quantms
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bigbio
Big datasets more than 200 GB mztab size are not supported.
Description of the bug
nf-core/quantms execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE (1)'
Caused by:
Process `NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE (1)` terminated with an error exit status (1)
Command executed:
set -x
set -e
# leaving here to ease debugging
ls -lcth *
echo ">>>>>>>>> Experimental Design <<<<<<<<<"
cat results/*openms_design.tsv
echo ">>>>>>>>> Running Multiqc <<<<<<<<<"
multiqc \
-f \
--config ./results/multiqc_config.yml \
\
\
\
--ignored_idxml \
--quantification_method feature_intensity \
./results \
-o .
cat <<-END_VERSIONS > versions.yml
"NFCORE_QUANTMS:QUANTMS:SUMMARYPIPELINE":
pmultiqc: $(multiqc --pmultiqc_version | sed -e "s/pmultiqc, version //g")
END_VERSIONS
Command exit status:
1
Command output:
413 JM1 413 42
414 KASUMI-2 414 42
415 KYM-1 415 42
416 KYSE-410 416 42
417 CL-34 417 42
418 NCI-H446 418 42
419 SK-N-AS 419 42
420 mixed 420 42
421 DAN-G 421 43
422 KNS-42 422 43
423 HEC-108 423 43
424 JeKo-1 424 43
425 JURKAT 425 43
426 MSTO-211H 426 43
427 OCUM-1 427 43
428 CCK-81 428 43
429 SNU-449 429 43
430 mixed 430 43
431 8505C 431 44
432 HCC-1833 432 44
433 Panc 04.03 433 44
434 J82 434 44
435 JHH-4 435 44
436 OVSAHO 436 44
437 RL 437 44
438 SNU-C5 438 44
439 SU-DHL-6 439 44
440 mixed 440 44
441 MFE-319 441 45
442 HD-MY-Z 442 45
443 HDQ-P1 443 45
444 JHH-6 444 45
445 L-428 445 45
446 LMSU 446 45
447 HUP-T4 447 45
448 SW 1783 448 45
449 UM-UC-3 449 45
450 mixed 450 45
451 SK-LU-1 451 46
452 Ishikawa (Heraklio) 02 ER- 452 46
453 SNG-M 453 46
454 GAMG 454 46
455 NCI-H929 455 46
456 Panc 02.03 456 46
457 RCH-ACV 457 46
458 SNU-423 458 46
459 SNU-1079 459 46
460 mixed 460 46
>>>>>>>>> Running Multiqc <<<<<<<<<
Warning: OPENMS_DATA_PATH environment variable not found and no share directory was installed. Some functionality might not work as expected.
Command error:
================================================================================
Traceback (most recent call last):
File "/usr/local/lib/python3.11/site-packages/multiqc/multiqc.py", line 689, in run
output = mod()
^^^^^
File "/usr/local/lib/python3.11/site-packages/pmultiqc/modules/quantms/quantms.py", line 189, in __init__
self.CalHeatMapScore()
File "/usr/local/lib/python3.11/site-packages/pmultiqc/modules/quantms/quantms.py", line 1006, in CalHeatMapScore
mztab_data = mztab.MzTab(self.out_mzTab_path)
^^^^^^^^^^^^^^^^^^^
AttributeError: 'QuantMSModule' object has no attribute 'out_mzTab_path'
================================================================================
DEBUG:multiqc.modules.custom_content.custom_content:No samples found: custom content (total_ion_chromatograms)
DEBUG:multiqc.modules.custom_content.custom_content:No samples found: custom content (base_peak_chromatograms)
DEBUG:multiqc.modules.custom_content.custom_content:No samples found: custom content (number_of_peaks)
DEBUG:multiqc.modules.custom_content.custom_content:No samples found: custom content (general_stats)
| custom_content | nf-core-quantms-methods-description: Found 1 sample (html)
INFO:multiqc.modules.custom_content.custom_content:nf-core-quantms-methods-description: Found 1 sample (html)
| custom_content | software_versions: Found 1 sample (html)
INFO:multiqc.modules.custom_content.custom_content:software_versions: Found 1 sample (html)
| custom_content | nf-core-quantms-summary: Found 1 sample (html)
INFO:multiqc.modules.custom_content.custom_content:nf-core-quantms-summary: Found 1 sample (html)
DEBUG:multiqc.utils.software_versions:Reading software versions from config.software_versions
DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' not found.
DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' not found for module 'nf-core/quantms Methods Description'.
DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-methods-description' not found for module 'nf-core/quantms Methods Description'.
DEBUG:multiqc:Reordering sections: anchor 'software_versions' not found for module 'nf-core/quantms Methods Description'.
DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-summary' not found for module 'nf-core/quantms Methods Description'.
DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' not found for module 'nf-core/quantms Software Versions'.
DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-methods-description' not found for module 'nf-core/quantms Software Versions'.
DEBUG:multiqc:Reordering sections: anchor 'software_versions' not found for module 'nf-core/quantms Software Versions'.
DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-summary' not found for module 'nf-core/quantms Software Versions'.
DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' not found for module 'nf-core/quantms Workflow Summary'.
DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-methods-description' not found for module 'nf-core/quantms Workflow Summary'.
DEBUG:multiqc:Reordering sections: anchor 'software_versions' not found for module 'nf-core/quantms Workflow Summary'.
DEBUG:multiqc:Reordering sections: anchor 'nf-core-quantms-summary' not found for module 'nf-core/quantms Workflow Summary'.
DEBUG:multiqc:Compressing plot data
| multiqc | Report : multiqc_report.html
INFO:multiqc:Report : multiqc_report.html
| multiqc | Data : multiqc_data
INFO:multiqc:Data : multiqc_data
DEBUG:multiqc:Moving data file from '/tmp/tmpj4s1blix/multiqc_data' to './multiqc_data'
DEBUG:multiqc:Full report path: multiqc_report.html
| multiqc | Plots : multiqc_plots
INFO:multiqc:Plots : multiqc_plots
DEBUG:multiqc:Moving plots directory from '/tmp/tmpj4s1blix/multiqc_plots' to './multiqc_plots'
| multiqc | Flat-image plots used. Disable with '--interactive'. See
docs.
| multiqc | MultiQC complete
INFO:multiqc:MultiQC complete
Work dir:
/hps/nobackup/juan/pride/reanalysis/absolute-expression/cell-lines/MSV000085836/work/eb/7791f6ff8eecc1b55b0fd398dfe07a
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
Command used and terminal output
No response
Relevant files
No response
System information
No response
