Slight differences in netmhccons_1_1_python_interface.py

Hello. As far as I can understand - the main reason for using your own netmhccons_1_1_python_interface.py are these lines:

    #process_status_code = p.wait()
    analysis_results, ignored_stderr = p.communicate()
    process_status_code = p.returncode

I have subprocess wait warnings in MHC_II installation, so I've tried to dig into you fix for MHC_I. Warning - just for context:

/usr/lib/python3.7/subprocess.py:883: ResourceWarning: subprocess 10 is still running
  ResourceWarning, source=self)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
./configure.py:28: ResourceWarning: unclosed file <_io.TextIOWrapper name=3 encoding='UTF-8'>
  result=os.popen(cmd).read()
ResourceWarning: Enable tracemalloc to get the object allocation traceback

I was curious what are other changes in the original file (and why you decided to overwrite it instead of replacing lines on the fly with sed for example) so I've checked original netmhccons_1_1_python_interface.py from IEDB_MHC_I-3.1 (link to download full archive). I'll attach file here: netmhccons_1_1_python_interface.zip (.zip due to GitHub don't allow me to attach .py).

Here is what I've found:

$ diff mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py netmhccons_1_1_python_interface.py
19,22c19
<     peptides_list = [peptide_list[i:i+500] for i in range(len(peptide_list))[::500]]
<     scores = ()
<     for peptide_list in peptides_list:
<         scores += predict_peptide_list(peptide_list, allele_length_pair)
---
>     scores = predict_peptide_list(peptide_list, allele_length_pair)
37c34
<     infile = tempfile.NamedTemporaryFile(prefix='netmhccons_', suffix='_input', delete=False, mode='w')
---
>     infile = tempfile.NamedTemporaryFile(prefix='netmhccons_', suffix='_input', delete=False)
49,50c46
<         # is the user_defined_allele a seuqnce list?
<         fasta_allele = SequenceOutput().to_fasta(allele)
---
>         fasta_allele = SequenceOutput(allele).to_fasta()
52c48
<                           prefix='netmhccons_', suffix='_usermhc', delete=False, mode='w')
---
>                           prefix='netmhccons_', suffix='_usermhc', delete=False)
67c63
<     logger.info('Calling netmhccons executable:\n%s', ' '.join(cmd))
---
>     logger.info('Calling netmhccons executable:\n{}'.format(' '.join(cmd)))
69c65
<     process_status_code = p.wait()
---
>     #process_status_code = p.wait()
71,72c67,68
<     analysis_results = analysis_results.decode()
<     scores = parse_pickpocket_output(analysis_results)
---
>     process_status_code = p.returncode
>     #scores = parse_pickpocket_output(analysis_results)
77a74
>     scores = parse_pickpocket_output(analysis_results)
85c82
<         logger.error('%s\n%s', msg, analysis_results)
---
>         logger.error(msg + '\n' + analysis_results)

Most of them are formatting and your change - but what about

<     peptides_list = [peptide_list[i:i+500] for i in range(len(peptide_list))[::500]]
<     scores = ()
<     for peptide_list in peptides_list:
<         scores += predict_peptide_list(peptide_list, allele_length_pair)
---
>     scores = predict_peptide_list(peptide_list, allele_length_pair)

and

<         # is the user_defined_allele a seuqnce list?
<         fasta_allele = SequenceOutput().to_fasta(allele)
---
>         fasta_allele = SequenceOutput(allele).to_fasta()

Can these differences be significant?

You are comparing the file to a version from IEDB 3.1. The IEDB version used in our 1.5 docker containers is 2.17 (we will update to a newer version in pVACtools 2.0). In IEDB 2.17 the only difference is the one to the child process handling.

So after pVACtools 2.0 you will use new netmhccons_1_1_python_interface.py from IEDB 3.1+ with your fix, correct?

Yes, in the pVACtools 2.0 images we will also update the netmhccons_1_1_python_interface.py to match the version of IEDB installed in that container with our fix applied.

Thanks for info, @susannasiebert Closing.

@susannasiebert Hello again. According to this line:

#COPY netmhccons_1_1_python_interface.py /opt/iedb/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py

you removed custom netmhccons_1_1_python_interface.py - but in this issue we discussed other method. Should we remove your custom netmhccons_1_1_python_interface.py from our docker images too? Or this is unexpected?

