Error executing process > 'sdrf_parsing (1)'
Caused by:
Process `sdrf_parsing (1)` terminated with an error exit status (1)
Command executed:
## -t2 since the one-table format parser is broken in OpenMS2.5
## -l for legacy behavior to always add sample columns
parse_sdrf convert-openms -t2 -l -s PXD012255-Sample-1.tsv > sdrf_parsing.log
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/bin/parse_sdrf", line 10, in <module>
sys.exit(main())
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/sdrf_pipelines/parse_sdrf.py", line 109, in main
cli()
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/click/core.py", line 829, in __call__
return self.main(*args, **kwargs)
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/click/core.py", line 1259, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/click/decorators.py", line 21, in new_func
return f(get_current_context(), *args, **kwargs)
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/sdrf_pipelines/parse_sdrf.py", line 36, in openms_from_sdrf
OpenMS().openms_convert(sdrf, raw, onetable, legacy, verbose, conditionsfromcolumns)
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/sdrf_pipelines/openms/openms.py", line 163, in openms_convert
variable_mods_string = self.openms_ify_mods(var_mods)
File "/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/conda/nf-core-proteomicslfq-1.1.0dev-dbfe576f0ba2eaab3a44c499db5d3312/lib/python3.8/site-packages/sdrf_pipelines/openms/openms.py", line 82, in openms_ify_mods
aa = ta.split(",") # multiply target site e.g., S,T,Y including potentially termini "C-term"
UnboundLocalError: local variable 'ta' referenced before assignment
Work dir:
/hps/nobackup2/proteomics/yperez_temp/proteogenomics_project/datasets/cell-lines/work/32/6f42c67549e5629673f5e7abc9e54b
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
Dataset PXD012255