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I'm trying to run a minimal experiment to test using the SDRF format to develop a TMT pipeline. I've tried copying the format as best I can, but I don't understand what is being flagged as incorrect here:
Command used and terminal output
Command:nextflow run bigbio/quantms -r dev -profile docker --input 20240521b_JR_TMT_HS_KO_MIN.sdrf.tsv --database /home/jack.rogan/Proteomics/Human_reference_proteome.fasta --add_decoys --search_engines comet --max_precursor_charge 5 --min_peptide_length 7 --FDR_level psm-level-fdrs --max_memory 48.GB --outdir 20240521b_JR_TMT_HS_KO_MIN_comet --acquisition_method dda --labelling_type "tmt10plex" --normalize true --msstats_remove_one_feat_prot false --msstatslfq_removeFewMeasurements falseOutput:ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING (20240521b_JR_TMT_HS_KO_MIN.sdrf.tsv)'Caused by: Process `NFCORE_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING (20240521b_JR_TMT_HS_KO_MIN.sdrf.tsv)` 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 \ --extension_convert raw:mzML,.gz:,.tar.gz:,.tar:,.zip: \ -s 20240521b_JR_TMT_HS_KO_MIN.sdrf.tsv \ \ 2>&1 | tee 20240521b_JR_TMT_HS_KO_MIN.sdrf_parsing.log mv openms.tsv 20240521b_JR_TMT_HS_KO_MIN.sdrf_config.tsv mv experimental_design.tsv 20240521b_JR_TMT_HS_KO_MIN.sdrf_openms_design.tsv cat <<-END_VERSIONS > versions.yml "NFCORE_QUANTMS:QUANTMS:CREATE_INPUT_CHANNEL:SDRFPARSING": sdrf-pipelines: $(parse_sdrf --version 2>&1 | awk -F ' ' '{print $2}') END_VERSIONSCommand exit status: 1Command output: PROCESSING: 20240521b_JR_TMT_HS_KO_MIN.sdrf.tsv" Factor columns: ['factor value[treatment]'] Characteristics columns (those covered by factor columns removed): ['characteristics[organism]', 'characteristics[organism part]', 'characteristics[sex]', 'characteristics[age]', 'characteristics[developmental stage]', 'characteristics[ethnic group]', 'characteristics[disease]', 'characteristics[cell line]', 'characteristics[cell type]', 'characteristics[infect]', 'characteristics[enrichment process]', 'characteristics[biological replicate]'] Conditions (5): dict_keys(['OE33_0pc_KO', 'OE33_25pc_KO', 'OE33_50pc_KO', 'OE33_75pc_KO', 'OE33_100pc_KO']) Files per condition: dict_values([1, 1, 1, 1, 1]) Traceback (most recent call last): File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/parse_sdrf.py", line 62, in openms_from_sdrf OpenMS().openms_convert(sdrf, onetable, legacy, verbose, conditionsfromcolumns, extension_convert) File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/openms/openms.py", line 446, in openms_convert self.writeTwoTableExperimentalDesign( File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/openms/openms.py", line 617, in writeTwoTableExperimentalDesign label = str(choice[label[label_index[raw]]]) ~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^ KeyError: 'TMT127N' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/bin/parse_sdrf", line 10, in <module> sys.exit(main()) ^^^^^^ File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/parse_sdrf.py", line 239, in main cli() File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/parse_sdrf.py", line 65, in openms_from_sdrf raise ValueError(msg) from ex ValueError: Error: 'TMT127N'Command error: WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. PROCESSING: 20240521b_JR_TMT_HS_KO_MIN.sdrf.tsv" Factor columns: ['factor value[treatment]'] Characteristics columns (those covered by factor columns removed): ['characteristics[organism]', 'characteristics[organism part]', 'characteristics[sex]', 'characteristics[age]', 'characteristics[developmental stage]', 'characteristics[ethnic group]', 'characteristics[disease]', 'characteristics[cell line]', 'characteristics[cell type]', 'characteristics[infect]', 'characteristics[enrichment process]', 'characteristics[biological replicate]'] Conditions (5): dict_keys(['OE33_0pc_KO', 'OE33_25pc_KO', 'OE33_50pc_KO', 'OE33_75pc_KO', 'OE33_100pc_KO']) Files per condition: dict_values([1, 1, 1, 1, 1]) Traceback (most recent call last): File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/parse_sdrf.py", line 62, in openms_from_sdrf OpenMS().openms_convert(sdrf, onetable, legacy, verbose, conditionsfromcolumns, extension_convert) File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/openms/openms.py", line 446, in openms_convert self.writeTwoTableExperimentalDesign( File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/openms/openms.py", line 617, in writeTwoTableExperimentalDesign label = str(choice[label[label_index[raw]]]) ~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^ KeyError: 'TMT127N' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/bin/parse_sdrf", line 10, in <module> sys.exit(main()) ^^^^^^ File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/parse_sdrf.py", line 239, in main cli() File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/local/lib/python3.12/site-packages/sdrf_pipelines/parse_sdrf.py", line 65, in openms_from_sdrf raise ValueError(msg) from ex ValueError: Error: 'TMT127N'Work dir: /mnt/bigdata/Jack/20240521b_JR_TMT_HS_KO_MIN/work/89/1cc0e0fc3d4400aff9683b5ca7a053Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line -- Check '.nextflow.log' file for details
Description of the bug
Hi,
I'm trying to run a minimal experiment to test using the SDRF format to develop a TMT pipeline. I've tried copying the format as best I can, but I don't understand what is being flagged as incorrect here:
Command used and terminal output
Relevant files
20240521b_JR_TMT_HS_KO_MIN.sdrf.tsv.txt
System information
Nextflow 24.04.1
Docker
Ubuntu
bigbio/quantms dev
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