mhcquant
mhcquant copied to clipboard
Published
20 hours ago •
nf-core
nf-core
error from '-profile test'
Description of the bug
Hi,
I got an error in the first step, 'profile test'. Here is the relevant report. Maybe there is something wrong with my singularity.
Command used and terminal output
$ nextflow run nf-core/mhcquant -r 2.5.0 -profile test,singularity --outdir ./result_test
N E X T F L O W ~ version 23.10.1
Launching `https://github.com/nf-core/mhcquant` [distracted_cori] DSL2 - revision: b80a5a4fbf [2.5.0]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/mhcquant v2.5.0-gb80a5a4
------------------------------------------------------
Core Nextflow options
revision : 2.5.0
runName : distracted_cori
containerEngine : singularity
launchDir : /dssg/home/acct-lulu0113/lulu0113-sd/IMpeptide/MHCquant
workDir : /dssg/home/acct-lulu0113/lulu0113-sd/IMpeptide/MHCquant/work
projectDir : /dssg/home/acct-lulu0113/lulu0113-sd/.nextflow/assets/nf-core/mhcquant
userName : lulu0113-sd
profile : test,singularity
configFiles :
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/HepG2_sample_sheet.tsv
outdir : ./result_test
Database Options
fasta : https://raw.githubusercontent.com/nf-core/test-datasets/mhcquant/testdata/UP000005640_9606.fasta
Mass Spectrometry Data Processing
fragment_mass_tolerance : 0.01
fixed_mods :
default_params_file_comet :
Rescoring
description_correct_features : 0
subset_max_train : 0
deeplc_calibration_bins : 20
deeplc_calibration_mode : idx_bin
ms2pip_model_name : Immuno-HCD
Quantification Options
skip_quantification : true
quantification_min_prob : 0
quantification_mz_window : 5
quantification_rt_window : 0
quantification_mapping_tolerance: 0
quantification_peak_width : 60
quantification_min_peak_width : 0.2
Institutional config options
config_profile_name : Test profile
config_profile_description : Minimal test dataset to check pipeline function
Max job request options
max_cpus : 2
max_memory : 6.GB
max_time : 6.h
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/mhcquant for your analysis please cite:
* The pipeline publication
https://doi.org/10.1021/acs.jproteome.9b00313
* The pipeline
https://doi.org/10.5281/zenodo.1569909
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/mhcquant/blob/master/CITATIONS.md
executor > local (6)
[5a/04d86f] process > NFCORE_MHCQUANT:MHCQUANT:INPUT_CHECK:SAMPLESHEET_CHECK (HepG2_sample_sheet.tsv) [100%] 1 of 1 ✔
[90/0ea659] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_DECOYDATABASE (3) [100%] 3 of 3 ✔
[- ] process > NFCORE_MHCQUANT:MHCQUANT:THERMORAWFILEPARSER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:TDF2MZML -
[6f/a32452] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (2) [ 0%] 0 of 2
executor > local (6)
[5a/04d86f] process > NFCORE_MHCQUANT:MHCQUANT:INPUT_CHECK:SAMPLESHEET_CHECK (HepG2_sample_sheet.tsv) [100%] 1 of 1 ✔
[90/0ea659] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_DECOYDATABASE (3) [100%] 3 of 3 ✔
[- ] process > NFCORE_MHCQUANT:MHCQUANT:THERMORAWFILEPARSER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:TDF2MZML -
[6f/a32452] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (2) [ 50%] 1 of 2, failed: 1
executor > local (6)
[5a/04d86f] process > NFCORE_MHCQUANT:MHCQUANT:INPUT_CHECK:SAMPLESHEET_CHECK (HepG2_sample_sheet.tsv) [100%] 1 of 1 ✔
[90/0ea659] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_DECOYDATABASE (3) [100%] 3 of 3 ✔
[- ] process > NFCORE_MHCQUANT:MHCQUANT:THERMORAWFILEPARSER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:TDF2MZML -
[6f/a32452] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (2) [ 33%] 1 of 3, failed: 1
executor > local (6)
[5a/04d86f] process > NFCORE_MHCQUANT:MHCQUANT:INPUT_CHECK:SAMPLESHEET_CHECK (HepG2_sample_sheet.tsv) [100%] 1 of 1 ✔
[90/0ea659] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_DECOYDATABASE (3) [100%] 3 of 3 ✔
[- ] process > NFCORE_MHCQUANT:MHCQUANT:THERMORAWFILEPARSER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:TDF2MZML -