This was an oversight on my end. I still need to recreate the file from the 3.1 IEDB base version of the file. The edited file from the 2.17 version is incompatible with IEDB 3.1 because it is still in python 2.

I apologize for the inconvenience. I will try to get this fixed this week.

Thank you for a quick answer. I'll leave this open till its fixed.

I rebuilt both the 2.0.1 and the latest container to include an updated version of the netmhccons_1_1_python_interface.py file. Let me know if you have any questions.

After update, I've got some errors:

2021-03-11:12:54:44,604 ERROR    [netmhccons_1_1_python_interface.py:78] Error calling netmhccons executable:
/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-A02:01 -length 9 -inptype 1 -f /tmp/netmhccons_5nrt2fd4_input
Traceback (most recent call last):
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 520, in <module>
    Prediction().main()
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 511, in main
    self.commandline_input(args)
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 135, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/soft/IEDB/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/soft/IEDB/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/soft/IEDB/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/soft/IEDB/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 79, in predict_peptide_list
    raise Exception(msg)
Exception: Error calling netmhccons executable:
/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-A02:01 -length 9 -inptype 1 -f /tmp/netmhccons_5nrt2fd4_input
2021-03-11:12:54:44,626 ERROR    [netmhccons_1_1_python_interface.py:78] Error calling netmhccons executable:
/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-B35:01 -length 9 -inptype 1 -f /tmp/netmhccons_la2vzdjc_input
Traceback (most recent call last):
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 520, in <module>
    Prediction().main()
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 511, in main
    self.commandline_input(args)
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 135, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/soft/IEDB/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/soft/IEDB/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/soft/IEDB/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/soft/IEDB/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 79, in predict_peptide_list
    raise Exception(msg)
Exception: Error calling netmhccons executable:
/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-B35:01 -length 9 -inptype 1 -f /tmp/netmhccons_la2vzdjc_input

An exception occured in thread 3: (<class 'subprocess.CalledProcessError'>, Command '['/usr/bin/python3', '/soft/IEDB/mhc_i/src/predict_binding.py', 'netmhccons', 'HLA-A*02:01', '9', '/output/MHC_Class_I/tmp/test_pvacbind.9.fa.split_1-7']' returned non-zero exit status 1.).
Traceback (most recent call last):
  File "/usr/local/bin/pvacbind", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.7/dist-packages/tools/pvacbind/main.py", line 65, in main
    args[0].func.main(args[1])
  File "/usr/local/lib/python3.7/dist-packages/tools/pvacbind/run.py", line 100, in main
    pipeline.execute()
  File "/usr/local/lib/python3.7/dist-packages/lib/pipeline.py", line 744, in execute
    self.call_iedb(chunks, length)
  File "/usr/local/lib/python3.7/dist-packages/lib/pipeline.py", line 680, in call_iedb
    p.print("Making binding predictions on Allele %s and Epitope Length %s with Method %s - File %s - Completed" % (a, epl, method, filename))
  File "/usr/local/lib/python3.7/dist-packages/pymp/__init__.py", line 148, in __exit__
    raise exc_t(exc_val)
TypeError: __init__() missing 1 required positional argument: 'cmd'

Here is result of diff command:

root@1671545ec929:/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable# diff netmhccons_1_1_python_interface.py netmhccons_1_1_python_interface.py.bak                                                                                                                                               
69,70c69                                                                                                                                                      
<     #process_status_code = p.wait()                                                                                                                         
<     process_status_code = p.returncode                                                                                                                      
---                                                                                                                                                           
>     process_status_code = p.wait()                                                                                                                          
73,74c72                                                                                                                                                      
<     #scores = parse_pickpocket_output(analysis_results)                                                                                                     
<                                                                                                                                                             
---                                                                                                                                                           
>     scores = parse_pickpocket_output(analysis_results)                                                                                                      
80,81d77                                                                                                                                                      
<                                                                                                                                                             
<     scores = parse_pickpocket_output(analysis_results)

Your changes look correct to me.

Unfortunately, I'm unable to reproduce the error you are seeing using our test data. Are you seeing the same error when using the official pvactools docker image? Would you be able to send me the input VCF you are running as well as the fill pVACseq command?

