egaffo / circompara Goto Github PK

Hi! I am running CirComPara with a subsample of my paired data (same size as the paired test data), but I am getting the following error

Quitting from lines 443-465 (circRNAs_analysis.Rmd) 
Error: Aesthetics must be either length 1 or the same as the data (1): x and fill
Backtrace:
     █
  1. └─rmarkdown::render(...)
  2.   └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  3.     └─knitr:::process_file(text, output)
  4.       ├─base::withCallingHandlers(...)
  5.       ├─knitr:::process_group(group)
  6.       └─knitr:::process_group.block(group)
  7.         └─knitr:::call_block(x)
  8.           └─knitr:::block_exec(params)
  9.             ├─knitr:::in_dir(...)
 10.             └─knitr:::evaluate(...)
 11.               └─evaluate::evaluate(...)
 12.                 └─evaluate:::evaluate_call(...)
 13.                   ├─base:::handle(...)
 14.                   ├─base::withCallingHandlers(...)
 15.                   ├─base::withVisible(value_fun(ev$value, ev$visible))
 16.                   └─knitr:::value_fun(ev$value, ev$visible)
 17.                     └─knitr:::fun(x, o
Interrumpted execution
scons: *** [circular_expression/circrna_analyze/circRNAs_analysis.html] Error 1

This is related to the "Barplot number of circRNAs per methods (sum over all samples)" graph in circRNA_analysis.Rmd.
Is it possible that the Barplot is not being produced because one (or more) method predicts 0 circRNAs?

I don't know what is causing this, if you have any clue I would really appreciate your help!

Hi, egaffo:
When I run Circompara, an error occured like this:
scons: *** Found dependency cycle(s):
File "*/CirComPara-circompara/tools/scons/scons-local-2.5.0/SCons/Taskmaster.py", line 1043, in cleanup.
How can I fixed this problem ?
Thank you very much !

Could you help me with the error below?

I am running CirComPara for the docker image that you have made available.

label: plot_circrnas_per_gene (with options)
List of 3
$ echo : logi FALSE
$ include : logi TRUE
$ fig.width: num 12

Quitting from lines 726-749 (circRNAs_analysis.Rmd)
Error in if (zero_range(as.numeric(limits))) { :
missing value where TRUE/FALSE needed
Calls: ... -> f -> -> f -> -> f
In addition: There were 29 warnings (use warnings() to see them)

Execution halted
scons: *** [circrna_analyze/circRNAs_analysis.html] Error 1
scons: building terminated because of errors.

Tnx

Hi, I am using the docker and I am having the following error:

(base) user@NGS:~/CirComPara$ sudo docker run --rm -it -v $(pwd):/ data egaffo/circompara-docker
scons: Reading SConscript files ...
'adapter' not defined for file./data/LNCAP-AD-rep1_1.fastq, sample S1. Sk ipping.
'adapter' not defined for file./data/LNCAP-AD-rep1_2.fastq, sample S1. Sk ipping.
'adapter' not defined for file./data/LNCAP-AD-rep2_1.fastq, sample S2. Sk ipping.
'adapter' not defined for file./data/LNCAP-AD-rep2_2.fastq, sample S2. Sk ipping.
'adapter' not defined for file./data/LNCAP-AI-rep1_1.fastq, sample S3. Sk ipping.
'adapter' not defined for file./data/LNCAP-AI-rep1_2.fastq, sample S3. Sk ipping.
'adapter' not defined for file./data/LNCAP-AI-rep2_1.fastq, sample S4. Sk ipping.
'adapter' not defined for file./data/LNCAP-AI-rep2_2.fastq, sample S4. Sk ipping.
TypeError: cannot concatenate 'str' and 'int' objects:
File "/CirComPara/src/ccp_main.scons", line 356:
exports = '''env_check_indexes''')
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 604:
return method(*args, **kw)
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 541:
return _SConscript(self.fs, *files, **subst_kw)
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 250:
exec file in call_stack[-1].globals
File "/CirComPara/src/ccp_check_indexes.scons", line 117:
exports = '''env_build_indexes ''')
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 604:
return method(*args, **kw)
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 541:
return _SConscript(self.fs, *files, **subst_kw)
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 250:
exec file in call_stack[-1].globals
File "/CirComPara/src/ccp_build_indexes.scons", line 67:
exports = '''env_index_hisat2 ''')
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 604:
return method(*args, **kw)
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 541:
return _SConscript(self.fs, *files, **subst_kw)
File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 250:
exec file in call_stack[-1].globals
File "/CirComPara/src/ccp_index_hisat2.scons", line 44:
''' ${TARGETS[0].dir}''' + os.path.sep + target_basename + ''' ''' + EXTRA_PARAMS

Do you have any suggestion to fix it?

thanks

I was able to run CirComPara for another set of libraries, but in this view the error below. Can they help with the error?

scons: Reading SConscript files ...
TypeError: 'Entry' object is not iterable:
File "/home/fabiano_d1f49/CirComPara/src/junk2_circpipe_multisample", line 307:
exports = '''env sample_cpus sample_genome_index '''
File "/home/fabiano_d1f49/CirComPara/tools/scons/scons-local-2.5.0/SCons/Script/SConscript.py", line 604:
return method(*args, **kw)
File "/home/fabiano_d1f49/CirComPara/tools/scons/scons-local-2.5.0/SCons/Script/SConscript.py", line 541:
return _SConscript(self.fs, *files, **subst_kw)
File "/home/fabiano_d1f49/CirComPara/tools/scons/scons-local-2.5.0/SCons/Script/SConscript.py", line 250:
exec file in call_stack[-1].globals
File "/home/fabiano_d1f49/CirComPara/src/junk2_circpipe", line 285:
sample_raw_reads = [f.abspath for f in unmapped_reads[1]]

Dear egaffo,
The "combined_circrnas.gtf" generated by CirComPara in circRNA_collection step showed confused results.
For example, the table below is simplified from a "combined_circrnas.gtf" file, in which CircRNA id "1:30217863-30218834:+" has 5 exons. However, there is one exon_number "5" whose start/end is different from other six exon_number "5" , and one exon_number "2" whose start/end is different from other seven exon_number "2", what does that mean ? I don't konw why the same exon's coordinate is different. The same situation also occured in other CircRNAs, but not all the CircRNAs identified by CirComPara pipline.
When I need to extract sequences of CircRNAs with tophat2, how can I deal with this situation? Should I drop the sequences of this abnormal exon, and just take sequences of the same exon index whose coordinate stays consistent ?

1:30217863-30218834:+ 30218756 30218834 . + . exon_number "6"
1:30217863-30218834:+ 30218756 30218834 . + . exon_number "6"
1:30217863-30218834:+ 30218636 30218677 . + . exon_number "5"
1:30217863-30218834:+ 30218636 30218677 . + . exon_number "5"
1:30217863-30218834:+ 30218636 30218677 . + . exon_number "5"
1:30217863-30218834:+ 30218636 30218677 . + . exon_number "5"
1:30217863-30218834:+ 30218636 30218834 . + . exon_number "5"
1:30217863-30218834:+ 30218636 30218677 . + . exon_number "5"
1:30217863-30218834:+ 30218636 30218677 . + . exon_number "5"
1:30217863-30218834:+ 30218493 30218544 . + . exon_number "4"
1:30217863-30218834:+ 30218493 30218544 . + . exon_number "4"
1:30217863-30218834:+ 30218493 30218544 . + . exon_number "4"
1:30217863-30218834:+ 30218493 30218544 . + . exon_number "4"
1:30217863-30218834:+ 30218338 30218417 . + . exon_number "3"
1:30217863-30218834:+ 30218338 30218417 . + . exon_number "3"
1:30217863-30218834:+ 30217863 30218248 . + . exon_number "2"
1:30217863-30218834:+ 30217863 30218248 . + . exon_number "2"
1:30217863-30218834:+ 30217863 30218248 . + . exon_number "2"
1:30217863-30218834:+ 30217863 30218233 . + . exon_number "2"

Dear Enrico,

Sorry to trouble you for a while. I have another question. I have run CirComPara with two methods findcirc and circexplorer, several folders and a number of output files are generated. I'm not sure if outputs by circompara have a file containing the circRNA sequences. I'm wondering if there is a script or tool that can be used to extract the DNA sequences of circRNAs detected. These circRNA sequences will be used for scanning miRNA binding sites. Any advice is very appreciated. Thank you very much!

Zhuofei

Function must_be_same (line 610 from CirComPara/tools/scons/scons-local-3.1.2/Scons/Node/FS.py) tries to look up for file named "ccp_dbs" which is actually a directory, so the function throws error. Another condition needs to be added to must_be_same function to avoid this. My quick fix was to add the following on line 622 in the same file.

elif klass.__name__== 'File' and self.__class__.__name__== 'Dir':
          return

hi, I am trying to install CirComPara but facing this issue during installation:
scons: Reading SConscript files ...
AttributeError: '_Environ' object has no attribute 'has_key':
File "/media/alphagenomics/Bay2/Softwares/CirComPara/src/ccp_install_tools.scons", line 18:
if not env['ENV'].has_key('VIRTUAL_ENV'):