Open ymatts opened 1 year ago
yafeng
commented
1 year ago @ymatts Hi, it seems the input file given to svmToTSV command caused the error. I suggest you locate to the work directory for the specific process
**[e1/236e28] process > svmToTSV (2)
check the input file, see it looks normal. Try run this command separately in this directory, see if you get same error.
Yafeng
ymatts
commented
1 year ago @yafeng Thank you very much for your response. I have tried executing as you suggested.
I would like to ask your suggestion this time about the following error output when I run
$bash .command.sh
in the directory where the file in issue is located.
from: can't read /var/mail/glob
.command.sh: line 3: syntax error near unexpected token `('
.command.sh: line 3: `mzidtsvfns = sorted(glob('mzidtsv*'))'Any advice you can give me when you have time would be greatly appreciated.
Best regards Yusuke
The following is a summary of what I have done for your reference.
1. Go to the work directory in issue and check the files. Three files were created.
2. check the contents of the file Visually, the file appeared to be generated correctly.
3. Independently execute the command in the directory containing the files in issue
I ran the nextflown intermediate script in each of the directories containing the three files above.
The results are as follows.
$ bash .command.run
The same error was output as the last time the whole process was run.
Traceback (most recent call last):
File "***/work2/43/ea8b0db1c692d9e43736093987c279/.command.sh", line 10, in <module>
for psm in sorted([(pid, float(p.find('{%s}svm_score' % ns['xmlns']).text), p) for pid, p in psms.items()], reverse=True, key=lambda x:x[1]):
File "***/work2/43/ea8b0db1c692d9e43736093987c279/.command.sh", line 10, in <listcomp>
for psm in sorted([(pid, float(p.find('{%s}svm_score' % ns['xmlns']).text), p) for pid, p in psms.items()], reverse=True, key=lambda x:x[1]):
AttributeError: 'NoneType' object has no attribute 'text'The results of the second command are as follows
$bash .command.sh
This error was newly confirmed in this run.
from: can't read /var/mail/glob
.command.sh: line 3: syntax error near unexpected token `('
.command.sh: line 3: `mzidtsvfns = sorted(glob('mzidtsv*'))'I checked and it seems that it is common for this error output to occur when the shell script to be executed (in this case .command.sh) does not have the shebang on the first line. I checked the .command.sh script, and the shebang was written correctly.
4. other For reference, here are the results of the run, the several lines of the file, and the script in issue(.command.sh). First, I went to the directory where the problem was occurring and checked the three output files:
$cd work2/43/ea8b0db1c692d9e43736093987c279
$ls -lh The following files were found.
*** xyz docker 126 Sep 21 17:03 filtprot -> ***/work2/b9/07aa3d4db11c24e1681a089af75ab3/filtprot
*** xyz docker 152 Sep 21 17:03 mzident1 -> ***/work2/0c/6d41dad785b56a982d05c5219d6d60/20220512_hela200ng_woFAIMS_01.mzid
*** xyz docker 130 Sep 21 17:03 mzidtsv1 -> ***/work2/f3/2c55fc48366f044a1f3585970c630d/out.mzid.tsvNext, I checked the file contents.
