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:
multiqc \
-f \
--config ./results/multiqc_config.yml \
\
\
\
--quantification_method spectral_counting \
./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:
(empty)
Command error:
╰──────────────────────────────────────────────────────────────────────────────╯
DEBUG:multiqc:Oops! The 'quantms' MultiQC module broke...
================================================================================
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3621, in get_loc
return self._engine.get_loc(casted_key)
File "pandas/_libs/index.pyx", line 136, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 163, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'opt_global_cv_MS:1002217_decoy_peptide'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/multiqc/multiqc.py", line 651, in run
output = mod()
File "/usr/local/lib/python3.9/site-packages/pmultiqc/modules/quantms/quantms.py", line 137, in __init__
self.parse_out_mzTab()
File "/usr/local/lib/python3.9/site-packages/pmultiqc/modules/quantms/quantms.py", line 1211, in parse_out_mzTab
psm = psm[psm['opt_global_cv_MS:1002217_decoy_peptide'] != 1]
File "/usr/local/lib/python3.9/site-packages/pandas/core/frame.py", line 3505, in __getitem__
indexer = self.columns.get_loc(key)
File "/usr/local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3623, in get_loc
raise KeyError(key) from err
KeyError: '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:
multiqc \
-f \
--config ./results/multiqc_config.yml \
\
\
\
--quantification_method spectral_counting \
./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:
(empty)
Command error:
╰──────────────────────────────────────────────────────────────────────────────╯
DEBUG:multiqc:Oops! The 'quantms' MultiQC module broke...
================================================================================
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3621, in get_loc
return self._engine.get_loc(casted_key)
File "pandas/_libs/index.pyx", line 136, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 163, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'opt_global_cv_MS:1002217_decoy_peptide'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/multiqc/multiqc.py", line 651, in run
output = mod()
File "/usr/local/lib/python3.9/site-packages/pmultiqc/modules/quantms/quantms.py", line 137, in __init__
self.parse_out_mzTab()
File "/usr/local/lib/python3.9/site-packages/pmultiqc/modules/quantms/quantms.py", line 1211, in parse_out_mzTab
psm = psm[psm['opt_global_cv_MS:1002217_decoy_peptide'] != 1]
File "/usr/local/lib/python3.9/site-packages/pandas/core/frame.py", line 3505, in __getitem__
indexer = self.columns.get_loc(key)
File "/usr/local/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3623, in get_loc
raise KeyError(key) from err
KeyError: 'opt_global_cv_MS:1002217_decoy_peptide'
================================================================================
| 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:Reordering sections: anchor 'pmultiqc' not found.
DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' 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 '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'.
| multiqc | Compressing plot data
INFO: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 '/hps/scratch/lsf_tmpdir/hl-codon-129-03/tmp0vmnod6_/multiqc_data' to './multiqc_data'
| multiqc | Plots : multiqc_plots
INFO:multiqc:Plots : multiqc_plots
DEBUG:multiqc:Moving plots directory from '/hps/scratch/lsf_tmpdir/hl-codon-129-03/tmp0vmnod6_/multiqc_plots' to './multiqc_plots'
| multiqc | MultiQC complete
INFO:multiqc:MultiQC complete
Work dir:
/hps/nobackup/juan/pride/reanalysis/phospho-datasets/PXD005173/work/6f/2e777ff6ab47e68944a1e599d4386b
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`'
================================================================================
| 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:Reordering sections: anchor 'pmultiqc' not found.
DEBUG:multiqc:Reordering sections: anchor 'pmultiqc' 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 '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'.
| multiqc | Compressing plot data
INFO: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 '/hps/scratch/lsf_tmpdir/hl-codon-129-03/tmp0vmnod6_/multiqc_data' to './multiqc_data'
| multiqc | Plots : multiqc_plots
INFO:multiqc:Plots : multiqc_plots
DEBUG:multiqc:Moving plots directory from '/hps/scratch/lsf_tmpdir/hl-codon-129-03/tmp0vmnod6_/multiqc_plots' to './multiqc_plots'
| multiqc | MultiQC complete
INFO:multiqc:MultiQC complete
Work dir:
/hps/nobackup/juan/pride/reanalysis/phospho-datasets/PXD005173/work/6f/2e777ff6ab47e68944a1e599d4386b
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
This is because in some versions of mzTab export from OpenMS the following field may not be avilable opt_global_cv_MS:1002217_decoy_peptide I suggest we actually handle this in the following way.
First by default define as DECOY peptide anything that in the accession of the protein has the following prefix DECOY_ . Then if opt_global_cv_MS:1002217_decoy_peptide is not available try to parse the protein accession and found if in any protein that prefix is found.
I got the following error:
This is because in some versions of mzTab export from OpenMS the following field may not be avilable
opt_global_cv_MS:1002217_decoy_peptideI suggest we actually handle this in the following way.First by default define as DECOY peptide anything that in the accession of the protein has the following prefix DECOY_ . Then if
opt_global_cv_MS:1002217_decoy_peptideis not available try to parse the protein accession and found if in any protein that prefix is found.