaded
drop/dlib7.out/Aligned.out.sorted.bam: 10000000 total reads; 19.7% intergenic; 36.4% touch exon; 5.14% touch intron; 0.268% touch not annotated regions; 551120 CBs read
drop/dlib7.out/Aligned.out.sorted.bam: 20000000 total reads; 14.2% intergenic; 35.2% touch exon; 5.23% touch intron; 0.354% touch not annotated regions; 807385 CBs read
drop/dlib7.out/Aligned.out.sorted.bam: 30000000 total reads; 12.6% intergenic; 35.9% touch exon; 5.89% touch intron; 0.676% touch not annotated regions; 1054520 CBs read
drop/dlib7.out/Aligned.out.sorted.bam: 40000000 total reads; 13.3% intergenic; 37.7% touch exon; 5.84% touch intron; 0.555% touch not annotated regions; 1316740 CBs read
drop/dlib7.out/Aligned.out.sorted.bam: 50000000 total reads; 12.5% intergenic; 37.7% touch exon; 5.5% touch intron; 0.484% touch not annotated regions; 1523297 CBs read
WARNING: Can't find chromosome 'JH584301.1'
WARNING: Can't find chromosome 'GL456379.1'
WARNING: Can't find chromosome 'GL456393.1'
WARNING: Can't find chromosome 'GL456366.1'
WARNING: Can't find chromosome 'GL456367.1'
WARNING: Can't find chromosome 'GL456213.1'
WARNING: Can't find chromosome 'GL456383.1'
WARNING: Can't find chromosome 'GL456360.1'
WARNING: Can't find chromosome 'GL456378.1'
WARNING: Can't find chromosome 'GL456389.1'
WARNING: Can't find chromosome 'GL456370.1'
WARNING: Can't find chromosome 'GL456390.1'
WARNING: Can't find chromosome 'GL456392.1'
WARNING: Can't find chromosome 'GL456382.1'
WARNING: Can't find chromosome 'GL456396.1'
WARNING: Can't find chromosome 'GL456368.1'
drop/dlib7.out/Aligned.out.sorted.bam: 53226123 total reads; 12.2% intergenic; 37.9% touch exon; 5.35% touch intron; 0.476% touch not annotated regions; can't parse 0.00553863% reads; 1589231 CBs read
Bams parsed: 23:46:53.
40620 CBs with more than 20 genes
top CBs:
12988 GGGGGGGGGGGGGGGG
4082 AGGAGTCGTTCACATA
4042 CCACGTTGCAACAAAT
3537 CGTGTACAGGTTTCTC
3474 CCGAGATCGATGTATT
3422 GTTCTGCTCCACATTA
3405 ATGGGCTCATGCATGG
3348 TGCTTGGGAGACACCA
3335 CATTCGGGATGACCGA
Start merge: 23:46:56.
Merge initialized: 23:46:56.
Total 2471 cells merged
Total 5847 cells excluded
Merge finished: 23:47:20.
Merge UMIs with N's: 23:47:20.
32302 cells processed. Merged 9571 UMIs from 9534 cells.
UMI merge finished: 23:47:25.
32302 cells are considered as real.
4897 CBs with more than 100 genes, which have UMIs of the requested type.
top CBs:
4105 AGGAGTCGTTCACATA
4063 CCACGTTGCAACAAAT
3567 CGTGTACAGGTTTCTC
3515 CCGAGATCGATGTATT
3439 GTTCTGCTCCACATTA
3436 ATGGGCTCATGCATGG
3367 CATTCGGGATGACCGA
3360 TGCTTGGGAGACACCA
3353 CCGAGATCCGCTAGTC
Done: 23:47:28.
22997 genes
top genes:
mt-Nd4 113333
Myo3a 106538
mt-Cytb 99032
S100a6 90587
mt-Nd1 90403
H19 81416
Saa3 72838
Col1a2 62978
Gm10076 62151
Rpl23 62003
Compiling diagnostic stats:
Reads per chromosome per cell;
Fill exon results
Fill intron results
Fill intergenic results
Saturation info;
Mean reads per UMI;
Merge targets;
Completed.
Compiling raw count matrix: 23:48:01.
23326 genes, 32302 cells.
Done: 23:48:05.
Compiling filtered count matrix: 23:48:05.
19283 genes, 4897 cells.
Done: 23:48:14.
Reads per UMI per gene;
Writing R data to drop/dlib7.out/cell.counts.bcconfig.rds ...: 23:49:20.
Completed: 23:49:55.
Compiling intron/exon matrices: 23:49:55.
Exon
18964 genes, 4897 cells.
Intron
16313 genes, 4897 cells.
Intron/exon spanning
4748 genes, 4897 cells.
Done: 23:50:10.
Writing R data to drop/dlib7.out/cell.counts.bcconfig.matrices.rds ...: 23:50:10.
Completed: 23:50:15.
All done: 23:50:48.
If you accidentally provide a ill-formatted configuration file (such as forgetting to specify the config and resulting in the first file being considered the config), you get a confusing error message:
input/sample.fq.tagged.1.tophat/accepted_hits.bam(1): expected <
An message like 'Error processing configuration file', would be must more useful.
When I try to install, I get the following errors that prevent installation in following steps. I want to know which libraries these packages are trying to link to so that I might specify the paths, but can't seem to figure out what the targets need. Any help would be appreciated.
WARNING: Target "DropTools" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Estimation" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TestEstimation" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TestEstimationMergeProbs" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TestTagsSearch" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TestTools" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "dropest" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "droptag" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
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