[61/5f3ea1] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (3) [ 66%] 2 of 3, failed: 2
executor > local (6)
[5a/04d86f] process > NFCORE_MHCQUANT:MHCQUANT:INPUT_CHECK:SAMPLESHEET_CHECK (HepG2_sample_sheet.tsv) [100%] 1 of 1 ✔
[90/0ea659] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_DECOYDATABASE (3) [100%] 3 of 3 ✔
[- ] process > NFCORE_MHCQUANT:MHCQUANT:THERMORAWFILEPARSER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:TDF2MZML -
[61/5f3ea1] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (3) [ 66%] 2 of 3, failed: 2
executor > local (6)
[5a/04d86f] process > NFCORE_MHCQUANT:MHCQUANT:INPUT_CHECK:SAMPLESHEET_CHECK (HepG2_sample_sheet.tsv) [100%] 1 of 1 ✔
[90/0ea659] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_DECOYDATABASE (3) [100%] 3 of 3 ✔
[- ] process > NFCORE_MHCQUANT:MHCQUANT:THERMORAWFILEPARSER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:TDF2MZML -
[61/5f3ea1] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (3) [ 66%] 2 of 3, failed: 2[- ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_PEPTIDEINDEXER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_IDMERGER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_PSMFEATUREEXTRACTOR -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_PERCOLATORADAPTER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_IDFILTER_Q_VALUE -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_TEXTEXPORTER -[- ] process > NFCORE_MHCQUANT:MHCQUANT:OPENMS_MZTABEXPORTER -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_MHCQUANT:MHCQUANT:MULTIQC -
-[nf-core/mhcquant] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (2)'
Caused by:
Process `NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER (2)` terminated with an error exit status (3)
Command executed:
CometAdapter -in HepG2_rep2_small.mzML \ -out HepG2_rep2_small.idXML \
-database UP000005640_9606_decoy.fasta \ -threads 2 \ -pin_out HepG2_rep2_small_pin.tsv \
\
-precursor_mass_tolerance 5 -fragment_mass_tolerance 0.01 -fragment_bin_offset 0.0 -instrument high_res -num_hits 1 -digest_mass_range 800:2500 -max_variable_mods_in_peptide 3 -missed_cleavages 0 -precursor_charge 2:3 -activation_method ALL -variable_modifications 'Oxidation (M)' -enzyme 'unspecific cleavage' -spectrum_batch_size 0 \
-fixed_modifications \
\ \
\ \
\
cat <<-END_VERSIONS > versions.yml
"NFCORE_MHCQUANT:MHCQUANT:OPENMS_COMETADAPTER": openms-thirdparty: $(echo $(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*$//' | sed 's/ -*//; s/ .*$//')
END_VERSIONS
Command exit status: 3
Command output:
The mzML file provided to CometAdapter is not indexed, but comet requires one. We will add an index by writing a temporary file. If you run this analysis more often, consider indexing your mzML in advance!
Command error: INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
IndexedMzMLDecoder::findIndexListOffset Error: Could not find element indexListOffset in the last 1023 bytes. Maybe this is not a indexedMzML.The mzML file provided to CometAdapter is not indexed, but comet requires one. We will add an index by writing a temporary file. If you run this analysis more often, consider indexing your mzML in advance! 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
/opt/conda/conda-bld/openms-meta_1691398820198/work/src/openms/source/FORMAT/HANDLERS/XMLHandler.cpp(130): While loading 'HepG2_rep2_small.mzML': input ended before all started tags were ended; last tag started is 'binary'( in line 76018 column 21927)
Error: Unable to read file (- due to that error of type Parse Error in: /opt/conda/conda-bld/openms-meta_1691398820198/work/src/openms/source/FORMAT/HANDLERS/XMLHandler.cpp@131-void OpenMS::Internal::XMLHandler::fatalError(ActionMode, const OpenMS::String&, OpenMS::UInt, OpenMS::UInt) const)
Work dir:
/dssg/home/acct-lulu0113/lulu0113-sd/IMpeptide/MHCquant/work/6f/a32452baa4c24bdca43862cef921ae
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
Relevant files
No response
System information
nextflow version 23.10.1 Singularity version: apptainer version 1.2.5-1.el8