$ head -n20 filtprot
Result:
<?xml version='1.0' encoding='UTF-8'?>
<percolator_output xmlns="http://per-colator.com/percolator_out/15" xmlns:p="http://per-colator.com/percolator_out/15" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://per-colator.com/percolator_out/15 https://github.com/percolator/percolator/raw/pout-1-5/src/xml/percolator_out.xsd" p:majorVersion="3" p:minorVersion="04" p:percolator_version="Percolator version 3.04.0">
<process_info>
<command_line>percolator -j percoin.xml -X perco.xml -N 500000 --decoy-xml-output -y</command_line>
<other_command_line/>
<pi_0_psms>0.467598</pi_0_psms>
<pi_0_peptides>0.527571</pi_0_peptides>
<psms_qlevel>37264</psms_qlevel>
<peptides_qlevel>28472</peptides_qlevel>
</process_info>
<psms>
<psm p:psm_id="20220512_hela200ng_woFAIMS_01_SII_102871_1_102871_3_1" p:decoy="false">
<svm_score>5.973</svm_score>
<q_value>2.529e-05</q_value>
<pep>1.003e-21</pep>
<exp_mass>1104.5200</exp_mass>
<calc_mass>1104.190</calc_mass>
<peptide_seq n="-" c="-" seq="QAESC[UNIMOD:4]DC[UNIMOD:4]LQGFQLTHSLGGGTGSGMGTLLLSK"/>
nagoya-bmhi@stratus052:~/projects/proj_abe/pan-cancer-proteogenomics-analysis-master/work2/43/ea8b0db1c692d9e43736093987c279$ head -n10 filtprot
<?xml version='1.0' encoding='UTF-8'?>
<percolator_output xmlns="http://per-colator.com/percolator_out/15" xmlns:p="http://per-colator.com/percolator_out/15" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://per-colator.com/percolator_out/15 https://github.com/percolator/percolator/raw/pout-1-5/src/xml/percolator_out.xsd" p:majorVersion="3" p:minorVersion="04" p:percolator_version="Percolator version 3.04.0">
<process_info>
<command_line>percolator -j percoin.xml -X perco.xml -N 500000 --decoy-xml-output -y</command_line>
<other_command_line/>
<pi_0_psms>0.467598</pi_0_psms>
<pi_0_peptides>0.527571</pi_0_peptides>
<psms_qlevel>37264</psms_qlevel>
<peptides_qlevel>28472</peptides_qlevel>
I checked next file:
head -n20 mzident1
Result:
<?xml version="1.0" encoding="UTF-8"?>
<MzIdentML xmlns="http://psidev.info/psi/pi/mzIdentML/1.1" id="MS-GF+" version="1.1.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzIdentML/1.1 http://www.psidev.info/files/mzIdentML1.1.0.xsd" creationDate="2022-09-21T03:54:23">
<cvList>
<cv fullName="PSI-MS" version="3.30.0" uri="https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo" id="PSI-MS"/>
<cv fullName="UNIMOD" uri="http://www.unimod.org/obo/unimod.obo" id="UNIMOD"/>
<cv fullName="UNIT-ONTOLOGY" uri="https://raw.githubusercontent.com/bio-ontology-research-group/unit-ontology/master/unit.obo" id="UO"/>
</cvList>
<AnalysisSoftwareList>
<AnalysisSoftware version="Release (v2022.04.18)" id="ID_software" name="MS-GF+">
<SoftwareName>
<cvParam cvRef="PSI-MS" accession="MS:1002048" name="MS-GF+"/>
</SoftwareName>
</AnalysisSoftware>
</AnalysisSoftwareList>
<SequenceCollection>
<DBSequence length="32" searchDatabase_ref="SearchDB_1" accession="COSMIC:ENST00000328974:TUBB8:p.E123Q:Substitution-Missense:1" id="DBSeq502834812">
<cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="COSMIC:ENST00000328974:TUBB8:p.E123Q:Substitution-Missense:1"/>
</DBSequence>
<DBSequence length="187" searchDatabase_ref="SearchDB_1" accession="ENSP00000261313.2" id="DBSeq602042350">
<cvParam cvRef="PSI-MS" accession="MS:1001088" name="protein description" value="ENSP00000261313.2 pep chromosome:GRCh38:12:118135858:118145584:1 gene:ENSG00000089220.4 transcript:ENST00000261313.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:PEBP1 description:phosphatidylethanolamine binding protein 1 [Source:HGNC Symbol;Acc:HGNC:8630]"/>Finally, I checked third file.