This is pVACbind error - not pVACseq - so not input VCF. This is full command:

python3 /usr/local/bin/pvacbind run -t 32 -e1 9,10 -e2 15 --allele-specific-binding-thresholds --iedb-install-directory /soft/IEDB /input/S1_S2_N_E_ORF6.fasta test_pvacbind "HLA-A*02:01,HLA-B*35:01,DRB1*11:01" MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC NetMHCcons NetMHCIIpan NetMHCpan PickPocket SMM SMMPMBEC SMMalign /output

Full FASTA:

>RBD
VEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTG
>S1_subunit_before_RBD
MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQT
>S1_subunit_after_RBD
LLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPRRARSVASQSIIAY
>S2_subunit
TQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT
>N_protein
MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSKRTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA
>E_protein
MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV
>ORF6
MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQLDEEQPMEI

Full run log:

 Command: 'python3 /usr/local/bin/pvacbind run -t 32 -e1 9,10 -e2 15 --allele-specific-binding-thresholds --iedb-install-directory /soft/IEDB /input/S1_S2_N_E_ORF6.fasta test_pvacbind "HLA-A*02:01,HLA-B*35:01,DRB1*11:01" MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC NetMHCcons NetMHCIIpan NetMHCpan PickPocket SMM SMMPMBEC SMMalign /output'.
  PID=232 (last job)
Executing MHC Class I predictions
Splitting FASTA into smaller chunks
Splitting FASTA into smaller chunks - Entries 1-7
Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-B*35:01.9.tsv_1-7 - Completed
2021-03-11:12:54:44,604 ERROR    [netmhccons_1_1_python_interface.py:78] Error calling netmhccons executable:
/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-A02:01 -length 9 -inptype 1 -f /tmp/netmhccons_5nrt2fd4_input
Traceback (most recent call last):
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 520, in <module>
    Prediction().main()
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 511, in main
    self.commandline_input(args)
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 135, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/soft/IEDB/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/soft/IEDB/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/soft/IEDB/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/soft/IEDB/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 79, in predict_peptide_list
    raise Exception(msg)
Exception: Error calling netmhccons executable:
/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-A02:01 -length 9 -inptype 1 -f /tmp/netmhccons_5nrt2fd4_input
2021-03-11:12:54:44,626 ERROR    [netmhccons_1_1_python_interface.py:78] Error calling netmhccons executable:
/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-B35:01 -length 9 -inptype 1 -f /tmp/netmhccons_la2vzdjc_input
Traceback (most recent call last):
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 520, in <module>
    Prediction().main()
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 511, in main
    self.commandline_input(args)
  File "/soft/IEDB/mhc_i/src/predict_binding.py", line 135, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/soft/IEDB/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/soft/IEDB/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/soft/IEDB/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/soft/IEDB/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 79, in predict_peptide_list
    raise Exception(msg)
Exception: Error calling netmhccons executable:
/soft/IEDB/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-B35:01 -length 9 -inptype 1 -f /tmp/netmhccons_la2vzdjc_input
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-A*02:01.9.tsv_1-7 - Completed
An exception occured in thread 3: (<class 'subprocess.CalledProcessError'>, Command '['/usr/bin/python3', '/soft/IEDB/mhc_i/src/predict_binding.py', 'netmhccons', 'HLA-A*02:01', '9', '/output/MHC_Class_I/tmp/test_pvacbind.9.fa.split_1-7']' returned non-zero exit status 1.).
Traceback (most recent call last):
  File "/usr/local/bin/pvacbind", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.7/dist-packages/tools/pvacbind/main.py", line 65, in main
    args[0].func.main(args[1])
  File "/usr/local/lib/python3.7/dist-packages/tools/pvacbind/run.py", line 100, in main
    pipeline.execute()
  File "/usr/local/lib/python3.7/dist-packages/lib/pipeline.py", line 744, in execute
    self.call_iedb(chunks, length)
  File "/usr/local/lib/python3.7/dist-packages/lib/pipeline.py", line 680, in call_iedb
    p.print("Making binding predictions on Allele %s and Epitope Length %s with Method %s - File %s - Completed" % (a, epl, method, filename))
  File "/usr/local/lib/python3.7/dist-packages/pymp/__init__.py", line 148, in __exit__
    raise exc_t(exc_val)
TypeError: __init__() missing 1 required positional argument: 'cmd'

Here is full run log with original file from IEBD:


  Command: 'python3 /usr/local/bin/pvacbind run -t 32 -e1 9,10 -e2 15 --allele-specific-binding-thresholds --iedb-install-directory /soft/IEDB /input/S1_S2_N_E_ORF6.fasta test_pvacbind "HLA-A*02:01,HLA-B*35:01,DRB1*11:01" MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC NetMHCcons NetMHCIIpan NetMHCpan PickPocket SMM SMMPMBEC SMMalign /output'.
  PID=232 (last job)
Executing MHC Class I predictions
Splitting FASTA into smaller chunks
Splitting FASTA into smaller chunks - Entries 1-7
Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-A*02:01.9.tsv_1-7 - Completed
Parsing binding predictions for Allele HLA-A*02:01 and Epitope Length 9 - Entries 1-7
Parsing prediction file for Allele HLA-A*02:01 and Epitope Length 9 - Entries 1-7
Parsing prediction file for Allele HLA-A*02:01 and Epitope Length 9 - Entries 1-7 - Completed
Parsing binding predictions for Allele HLA-B*35:01 and Epitope Length 9 - Entries 1-7
Parsing prediction file for Allele HLA-B*35:01 and Epitope Length 9 - Entries 1-7
Parsing prediction file for Allele HLA-B*35:01 and Epitope Length 9 - Entries 1-7 - Completed
Splitting FASTA into smaller chunks
Splitting FASTA into smaller chunks - Entries 1-7
Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-A*02:01.10.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-A*02:01.10.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-A*02:01.10.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-A*02:01.10.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-A*02:01.10.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-A*02:01.10.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-A*02:01.10.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-B*35:01.10.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-B*35:01.10.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-B*35:01.10.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-B*35:01.10.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-B*35:01.10.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-B*35:01.10.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-B*35:01.10.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-B*35:01.10.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-A*02:01.10.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-A*02:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method SMMPMBEC - File /output/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-B*35:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-A*02:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method SMM - File /output/MHC_Class_I/tmp/test_pvacbind.smm.HLA-B*35:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-B*35:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method NetMHC - File /output/MHC_Class_I/tmp/test_pvacbind.ann.HLA-A*02:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-B*35:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method PickPocket - File /output/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-A*02:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-A*02:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method NetMHCcons - File /output/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-B*35:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-B*35:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method MHCnuggetsI - File /output/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-A*02:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-A*02:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method NetMHCpan - File /output/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-B*35:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 10 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-B*35:01.10.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 10 with Method MHCflurry - File /output/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-A*02:01.10.tsv_1-7 - Completed
Parsing binding predictions for Allele HLA-A*02:01 and Epitope Length 10 - Entries 1-7
Parsing prediction file for Allele HLA-A*02:01 and Epitope Length 10 - Entries 1-7
Parsing prediction file for Allele HLA-A*02:01 and Epitope Length 10 - Entries 1-7 - Completed
Parsing binding predictions for Allele HLA-B*35:01 and Epitope Length 10 - Entries 1-7
Parsing prediction file for Allele HLA-B*35:01 and Epitope Length 10 - Entries 1-7
Parsing prediction file for Allele HLA-B*35:01 and Epitope Length 10 - Entries 1-7 - Completed
Combining Parsed Prediction Files
Completed
Creating aggregated report
Completed
Calculating Manufacturability Metrics
Completed
Running Binding Filters
Completed
Running Top Score Filter
Completed

Done: Pipeline finished successfully. File /output/MHC_Class_I/test_pvacbind.filtered.tsv contains list of filtered putative neoantigens.

