egaffo / mirandmore2 Goto Github PK

I am trying to run mir&more2 pipeline on our data and everytime while running install_mnm2 file, I always get an error at line no. 29 which says that scons: command not found. I have checked that module is already install but it is not working. Even I manually set the symbolic link that was done at line no. 23 still the error persists. I have attached the screenshot of the error. Please suggest. Thanks.

[EDIT-1] : Adding little bit more about how I debug it. I run the command python scon.py from $TOOL_DIR/scons/ directory to check if the module is working and yes it is working fine but the symbolic link at line_no 23 of install_mnm2 script may not be properly (or effectively) working because by calling scons from command prompt it is calling only $TOOL_DIR/scons/scons.py without telling bash how to run it (i.e. without python) (please let me know If I missed anything)

While running mirandmore2 pipeline on my data, I have got the following error:

Negative repeat count does nothing at /mnt/disk2/Mirpipe/mirandmore2/bin/miRDeep2_core_algorithm.pl line 1458, <FILENAME> line 4192087.
Negative repeat count does nothing at /mnt/disk2/Mirpipe/mirandmore2/bin/miRDeep2_core_algorithm.pl line 1458, <FILENAME> line 5548059.
[fai_build_core] ignoring duplicate sequence "hsa-mir-6511b-1-ext" at byte offset 150195
WARNING: duplicated precursorname for hsa-mir-6511b-1-ext. Will change into hsa-mir-6511b-1-ext|MI0022552_2
Traceback (most recent call last):
  File "/mnt/disk2/Mirpipe/mirandmore2/bin/gff2maturetable.py", line 225, in <module>
    gff2maturetable([args.mature_table], [args.gff], env)
  File "/mnt/disk2/Mirpipe/mirandmore2/bin/gff2maturetable.py", line 56, in gff2maturetable
    mirna_pre_id = re.findall(r'Derives_from=([^;]*)',items[8])[0].strip()
IndexError: list index out of range
scons: *** [mirandmore_dbs/annotation_files/extended_annotation/mature-table.txt] Error 1

Unfortunately, I am not able to understand why this error occurred and how to debug. Need suggestions. Thanks.

Hi there,

Excited to give this tool a shot, but encountering some difficulties with the installation process. This may be compounded by the fact that I don't have sudo access on our group's cluster, but tried my best to install the appropriate dependencies through conda/locally. The error I'm encountering is thrown after cloning the repository and running the install script; I copy the relevant output below. It looks like one of the build steps involving Perl is looking for an EXTERN.h file that doesn't exist/isn't created when I try to install. Could you let me know what you think? I'm on a CentOS Linux 7 HPC, if that's helpful.

./install_mnm2

..........
/users/tcarroll/sharedscratch/bin/git/mirandmore2
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
cd dirname tools/ViennaRNA-2.4.14/Makefile && make -j
make all-recursive
make[1]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14' Making all in src make[2]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src'
Making all in ViennaRNA
make[3]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/ViennaRNA' Making all in static make[4]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/ViennaRNA/static'
make all-am
make[5]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/ViennaRNA/static' make[5]: Nothing to be done for all-am'.
make[5]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/ViennaRNA/static' make[4]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/ViennaRNA/static'
make[4]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/ViennaRNA' make[4]: Nothing to be done for all-am'.
make[4]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/ViennaRNA' make[3]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/ViennaRNA'
Making all in bin
make[3]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/bin' CCLD RNAfold make[3]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/bin'
Making all in Utils
make[3]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/Utils' make[3]: Nothing to be done for all'.
make[3]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src/Utils' make[3]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src'
make[3]: Nothing to be done for all-am'. make[3]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src'
make[2]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/src' Making all in man make[2]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/man'
make[2]: Nothing to be done for all'. make[2]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/man'
Making all in misc
make[2]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/misc' make[2]: Nothing to be done for all'.
make[2]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/misc' Making all in doc make[2]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/doc'
make[2]: Nothing to be done for all'. make[2]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/doc'
Making all in RNA-Tutorial
make[2]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/RNA-Tutorial' make[2]: Nothing to be done for all'.
make[2]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/RNA-Tutorial' Making all in interfaces make[2]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/interfaces'
Making all in Perl
make[3]: Entering directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/interfaces/Perl' CXX RNA_la-RNA_wrap.lo RNA_wrap.cpp:762:20: fatal error: EXTERN.h: No such file or directory #include "EXTERN.h" ^ compilation terminated. make[3]: *** [RNA_la-RNA_wrap.lo] Error 1 make[3]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/interfaces/Perl'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14/interfaces' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory /mnt/lustre/users/tcarroll/bin/git/mirandmore2/tools/ViennaRNA-2.4.14'
make: *** [all] Error 2
scons: *** [tools/ViennaRNA-2.4.14/src/bin/RNAfold] Error 2
scons: building terminated because of errors.