head -n20 mzidtsv1
Result:
#SpecFile SpecId ScanNum ScanTime(Min) FragMethod Precursor IsotopeError PrecursorError(ppm) Charge Peptide Protein DeNovoScore MSGFScore SpecEValue EValue QValue PepQValue
20220512_hela200ng_woFAIMS_01.mzML scan=102871 102871 77.36203 HCD 1104.51575 1 -6.28241 3 QAESC+57.021DC+57.021LQGFQLTHSLGGGTGSGMGTLLLSK COSMIC:ENST00000328974:TUBB8:p.E123Q:Substitution-Missense:1 327 325 7.4168E-39 2.6297E-30 0.0 0.0
20220512_hela200ng_woFAIMS_01.mzML scan=103252 103252 77.61435 HCD 868.68536 0 0.49183 4 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK ENSP00000261313.2 243 233 1.274E-37 4.517E-29 0.0 0.0
20220512_hela200ng_woFAIMS_01.mzML scan=101815 101815 76.65645 HCD 1104.51758 1 -4.62413 3 QAESC+57.021DC+57.021LQGFQLTHSLGGGTGSGMGTLLLSK COSMIC:ENST00000328974:TUBB8:p.E123Q:Substitution-Missense:1 342 338 1.9869E-37 7.0448E-29 0.0 0.0
20220512_hela200ng_woFAIMS_01.mzML scan=92212 92212 70.25015 HCD 868.68555 0 0.70262 4 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK ENSP00000261313.2 245 239 3.9352E-37 1.3953E-28 0.0 0.0
20220512_hela200ng_woFAIMS_01.mzML scan=113071 113071 84.21866 HCD 1137.86035 0 -1.39465 3 TTIPEEEEEEEEAAGVVVEEELFHQQGTPR ENSP00000261366.5 295 289 9.0405E-37 3.1719E-28 0.0 0.0
20220512_hela200ng_woFAIMS_01.mzML scan=98198 98198 74.24255 HCD 964.8396 0 1.83453 3 PAVVAPAPVVEAVSTPSAAFPSDATAENVK CanProVar_rs184666535_ILF3_S482L_missense_8 204 200 6.0905E-36 2.1369E-27 0.0 0.0
20220512_hela200ng_woFAIMS_01.mzML scan=102721 102721 77.26036 HCD 868.68597 0 1.19445 4 WSGPLSLQEVDEQPQHPLHVTYAGAAVDELGK ENSP00000261313.2 233 216 8.1685E-36 2.8962E-27 0.0 0.0
20220512_hela200ng_woFAIMS_01.mzML scan=125541 125541 92.64829 HCD 1091.17517 0 -1.56618 3 VADEDDVDNEEAALLHEEATMTIEELLTR ENSP00000342778.4 368 345 1.2355E-35 4.3101E-27 0.0 0.0
20220512_hela200ng_woFAIMS_01.mzML scan=72302 72302 56.99773 HCD 758.56421 0 1.52877 5 LVQAFQYTDEHGEVC+57.021PAGWKPGSDTIKPNVDDSK ENSP00000301522.2 199 178 1.7509E-35 6.268E-27 0.0 0.0Finally, paste the contents of the shell script ".command.sh".
I have confirmed that
$/usr/bin/env python3
will launch python correctly.
#!/usr/bin/env python3
from glob import glob
mzidtsvfns = sorted(glob('mzidtsv*'))
mzidfns = sorted(glob('mzident*'))
from app.readers import pycolator, xml, tsv, mzidplus
import os
ns = xml.get_namespace_from_top('filtprot', None)
psms = {p.attrib['{%s}psm_id' % ns['xmlns']]: p for p in pycolator.generate_psms('filtprot', ns)}
decoys = {True: 0, False: 0}
for psm in sorted([(pid, float(p.find('{%s}svm_score' % ns['xmlns']).text), p) for pid, p in psms.items()], reverse=True, key=lambda x:x[1]):
pdecoy = psm[2].attrib['{%s}decoy' % ns['xmlns']] == 'true'
decoys[pdecoy] += 1
try:
psms[psm[0]] = {'decoy': pdecoy, 'svm': psm[1], 'qval': decoys[True]/decoys[False]} # T-TDC
except ZeroDivisionError:
psms[psm[0]] = {'decoy': pdecoy, 'svm': psm[1], 'qval': 1.0} # T-TDC
decoys = {'true': 0, 'false': 0}
for svm, pep in sorted([(float(x.find('{%s}svm_score' % ns['xmlns']).text), x) for x in pycolator.generate_peptides('filtprot', ns)], reverse=True, key=lambda x:x[0]):
decoys[pep.attrib['{%s}decoy' % ns['xmlns']]] += 1
try:
[psms[pid.text].update({'pepqval': decoys['true']/decoys['false']}) for pid in pep.find('{%s}psm_ids' % ns['xmlns'])]
except ZeroDivisionError:
[psms[pid.text].update({'pepqval': 1.0}) for pid in pep.find('{%s}psm_ids' % ns['xmlns'])]
oldheader = tsv.get_tsv_header(mzidtsvfns[0])
header = oldheader + ['percolator svm-score', 'PSM q-value', 'peptide q-value']
with open('mzidperco', 'w') as fp:
fp.write('\t'.join(header))
for fnix, mzidfn in enumerate(mzidfns):
mzns = mzidplus.get_mzid_namespace(mzidfn)
siis = (sii for sir in mzidplus.mzid_spec_result_generator(mzidfn, mzns) for sii in sir.findall('{%s}SpectrumIdentificationItem' % mzns['xmlns']))
for specidi, psm in zip(siis, tsv.generate_tsv_psms(mzidtsvfns[fnix], oldheader)):