Executing MHC Class II predictions
Splitting FASTA into smaller chunks
Splitting FASTA into smaller chunks - Entries 1-7
Completed
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method NNalign - File /output/MHC_Class_II/tmp/test_pvacbind.nn_align.DRB1*11:01.15.tsv_1-7
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method NetMHCIIpan - File /output/MHC_Class_II/tmp/test_pvacbind.NetMHCIIpan.DRB1*11:01.15.tsv_1-7
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method SMMalign - File /output/MHC_Class_II/tmp/test_pvacbind.smm_align.DRB1*11:01.15.tsv_1-7
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method MHCnuggetsII - File /output/MHC_Class_II/tmp/test_pvacbind.MHCnuggetsII.DRB1*11:01.15.tsv_1-7
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method SMMalign - File /output/MHC_Class_II/tmp/test_pvacbind.smm_align.DRB1*11:01.15.tsv_1-7 - Completed
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method NNalign - File /output/MHC_Class_II/tmp/test_pvacbind.nn_align.DRB1*11:01.15.tsv_1-7 - Completed
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method MHCnuggetsII - File /output/MHC_Class_II/tmp/test_pvacbind.MHCnuggetsII.DRB1*11:01.15.tsv_1-7 - Completed
Making binding predictions on Allele DRB1*11:01 and Epitope Length 15 with Method NetMHCIIpan - File /output/MHC_Class_II/tmp/test_pvacbind.NetMHCIIpan.DRB1*11:01.15.tsv_1-7 - Completed
Parsing binding predictions for Allele DRB1*11:01 and Epitope Length 15 - Entries 1-7
Parsing prediction file for Allele DRB1*11:01 and Epitope Length 15 - Entries 1-7
Parsing prediction file for Allele DRB1*11:01 and Epitope Length 15 - Entries 1-7 - Completed
Combining Parsed Prediction Files
Completed
Creating aggregated report
Completed
Calculating Manufacturability Metrics
Completed
Running Binding Filters
Completed
Running Top Score Filter
Completed

Done: Pipeline finished successfully. File /output/MHC_Class_II/test_pvacbind.filtered.tsv contains list of filtered putative neoantigens.

Creating combined reports
Creating aggregated report
Completed
Running Binding Filters
Completed
Running Top Score Filter
Completed

Done: Pipeline finished successfully. File /output/combined/test_pvacbind.filtered.tsv contains list of filtered putative neoantigens.```

Errors in original pvactools image:

root@b8de4f01bd19:/opt/iedb# pvacbind run -t 32 -e1 9,10 -e2 15 --allele-specific-binding-thresholds --iedb-install-directory $PWD /inputs/tests/input_data/S1_S2_N_E_ORF6.fasta test_pvacbind "HLA-A*02:01,HLA-B*35:01,DRB1*11:01" MHCflurry MHCnuggetsI MHCnuggetsII NNalign NetMHC NetMHCcons NetMHCIIpan NetMHCpan PickPo
cket SMM SMMPMBEC SMMalign /opt/
Executing MHC Class I predictions
Splitting FASTA into smaller chunks
Splitting FASTA into smaller chunks - Entries 1-7
Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCnuggetsI - File /opt/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - File /opt/MHC_Class_I/tmp/test_pvacbind.ann.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCcons - File /opt/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCpan - File /opt/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method PickPocket - File /opt/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMM - File /opt/MHC_Class_I/tmp/test_pvacbind.smm.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMMPMBEC - File /opt/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCflurry - File /opt/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCnuggetsI - File /opt/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHC - File /opt/MHC_Class_I/tmp/test_pvacbind.ann.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCcons - File /opt/MHC_Class_I/tmp/test_pvacbind.netmhccons.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCpan - File /opt/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method PickPocket - File /opt/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMM - File /opt/MHC_Class_I/tmp/test_pvacbind.smm.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMMPMBEC - File /opt/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-B*35:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCflurry - File /opt/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-A*02:01.9.tsv_1-7
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMM - File /opt/MHC_Class_I/tmp/test_pvacbind.smm.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMMPMBEC - File /opt/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method SMMPMBEC - File /opt/MHC_Class_I/tmp/test_pvacbind.smmpmbec.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method SMM - File /opt/MHC_Class_I/tmp/test_pvacbind.smm.HLA-B*35:01.9.tsv_1-7 - Completed
2021-03-11:14:50:28,22 ERROR    [netmhccons_1_1_python_interface.py:78] Error calling netmhccons executable:
/opt/iedb/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-A02:01 -length 9 -inptype 1 -f /tmp/netmhccons_15bwq1qp_input
Traceback (most recent call last):
  File "/opt/iedb/mhc_i/src/predict_binding.py", line 520, in <module>
    Prediction().main()
  File "/opt/iedb/mhc_i/src/predict_binding.py", line 511, in main
    self.commandline_input(args)
  File "/opt/iedb/mhc_i/src/predict_binding.py", line 135, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/opt/iedb/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/opt/iedb/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/opt/iedb/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/opt/iedb/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 79, in predict_peptide_list
    raise Exception(msg)
Exception: Error calling netmhccons executable:
/opt/iedb/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-A02:01 -length 9 -inptype 1 -f /tmp/netmhccons_15bwq1qp_input
2021-03-11:14:50:28,52 ERROR    [netmhccons_1_1_python_interface.py:78] Error calling netmhccons executable:
/opt/iedb/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-B35:01 -length 9 -inptype 1 -f /tmp/netmhccons_mn0dz2bi_input
Traceback (most recent call last):
  File "/opt/iedb/mhc_i/src/predict_binding.py", line 520, in <module>
    Prediction().main()
  File "/opt/iedb/mhc_i/src/predict_binding.py", line 511, in main
    self.commandline_input(args)
  File "/opt/iedb/mhc_i/src/predict_binding.py", line 135, in commandline_input
    mhc_scores = mhc_predictor.predict(input.input_protein.as_amino_acid_text())
  File "/opt/iedb/mhc_i/src/seqpredictor.py", line 903, in predict
    scores.append(predictor.predict_sequence(sequence,pred))
  File "/opt/iedb/mhc_i/src/seqpredictor.py", line 479, in predict_sequence
    scores = predict_netmhccons(sequence, (allele_name_or_sequence, self.length))
  File "/opt/iedb/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 22, in predict_sequence
    scores += predict_peptide_list(peptide_list, allele_length_pair)
  File "/opt/iedb/mhc_i/src/../method/netmhccons-1.1-executable/netmhccons_1_1_executable/netmhccons_1_1_python_interface.py", line 79, in predict_peptide_list
    raise Exception(msg)
Exception: Error calling netmhccons executable:
/opt/iedb/mhc_i/method/netmhccons-1.1-executable/netmhccons_1_1_executable/netMHCcons -a HLA-B35:01 -length 9 -inptype 1 -f /tmp/netmhccons_mn0dz2bi_input
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHC - File /opt/MHC_Class_I/tmp/test_pvacbind.ann.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHC - File /opt/MHC_Class_I/tmp/test_pvacbind.ann.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method PickPocket - File /opt/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method PickPocket - File /opt/MHC_Class_I/tmp/test_pvacbind.pickpocket.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method NetMHCpan - File /opt/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method NetMHCpan - File /opt/MHC_Class_I/tmp/test_pvacbind.netmhcpan.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCnuggetsI - File /opt/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCnuggetsI - File /opt/MHC_Class_I/tmp/test_pvacbind.MHCnuggetsI.HLA-A*02:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-B*35:01 and Epitope Length 9 with Method MHCflurry - File /opt/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-B*35:01.9.tsv_1-7 - Completed
Making binding predictions on Allele HLA-A*02:01 and Epitope Length 9 with Method MHCflurry - File /opt/MHC_Class_I/tmp/test_pvacbind.MHCflurry.HLA-A*02:01.9.tsv_1-7 - Completed
An exception occured in thread 3: (<class 'subprocess.CalledProcessError'>, Command '['/usr/local/bin/python', '/opt/iedb/mhc_i/src/predict_binding.py', 'netmhccons', 'HLA-A*02:01', '9', '/opt/MHC_Class_I/tmp/test_pvacbind.9.fa.split_1-7']' returned non-zero exit status 1.).
Traceback (most recent call last):
  File "/usr/local/bin/pvacbind", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.7/site-packages/tools/pvacbind/main.py", line 65, in main
    args[0].func.main(args[1])
  File "/usr/local/lib/python3.7/site-packages/tools/pvacbind/run.py", line 100, in main
    pipeline.execute()
  File "/usr/local/lib/python3.7/site-packages/lib/pipeline.py", line 744, in execute
    self.call_iedb(chunks, length)
  File "/usr/local/lib/python3.7/site-packages/lib/pipeline.py", line 680, in call_iedb
    p.print("Making binding predictions on Allele %s and Epitope Length %s with Method %s - File %s - Completed" % (a, epl, method, filename))
  File "/usr/local/lib/python3.7/site-packages/pymp/__init__.py", line 148, in __exit__
    raise exc_t(exc_val)
TypeError: __init__() missing 1 required positional argument: 'cmd'

Ok, I moved the order of some of those calls in the wrapper around and I think that fixed it. The 2.0.1 and latest images are currently rebuilding. You can check https://hub.docker.com/repository/docker/griffithlab/pvactools for the status. Please make sure to pull the latest image built before running these docker containers so that you get the update.

Thank you, I'll check tomorrow and report here.

Everything working fine, thanks. Closing.

griffithlab / docker-pvactools

Slight differences in netmhccons_1_1_python_interface.py #30