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hillerlab / TOGA

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
MIT License
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"CESAR wrapper command crashed" #119

Open mprincipato opened 10 months ago

mprincipato commented 10 months ago

Hello, dev team!

I'm very new to TOGA, and I'm trying it out on some public data for a class project.

When I run it on my personal Windows machine (using Windows Subsystem for Linux), it runs for about eight and a half hours before saying:

`### CESAR jobs done ###

Checking whether all CESAR results are complete !!CRITICAL: Too many (4576) CESAR jobs died, please check your input data and re-run TOGA !!CRITICAL: Too many (4576) CESAR jobs died, please check your input data and re-run TOGA Program finished with exit code 1`

When I look in the CESAR job logs, I find several error messages like this: (Slightly edited to remove personal information.) 

!!CESAR wrapper command crashed: /home/m/code/TOGA/CESAR_wrapper.py ENST00000356220 70 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/toga_filt_ref_annot.hdf5 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/genome_alignment.bst /home/m/code/toga_input/hg38.2bit /home/m/code/toga_input/HLpipKuh2.2bit --cesar_binary /home/m/code/TOGA/CESAR2.0/cesar --uhq_flank 50 --temp_dir /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/cesar_temp_files --check_loss --alt_frame_del CESAR failed run for ['/home/m/code/TOGA/CESAR2.0/cesar', '/dev/stdin', '-x', '3']:  
!!FAILED COMMAND: /home/m/code/TOGA/CESAR_wrapper.py ENST00000356220 70 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/toga_filt_ref_annot.hdf5 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/genome_alignment.bst /home/m/code/toga_input/hg38.2bit /home/m/code/toga_input/HLpipKuh2.2bit --cesar_binary /home/m/code/TOGA/CESAR2.0/cesar --uhq_flank 50 --temp_dir /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/cesar_temp_files --check_loss --alt_frame_del
!!At attempt 0
!!CESAR wrapper command crashed: /home/m/code/TOGA/CESAR_wrapper.py ENST00000356220 70 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/toga_filt_ref_annot.hdf5 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/genome_alignment.bst /home/m/code/toga_input/hg38.2bit /home/m/code/toga_input/HLpipKuh2.2bit --cesar_binary /home/m/code/TOGA/CESAR2.0/cesar --uhq_flank 50 --temp_dir /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/cesar_temp_files --check_loss --alt_frame_del CESAR failed run for ['/home/m/code/TOGA/CESAR2.0/cesar', '/dev/stdin', '-x', '3']:  
!!FAILED COMMAND: /home/m/code/TOGA/CESAR_wrapper.py ENST00000356220 70 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/toga_filt_ref_annot.hdf5 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/genome_alignment.bst /home/m/code/toga_input/hg38.2bit /home/m/code/toga_input/HLpipKuh2.2bit --cesar_binary /home/m/code/TOGA/CESAR2.0/cesar --uhq_flank 50 --temp_dir /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/cesar_temp_files --check_loss --alt_frame_del
!!At attempt 1
!!FAILED TO EXECUTE COMMAND /home/m/code/TOGA/CESAR_wrapper.py ENST00000356220 70 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/toga_filt_ref_annot.hdf5 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/genome_alignment.bst /home/m/code/toga_input/hg38.2bit /home/m/code/toga_input/HLpipKuh2.2bit --cesar_binary /home/m/code/TOGA/CESAR2.0/cesar --uhq_flank 50 --temp_dir /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/cesar_temp_files --check_loss --alt_frame_del in 2 attempts
cesar_runner::cesar_job_1_0: return code: 1
cesar_runner::cesar_job_1_0: CESAR JOB FAILED: /home/m/code/TOGA/CESAR_wrapper.py ENST00000356220 70 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/toga_filt_ref_annot.hdf5 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/genome_alignment.bst /home/m/code/toga_input/hg38.2bit /home/m/code/toga_input/HLpipKuh2.2bit --cesar_binary /home/m/code/TOGA/CESAR2.0/cesar --uhq_flank 50 --temp_dir /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/cesar_temp_files --check_loss --alt_frame_del
cesar_runner::cesar_job_1_0: ERROR MESSAGE: CESAR wrapper command crashed: /home/m/code/TOGA/CESAR_wrapper.py ENST00000356220 70 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/toga_filt_ref_annot.hdf5 /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/genome_alignment.bst /home/m/code/toga_input/hg38.2bit /home/m/code/toga_input/HLpipKuh2.2bit --cesar_binary /home/m/code/TOGA/CESAR2.0/cesar --uhq_flank 50 --temp_dir /home/m/code/TOGA/TOGA_project_on_2023.11.12_at_13:58:58/temp/cesar_temp_files --check_loss --alt_frame_del CESAR failed run for ['/home/m/code/TOGA/CESAR2.0/cesar', '/dev/stdin', '-x', '3']:

Here was the command I originally used to run TOGA: ./toga.py ../toga_input/hg38.HLpipKuh2.allfilled.chain supply/hg38.wgEncodeGencodeCompV34.bed ../toga_input/hg38.2bit ../toga_input/HLpipKuh2.2bit --kt -i supply/hg38.wgEncodeGencodeCompV34.isoforms.txt --cesar_mem_limit 5 --cesar_jobs_num 500

Do you have any guesses what might be going wrong to cause the CESAR wrapper command to crash?

As far as my inputs go, I got hg38.HLpipKuh2.allfilled.chain and HLpipKuh2.fa from this Bat1K page, and I converted HLpipKuh2.fa to 2bit using faToTwoBit.

kirilenkobm commented 10 months ago

Hi @mprincipato

CESAR distribution provides a few test samples Could you pls try running CESAR on a couple of them? Like https://github.com/hillerlab/CESAR2.0/blob/master/extra/example4.fa

Then pls try cat XXX.fa | ./cesar /dev/stdin

I suspect the current implementation is not quite compatible with WSL. (but I need to check the docs, probably there is a simple way to adjust subprocess calls to make it work)

mprincipato commented 10 months ago

Thank you, @kirilenkobm !

I spotted one thing in the documentation (the fact that Python 3.11 was recommended, but my default version was Python 3.10.12) and went down an ill-advised rabbit hole trying to set my default Python3 to 3.11 and wound up breaking things further. I think I was able to undo what I did, though, and these results are from running CESAR after that!

example1.fa

m@MPC:~/code/TOGA/CESAR2.0$ ./cesar extra/example1.fa
>referenceExon
                                                                                                    gCCTGGGAACTTCACCTACCACATCCCTGTCAGTAGTGGCACCCCACTGCACCTCAGCCTGACTCTGCAGATGaa                                                                 
>mouse
ctttcctcatttcctcaggcttcagtatagcatgaggctgaggaggagagagggagaccggcaaagtggccttgcttaggtaccatctttgcccctttagGCTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGAAgtgagtgctggtgtgtgggtatgtgtgggggaccatgtggaagccctcagaaaagtgaaagccaagtgcttactaaatttattacgtggagggtccaggc

example4.fa

m@MPC:~/code/TOGA/CESAR2.0$ ./cesar extra/example4.fa
>referenceExon
                                                                                                                                                                                                                                                                                                                                 ---CCCCTGTCCCGCTGGTTGAGATCTGTGGGGGTCTTCCTGCTGCCAGCCCCCTACTGGGCACCCCGGGAGAGGTGGCTGGGTTCCCTACGGCGGCCCTCCCTGGTGCACGGGTACCCAGTCCTG---GCCTGGCACAGTGCCCGCTGCTGGTGCCAAGCGTGGACAGAGGAACCTcg                                                                                  aGCCCTTTGCTCCTCCCTCAGAATGAACGGAGACCAGAATTCAGATGTTTATGCCCAAGAAAAGCAGGATTTCGTTCAGCACTTCTCCCAGATCGTTAGGGTGCTGACTGAGGATGAGATGGGGCACCCAGAGATAGGAGATGCTATTGCCCGGCTCAAGGAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      GTCCTGGAGTACAATGCCATTGGAGGCAAGTATAACCGGGGTTTGACGGTGGTAGTAGCATTCCGGGAGCTGGTGGAGCCAAGGAAACAGGATGCTGATAGTCTCCAGCGGGCCTGGACTGTGGGCTGGTGTGTGGAACTG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    CTGCAAGCTTTCTTCCTGGTGGCAGATGACATCATGGATTCATCCCTTACCCGCCGGGGACAGATCTGCTGGTATCAGAAG>>>>>>>>>>>>>>>>>>>CCGGGCGTGGGTTTGGATGCCATCAATGATGCTAACCTCCTGGAAGCATGTATCTACCGCCTGCTGAAGCTCTATTGCCGGGAGCAGCCCTATTACCTGAACCTGATCGAGCTCTTCCTGCAG>>>>>>>>>>>>>>>>>>>AGTTCCTATCAGACTGAGATTGGGCAGACCCTGGACCTCCTCACAGCCCCCCAGGGCAATGTGGATCTTGTCAGATTCACTGAAAAGag                                                                                     gTACAAATCTATTGTCAAGTACAAGACAGCTTTCTACTCCTTCTACCTTCCTATAGCTGCAGCCATGTACATG                                                                                                                                                                                                                                                                                                                                                                                                                                                         GCAGGAATTGATGGCGAGAAGGAGCACGCCAATGCCAAGAAGATCCTGCTGGAGATGGGGGAGTTCTTTCAGATTCAG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            GATGATTACCTTGACCTCTTTGGGGACCCCAGTGTGACCGGCAAAATTGGCACTGACATCCAGGACAACAAATGCAGCTGGCTGGTGGTTCAGTGTCTGCAACGGGCCACTCCAGAACAGTACCAGATCCTGAAG                                                                                                                                                                                                                                                                                                                                                                                      GAAAATTACGGGCAGAAGGAGGCTGAGAAAGTGGCCCGGGTGAAGGCGCTATATGAGGAGCTGGATCTGCCAGCAGTGTTCTTGCAATATGAGGAAGACAGTTACAGCCACATTATGGCTCTCATTGAACAGTACGCAGCACCCCTGCCCCCAGCCGTCTTTCTGGGGCTTGCGCGCAAAATCTACAAGCGGAGAAAG                                                                                                                                                                                                         
>rn6
aatagtgtcactttaggaccttccatcccataattctccgtaccgaattgtagtgaacgcagctttggaagtagaaagcgttcagttttagccatttgcggtttaagtgaagatctgttggctctcagtcactccgatatactttttatttcctgtgtgttatttatgtaattcttgaatttagaaacagggtggggcattctaatgcattctaaaagcttgggttgcggggtaccttaggtaacagccaccaagcatctgccttcggtgcttgctcctgcagggagtgcttggtgtcccccacccccatgcccacccaggATGCCCCTGTCCCGCTGGCTGAGATCTCTGGGGGTCTTCCTGCTGCCAGCCCCCTGCTGGGCACCCCGGGAGAGGTGGCTTGGTTACCTACAACGACCCTCCCTGGCATATGGGTGTCCAGTCCTTGGGGCTTGGCACAGTGCCCGCTGGTGGTGCCAAGTGTGGACAGAGGAGCCTCGgtgagtgtggttggggtgtggggcttcggggagggaagcaccggagccaccctctcactcatttgtgtgttttttccctcagAGCATTTAGCTCCTCTGTCAGAATGAATGGGGACCAGAAACTGGATGTTCATAACCAAGAAAAGCAGAATTTCATCCAGCACTTCTCCCAGATTGTCAAGGTGCTGACTGAGGATGAACTGGGACACCCAGAGAAGGGAGATGCTATTACCCGGATCAAAGAGgtgagggattcaggactgaagaagtcagtagaggtgtggattcgctgccagggttttgataagagcagaagtaacgtttttacctgtgggtcccgactgtacttcaacccacccagatatttggctccctgactttggaccatcccatcagctttgcttgagagcagagccctggacgtcatggtttgattttatgccctgagactataagataggatcttagcagataccaaaaggctgttggcactgaggcctgagggaagttactgtattgttaaagtctgctctaaaaagggagttgttcctcttctgcttgagttacctatttccctccagtctcttgagtttattttctttttttttggggggggggggtctttttttcggagctggggaccgaacccagggccttccgcttcctaggtaagcgctctaccactgagctaaatccccagccccttgagtttattttcttttcttttttttttttttttttttggttctctttttcggagctggggaccgaacccagggccttgtgcttcctaggtaagcgctctaccactgagctaaatccccagccccttgagtttattttcttaagacagagtttcaatttcttttttttttttttttttttttttttttggttcttttttcggagctggggaccgaacccagggcctttcgcttcctaggcaagcgctctaccactgaactaaatccccagccccgagtttcaatttcttttttttttttttttttttttttttggttcgttttttcggagctggggaccgaacccagggccttgcgcttcctaggtaagtgctctaccactgagctaaatccccagccccgagtttcaatttctaaacccacatgtcctcacacacacaaccccctgcctcagcctactgtgtgctgtatcaattacagtacatgtctagattgggaattctttttttttttttttttcaaaaaaagatttattatatataagaacactgtagctgtcttcagatacaccagaagaaggcatcggatcccattacagatggttgtgagccaccatgtggttgctgggaattgaactcagaacctctggaagagcagtcagtgctcttaaccactgaaccatctctccagcccaggaaacttttttttttttttttttttttttttttttttttttttttttttttttttgggttctttttttcggagctggggaccgaacccagggccttgcgcttcctaggtaagcgctctaccactgagctaaatccccagcccccaggaaacttttttttaaagacatacattttttttaaaaaattgtgcattgactttttgcctgcctctgtgtgtgtgtgtgtgtgtgtacacacttgtgagctgccatgtaggtgctgggaattgaacccaggtcctctggaggggcagtcagtgctcttcactgccaagccatctctagcctggggaattcttttttttataaatgtctcatctttgaggaaaacaccaaggagaattttctttgtctatactgtgcaggtattaaagagctatctctttagttagttagggctgctgtctggcagaaggcacagttgagaaggctccaggaggaggacattagaagggttagacgtagccctgactcttgctgtcccttcaatgccttcttttggctaactttggagaagccttgtcttttgttttgtttctttgttttctgtagccaaggctgtccagaactcattctgtatctgaggctggcctcatactcatcagtctgcctgcctccctgctgagtattgagcttataggagttagccatcactctacgctagggcccttgtcttcactacaagcttgtttgcaggtggtccaagttctcggcttgagggaagaactgggggtatgttatgtagcaggtacttgggttccatatgctataggactttggagaagaaatgaagaggggactgacccagggactccccaaggggagttggggttcaaagagggagaaggaaaggggaaacctcttcaggtcccttctgtgtggaccctgatgtcctctcaccctgcctcagGTCCTGGAGTACAACACTGTAGGAGGCAAGTACAATCGGGGTCTGACGGTGGTACAGACCTTCCAGGAACTGGTGGAACCAAGGAAACAGGATGCTGAGAGCCTACAGCGGGCCCTGACGGTGGGCTGGTGTGTAGAACTGgtaagagcggtcggagaagcagagttcccacagttggggcttccttggtgaggagcagaagcttgtttcttgcttgtgttgatgtgtgagtctcttgtgtgctacagtcattcgggcagtgtggatcccttcaggggctgacagatgggcacagagagttttcagaaatgctcaccttaaatatcaccatgtggtggtgtcccatgcctttgatcttatctcagggagcagaggcaagtggatctctatgagttctaggctagcctgatctatagagtaagttctaggatggccagggctactcaagaaaccctagtttcaaataacagaaaccttaaattcttaaacttaacaaagaagacatgccattaaaaaagaaagtagacttttaaagtctggttagatggcttggccggtgagagcatttgccatcagaagagccgaatgtgtgagccagggccgtagaaacccagttgtgtctctggacacagaatctgcatggtaggtagagccagcaggctggccaggctgcctggctcagtgagagagaccctgtttcaaaggaacattgatgtgatagacaggacacctggcatcttcctttggcttctccgcccctgttttcatgcccacactgaatgcacccaagtgtgtgcttggtggtacacatctgtaatacatacactcacctagtgctggggcatggagataggcgggtccccagagttcgctggcaagctaggttagccaatcagtcagttccgggctcagaaaggtttgtctcccaaaactgaggacacctgatactcacctcttgctgctacagatgcgcccagttcagatgcccatccatatatacaacttgtgacacagacacaagcacacaaggcctgctgggcaggcaggcaggcagacacacttgtgttcagtttctcactatctatatgacaactgtgtgcatctgttgcacccttcccggagttgggatagatgtgcagatcctggagcttgttggccagtctgaccatttcagtgaccaccctgtctcaaagaataaggtggagaggctggagagatgggccagtgtttaagagctctggctgcttttccagaggaccggggttcagtggttagggatctgacaccctcttctggccttcatgggcaccaggcatgcacatggttagcagacagacttgcagaccagcaccagtgcatttaaaataagtagtcctctgtttggcagcacatatactgaaattggaacaatacagagaagattagcttggcccctttgtaaggatgacacaaattcatgaggcagtcactctctttttttcctttctgtcttttcatttctatcaaatgtgtgaaaaaatacataaagattggttataaccaaaaatatgttatataaaattttaaaaatgaggaagacatctcacagaattcccccaaaatgaggacatccaaggtcgacctctgacctccacatgattgcatttgtaactcatgtacacagagcacatgcatacatgaaacatgtgtgcacaatataatatgtgcacacaattctacaaatctataataacatgtatgcatacactacacacatgcacacatgtacacacataaacagttcagatcactggcatgttcacttaatgaaatgattttccagagtgaattaaaagctgcttccctaatgtagggtacgtgctccacctatggctctgattttcagtcctggctcttgaatgtctgactttgttgtttcctgggtgggtgagaggtttccaatttggtattgaagtccagggccttgtctattgtaagcacgctcttatcccttaactatgtccctgccctttggtttcggtttttgatttttcactggctgtcctggaacttactctgtagatcaggctggcctcaaactcagctccacctgccctatctcccaagtgctgggattagaggtgagcgccaccagtgcctggctgtttttgtttatgagacaaggtctcactgtgtacagctcacacatactcaagatcatctcgcttcagccttccaagtgctgggatcatagatgtgtgccatcacgcctgactcatactgacttactaaattattggtctattaaatagaccagtttgcggtgtttggatgatgtaacgatagacttctgttgagaatcataggggtggaaggatgagtcaaagttctggagccctgagtttgatccttagaacccatgtaagaagtgaactgactcccagaagtcaccctctgacatcactgcatgctgtgacgtgtgagcatccacaccgagacacaccttcctcacccctgactagtgaggggctggcagtgtggttctagtgggtaaaggcactctgtcgaaagcccagcaaagtgagttctgtcccaggattcatgggaagatggaaagagaaaaacaactcctagaaattgtcctctgacctttatttgtgtgctgtggcatgtatgtgcccttgcacacaataataatagaagtttgttaaaacagaaaaaaaatagataattttgttgtgggggtcaaaagccttccatcccatatgtaaggccctgggttccatcctcagcactttaacacagtaaagccaaggcatgcagttaaagcaattgccacgtaacaaacgggtagccttgccggaaggtgcgtgggccagtgttcaggagatgggctgaggaccttgagatcgaagccagcctggccttcataccgaggttctgtctcaaggaatcaaaacccaaaagtgtcctggatgttgttgagtgttcagtcttccatctccctaatagagagcgcgtgggaggcaccactctgtggtcagggctaggctctgggaatacctgaggagccagcattgctgaactggaagagcatttaccagcaggcagagtggctcagtggtagcatgaggtcccgggttcagcactcgcagtgcacagaaccaaacatgacagtagacagctgtgacctcggcacctgggaaggagcggtaaaggcagaagtacagatccttggccacggagggactttggctcatctaagggaagacgccattgattgccaaggcggtgctcttggggtggtgctcctggaagtgtgactctcatagcccgtcactgagggaagtcagaatgggagttgatccagatgccgtgcagagtgatggtgactggtttgttcccacagctttctcagcctgttcccttacacaccccagaactgtctgcccagggatgcagcacccactgtgaaaatgcctcacagccttgctagaagccagtctggtgagggcatttttttcagttgaggctcccttttgccaaatgactatagcttgggtcaagttgacctcaaactagccaacacagtcacttactggaacaaaagttacggatgttttgggtaagagtgaggtacgtgaaggtgtttcatactcaacttactaccgagggagtcctagagccgattagaggcggcagagctgtgttttagtctgttagcctgaaaatgagggtgcagacatgggatcctgtaatctgtcagagttcccataaccaccccttccacccagtgcacggcagtggccagggcagcagccgtcactgagagagggcccctttcagagccctggggtcttactgtgttccttctccagCTCCAGGCTTTCTTCCTCGTGTTAGATGACATCATGGACTCTTCCCACACTCGCCGGGGGCAGATCTGCTGGTATCAGAAG-------------------CCGGGCATAGGCTTGGATGCCATCAACGATGCTCTGCTTCTGGAAGCCGCTATCTACCGCCTGCTTAAGTTCTACTGCAGGGAGCAGCCCTACTACCTCAACCTGCTGGAGCTCTTTCTACAG-------------------AGTTCCTATCAGACTGAGATCGGGCAGACTCTCGACCTCATCACAGCACCCCAGGGCCAAGTGGATCTTGGTAGATACACTGAAAAGAGgtgaggcccctggcaaccatgtgtagactttgaggcactcaacatgggcctagcccttaggagtgcatcttctcccctgactcagGTACAAATCTATCGTCAAGTACAAGACAGCTTTCTACTCTTTCTACCTGCCTATCGCGGCTGCCATGTACATGgtgagtcagtggcacctccactcttttcccttgggggcattgggatgggaggacatggagtagacattcagggtatgatggtataacttggagcaagccacccagtccctctgacactggaaagtgagcagagctgagtcctatctgagtgggaggggcagaggaaaatttaggctgagcaagagactaggtgtggcggtggctcttgggtccatcctggccagcctcttcaggttttctcttcattttgtaagaggttggagttggaagtggagctgtaatggctttccaggggaagatggcctgatgccttcagaatggattcattccttaggcctcccggggaggggctgaggttggactgcagttacgcagaacccatggaaagtgtcaagaagggcagggtgctgtggccatgctgccttacctgtctccctgtagGCTGGAATTGATGGGGAGAAGGAACACGCTAATGCCCTGAAGATCCTGCTGGAGATGGGCGAGTTCTTCCAGATCCAGgtaggagggtctgcagcgggaagtaataagaggattttccaccccacgctatgccgggcaccatggggtgttctcatctcggcagactgtgacccattgttcttaacactctccacccgactcgctaagttcccgtggtgggtcgctgccactccagccccatttaacaactgcccacctcacggttggctgtcacagatatctataccctggcaaaatcaaaactctagaggcttgtaatttattaatcagatttatatcagtaaattctcaccccacaaaacgcccacataataaactcagagccaattgatactgatataaagggcccacctagataagatgtcctgtagtcatctatcccttatataatactcatagttacccgtggctgtttaaagctacacggatccgggtggtcctcttcctccgtcttccttctccccttcctgtgctctttgtctctagaattctcggcccacttttctttttcactgtccaatcacaggctcttgccttgtcttctacctgcccttccctgcttacagacagcagtgtacacaggtcctccagccacactgcatggagcttctcatctctcctttctgcctgctccctagGACGACTACCTTGATCTCTTTGGAGACCCCAGTGTGACCGGAAAGGTCGGCACTGACATCCAGGACAACAAATGCAGCTGGCTGGTGGTTCAGTGTCTGCTACGAGCCACTCCTCAGCAGCGCCAGATCTTAGAGgtgcccaagtggggcttgggggtggcatgtccctttgctaagaggggatgggggaggagtggttagaacagtgattttgctgtccaggagacatttgggagctcagtgcaatttggtgtatgtgctgaaggtagcaggcaggaccaggaagattttgtacagtgccagacaacacatgcccagtaactgtcagtggtgtcgaggctgagaatccatagaggaagtagaatcctgagccaatgcctgaactttggggttggggaggcaatgcttgagattggattcccagagagagagctttgccagtgttctggaatgtaggagttgtgagggcctttgaatccagccaaaaaaagctgtttctctgcttccagGAGAATTATGGGCAGAAGGACCCAGAAAAAGTGGCGCGGGTGAAAGCACTGTACGAGGAGCTGGATCTGCGGAGTGTGTTCTTCAAGTACGAGGAAGACAGTTACAACCGCCTCAAGAGTCTCATAGAGCAGTGCTCCGCGCCCCTGCCCCCATCCATCTTCCTGGAACTAGCAAACAAGATCTACAAGCGGAGAAAGtaacctcgaattgtagaggctgcgagggaggggtctcaataaattattgttcaacatcctgtggttttatgcttgtgtcaggagttcaaaatggaggggtgggagagggcaacttggaatccaggttggcaaaagaattccttgagacccaaagctgctgcgttgttagatgggtgacataggcacagcgtcaagtgttgcgtggaggttgggaggcggtcctgagctatgccacgcccatgcgtgaaggggtgcggctgcgcagccactgggttttgctggtgcccctcccctccgctctg

Then I tried cat extra/example1.fa | ./cesar /dev/stdin, and here's what I got: 

m@MPC:~/code/TOGA/CESAR2.0$ cat extra/example1.fa | ./cesar /dev/stdin
>referenceExon
                                                                                                    gCCTGGGAACTTCACCTACCACATCCCTGTCAGTAGTGGCACCCCACTGCACCTCAGCCTGACTCTGCAGATGaa                                                                 
>mouse
ctttcctcatttcctcaggcttcagtatagcatgaggctgaggaggagagagggagaccggcaaagtggccttgcttaggtaccatctttgcccctttagGCTTGGCAACTTCACCTACCACATCCCTGTCAGCAGCAGCACACCACTGCACCTCAGCCTGACCCTGCAGATGAAgtgagtgctggtgtgtgggtatgtgtgggggaccatgtggaagccctcagaaaagtgaaagccaagtgcttactaaatttattacgtggagggtccaggc

Does anything look unusual here? Any red flags for what might be going on?

kirilenkobm commented 8 months ago

@mprincipato

I apologise for the long delay... And also, I would recommend using virtualenv to manage python versions between different projects =).

I should say, there are absolutely 0 red flags in the provided output, which makes everything more complicated. The part that crashes is /home/m/code/TOGA/CESAR2.0/cesar /dev/stdin -x 3. It consumes the input directly from stdin, without creating any temporary input files. My guess was that it does not work on WSL, however, it seems like there is another reason for such a behaviour. I need to add some additional logging and maybe provide an option to create these temporary input files. Will keep you updated.