# percolator psm ID is: samplename_SII_scannr_rank_scannr_charge_rank
print(specidi)
print(psm)
scan, rank = specidi.attrib['id'].replace('SII_', '').split('_')
outpsm = {k: v for k,v in psm.items()}
spfile = os.path.splitext(psm['#SpecFile'])[0]
try:
percopsm = psms['{fn}_SII_{sc}_{rk}_{sc}_{ch}_{rk}'.format(fn=spfile, sc=scan, rk=rank, ch=psm['Charge'])]
except KeyError:
continue
if percopsm['decoy']:
continue
fp.write('\n')
outpsm.update({'percolator svm-score': percopsm['svm'], 'PSM q-value': percopsm['qval'], 'peptide q-value': percopsm['pepqval']})
fp.write('\t'.join([str(outpsm[k]) for k in header]))
I am referring it to @glormph. He contributed to the code of this specific process. Hi, Jorrit! Can you have a look at this issue?
glormph
commented
1 year ago Hi @yafeng, nice to hear from you, hope all is OK! It took me a while before realizing this is not our old ipaw, but a new repo! :D
@ymatts So, the from app.readers import ... line is referring to our msstitch library, which we (in our @lehtiolab/proteogenomics-analysis-workflow ) use inside a conda env in a docker container. Judging from your command line -profile docker,standard \ you also run docker, and I don't see any errors about this line, so it should be fine. But I'm not sure which container you're in (in this repo I don't see a nextflow.config file for example).
Indeed, if you rerun, use bash .command.run, which will setup the nextflow environment you have to run .command.sh. Yu can change code inside the .command.sh if you want, .command.run will use it and also sets up any containers you use etc. In this case .command.sh is a python script and not bash, so the error from: can't read /var/mail/glob is no problem.
The error seems to be that the XML parser encounters a None element when sorting PSMs from percolator in the filtprot file. It does .text to get the text from an <svm_score/> element, and that is instead a None. I'm not sure why, and when you showed the results of head -n20 filtprot it looked fine for that one PSM which was in the first lines. So maybe there's a PSM without a percolator svm score, inside the filtprot file, which would be strange. That file is generated inside the filterPercolator process here: https://github.com/yafeng/pan-cancer-proteogenomics-analysis/blob/master/ipaw.hg38.nf#L295
To look at that PSM, insert this code right after decoys = {True: 0, False: 0} into .command.sh and rerun with bash .command.run:
for p in psms.values():
try:
p.find('{%s}svm_score' % ns['xmlns']).text
except AttributeError:
print(etree.tostring(p, pretty_print=True))Then you can see how the PSMs look which are erroring.
ymatts
commented
1 year ago @yafeng Thank you for your response.
@glormph Hello and thank you for your time. I inserted the code you suggested into .command.sh and ran it again.
$bash .command.sh
However, I am getting the following error. I would be very grateful if you could tell me how to deal with it when you have time.
File "work2/43/ea8b0db1c692d9e43736093987c279/.command.sh", line 13, in <module>
p.find('{%s}svm_score' % ns['xmlns']).text
AttributeError: 'NoneType' object has no attribute 'text'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/nagoya-bmhi/projects/proj_abe/pan-cancer-proteogenomics-analysis-master/work2/43/ea8b0db1c692d9e43736093987c279/.command.sh", line 15, in <module>
print(etree.tostring(p, pretty_print=True))
NameError: name 'etree' is not definedAlso, in response to the comment that it is unclear which container was used, the contents of nextflow.config, Dockerfile and environment.yml are pasted below.
you also run docker, and I don't see any errors about this line, so it should be fine. But I'm not sure which container you're in (in this repo I don't see a nextflow.config file for example).
params {
//container = 'glormph/ipaw:dev' // Container slug. Stable releases should specify release tag!
container = 'glormph/ipaw:0.4' // Container slug. Stable releases should specify release tag!
outdir = './results'
tracedir = "${params.outdir}/pipeline_info"
awsqueue = false
awsregion = 'eu-west-1'
// VarDB v.1 headers
novheaders = '^PGOHUM;^lnc;^decoy_PGOHUM;^decoy_lnc'
varheaders = '^COSMIC;^CanProVar;^decoy_COSMIC;^decoy_CanProVar'
}
profiles {
standard {
includeConfig 'conf/base.config'
}
conda { process.conda = "$baseDir/environment.yml" }
docker {
docker.enabled = true
docker.fixOwnership = true
docker.runOptions = '-u $(id -u):$(id -g)'
}
singularity {
singularity.enabled = true
}
lehtio {
includeConfig 'conf/base.config'
includeConfig 'conf/lehtio.config'
}
uppmax {
includeConfig 'conf/base.config'
includeConfig 'conf/uppmax.config'
}
testing {
includeConfig 'conf/base.config'
}
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if(type == 'memory'){
try {
if(obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if(type == 'time'){
try {
if(obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if(type == 'cpus'){
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}
FROM nfcore/base
LABEL description="Docker image containing all requirements for IPAW pipeline"COPY envs /envs/ RUN conda env create -f /envs/environment.yml && conda clean -a
RUN git clone https://github.com/yafeng/SpectrumAI /SpectrumAI RUN cd /SpectrumAI && git pull && git reset --hard b8e7001807d834db633c30d265ef6e8361cdcb3c
ENV PATH /opt/conda/envs/ipaw-0.4/bin:$PATH
- enviornment.yml:name: ipaw-0.4 channels:
I also briefly parsed the filtprot and checked the svm_score. In particular, no missing, nulls, etc. were found, and at first glance there appears to be no problem.
A simple table of filtprot:. filtprot_table.txt
R script written to check:.
setwd("work2/43/ea8b0db1c692d9e43736093987c279/")
# scan row by row
rawdat <- scan("filtprot",what = "character",sep = "\n")
# convert table psm
psm_st <- grep("^<psm",rawdat)
psm_ed <- grep("</psm>",rawdat)
length(psm_st)==length(psm_ed) # check whether there is any missing tag
psm_li <- vector("list",length(psm_st))
for(i in seq_along(psm_st)){
tmp <- gsub(" ","",rawdat[psm_st[i]:psm_ed[i]])
psm <- tmp[grep("^<psm",tmp)]
svmscore <- tmp[grep("^<svm_score",tmp)]
q_value <- tmp[grep("^<q_value",tmp)]
disp <- c(psm,svmscore,q_value)
psm_li[[i]] <- disp
}
psm_df <- do.call(rbind,psm_li)
psm_df
# convert table peptide
pep_st <- grep("^<peptide",rawdat)
pep_ed <- grep("</peptide>",rawdat)
length(pep_st)==length(pep_ed) # check whether there is any missing tag
pep_li <- vector("list",length(pep_st))
for(i in seq_along(pep_st)){
tmp <- gsub(" ","",rawdat[pep_st[i]:pep_ed[i]])
pep <- tmp[grep("^<peptide",tmp)]
svmscore <- tmp[grep("^<svm_score",tmp)]
q_value <- tmp[grep("^<q_value",tmp)]
disp <- c(pep,svmscore,q_value)
pep_li[[i]] <- disp
}
pep_df <- do.call(rbind,pep_li)
output <- data.frame(rbind(psm_df,pep_df))
colnames(output) <- c("header","svm_score","q_value")
output[,2] <- gsub("<svm_score>|</svm_score>","",output[,2])
output[,3] <- gsub("<q_value>|</q_value>","",output[,2])
output[,2] <- as.numeric(output[,2])
output[,3] <- as.numeric(output[,3])
all(!is.na(output[,2])) # TRUE
all(!is.nan(output[,2])) #TRUE
all(!is.null(output[,2])) # TRUE
write.table(output,file = "filtprot_table.txt",sep="\t",row.names = FALSE,col.names = TRUE)
Best regards Yusuke
yafeng
commented
1 year ago @glormph Glad to hear your response too! This workflow was modified based it your previous version. I used it to search public datasets.
Regarding the svmtoTSV process, i have not seen this error before.
@ymatts Since you have the input file, I suggest to copy the python script and run it in standalone version, such as
python3 svmtoTSV.py input.id output.tsv
just to see if the error is related to nextflow environment or python library/version ... @glormph may have better advice, he is a more experienced nextflow player :)
glormph
commented
1 year ago Thanks, now I understand it a bit better! The run environment seems to be more or less the same as in our old pipeline. It's still a strange error though. Even if we find the problem, it can have been caused in another NF process upstream, and we may need to look there too :(
As for the new error message from the code we added, etree needs importing, so you can add the line from lxml import etree to the top of the "extra" python code and run bash .command.run again.
ymatts
commented
1 year ago @yafeng
Thank you so much for your time. I am trying to attempt python standalone as you suggested, but I am stuck on elementary errors with msstitch as I have been able to install it but cannot resolve the error on import.
As you pointed out , I need to determine if this is a python or NX-specific issue, so now I am continuing to work on addressing the error.
When I executed pip3 install msstitch
Requirement already satisfied: msstitch in **/.local/lib/python3.6/site-packages
Requirement already satisfied: numpy in **/.local/lib/python3.6/site-packages (from msstitch)
Requirement already satisfied: biopython in **/.local/lib/python3.6/site-packages (from msstitch)
Requirement already satisfied: lxml in **/.local/lib/python3.6/site-packages (from msstitch),but I cannot import the module in python:
>>> import msstitch
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'msstitch'
>>> export PYTHONPATH=*/.local/lib/python3.6/site-packages
File "<stdin>", line 1
export PYTHONPATH=*/.local/lib/python3.6/site-packages
^
SyntaxError: invalid syntax@glormph Thank you again for your time.
I am new to NX and apologize for the hassle, but if there is an efficient way to proceed in dealing with the error, please let me know and I will follow your instructions.
Even if we find the problem, it can have been caused in another NF process upstream, and we may need to look there too :(
Now, I added the following line to .comman.sh as you instructed and ran it
from lxml import etree
for p in psms.values():
try:
p.find('{%s}svm_score' % ns['xmlns']).text
except AttributeError:
print(etree.tostring(p, pretty_print=True))The output is as follows error.txt
I can't interpret it, but when I looked at the entire line of the file, there was what appeared to be a partially blank line (at the end of line 3 in the example below).
b'<ns40242:psm xmlns:ns40242="http://per-colator.com/percolator_out/15"/>\n'
b'<ns40243:psm xmlns:ns40243="http://per-colator.com/percolator_out/15"/>\n'
b'<ns40252:psm xmlns:ns40252="http://per-colator.com/percolator_out/15"/>\n \n\n\n\n'
b'<ns40261:psm xmlns:ns40261="http://per-colator.com/percolator_out/15"/>Computer'
b'<ns40271:psm xmlns:ns40271="http://per-colator.com/percolator_out/15"/>Computer'
b'<ns40282:psm xmlns:ns40282="http://per-colator.com/percolator_out/15"/>\n'Is it possible to identify the cause and fix it from here? I would appreciate a reply when you have time.
Best regards Yusuke
glormph
commented
1 year ago This is strange and I'm not sure where the error is. Now it looks like there are PSMs in the perco.xml input file to this process without svm score, or without much at all. Can you attach the filtprot file which contains the percolator XML?
I am afraid to contact you at such short notice.
I am interested in the pipeline that you kindly published, and I am running it using label free data, but I am having trouble resolving some of the errors (in the svmToTSV section).
If possible, I would be very happy if you could give me some suggestions on how to solve the problem.
The error seemed to be happening at svmToTSV.
I am trying to test the Python code written there first to confirm that it works.
My question is, are all of the following modules available? I couldn't find them by searching, so if you could tell me how to get them, that would be great.
// The above modules were imported in the python code in svmToTSV in ipaw.hg38.nf, but I could not find them.
L349. from app.readers import pycolator, xml, tsv, mzidplusThank you for your time and patience. Best regards Yusuke
For your reference, I would also like to describe the analysis environment, the overall execution status and the error status.
The analysis environment is Ubuntu 18.04 LTS and the version of Nextflow is 21.04.1. The overall execution was as follows
Parameter setup:
Executed command and parameters:
Output: