flowchart TB
subgraph " "
v0["Channel.fromPath"]
v1["Channel.fromPath"]
v2["Channel.fromPath"]
v8["Channel.fromPath"]
v24["Channel.of"]
end
v3([prepInputFiles])
v4([filesummary])
subgraph " "
v5[" "]
v29["network_graphml_singleton_ch"]
v31[" "]
v32[" "]
v34[" "]
v36[" "]
end
v6([mscluster])
v7([massqlFilterSpectra])
v9([librarySearchData])
v11([librarymergeResults])
v13([summaryLibrary])
v16([librarygetGNPSAnnotations])
v18([networkingGNPSPrepParams])
v20([calculatePairs])
v22([filterNetwork])
v23([enrichNetworkEdges])
v25([createMetadataFile])
v26([calculateGroupings])
v27([enrichClusterSummary])
v28([createNetworkGraphML])
v30([splitNetworkComponents])
v33([createFeatureTable])
v35([PrepareForModiFinder])
v10(( ))
v12(( ))
v14(( ))
v17(( ))
v19(( ))
v21(( ))
v0 --> v3
v0 --> v4
v0 --> v6
v0 --> v25
v1 --> v3
v1 --> v25
v2 --> v3
v3 --> v4
v3 --> v25
v3 --> v6
v4 --> v5
v6 --> v7
v6 --> v26
v6 --> v23
v6 --> v33
v7 --> v9
v7 --> v18
v7 --> v20
v8 --> v9
v8 --> v13
v9 --> v10
v10 --> v11
v11 --> v12
v13 --> v14
v12 --> v16
v14 --> v16
v16 --> v17
v18 --> v19
v19 --> v20
v20 --> v21
v21 --> v22
v22 --> v23
v23 --> v27
v23 --> v28
v23 --> v35
v24 --> v25
v25 --> v26
v26 --> v27
v17 --> v27
v27 --> v28
v17 --> v28
v28 --> v30
v28 --> v29
v30 --> v32
v30 --> v31
v33 --> v34
v17 --> v35
v35 --> v36
job_parameters.yaml 0000644 0000000 0000000 00000002405 15027232056 013440 0 ustar root root OMETAFLOW_SERVER: http://ometaflow-launchserver:4000
OMETALIBRARY_SERVER: http://ometalibrary-web:5000/library
OMETAMASST_SERVER: http://ometamasst-web:5000/masst
OMETATASK: 2e83f115114a4a9c97caa28384cd5f55
OMETAUSER: jouteurestaque
create_time: 2025-06-26 04:57:15 PDT-0700
description: PFO4DA_classical_tolookatCHINAstuff_massQLfiltering
fragment_tolerance: '0.05'
input_libraries: /data/nf_data/server/nf_tasks/2e83f115114a4a9c97caa28384cd5f55/input_libraries
input_spectra: /data/nf_data/server/nf_tasks/2e83f115114a4a9c97caa28384cd5f55/input_spectra
library_analog_search: '0'
library_min_cosine: '0.7'
library_min_matched_peaks: '0.7'
library_topk: '1'
massql_filter: QUERY scaninfo(MS2DATA) WHERE MS2PROD=85.029
metadata_filename: NO_FILE
metadata_per_file_grouping: 'Yes'
min_cluster_size: '0'
min_peak_intensity: '0.0'
networking_max_shift: '1999'
networking_min_cosine: '0.7'
networking_min_matched_peaks: '6'
pm_tolerance: '0.05'
precursor_filter: '1'
publishdir: /data/nf_data/server/nf_tasks/2e83f115114a4a9c97caa28384cd5f55
redu_metadata_integration: 'No'
task: 2e83f115114a4a9c97caa28384cd5f55
topology_maxcomponent: '100'
topology_topk: '10'
usi: ''
window_filter: '1'
workflow_version: SERVER:2025.06.17;WORKFLOW:2025.01.14
workflowname: classical_networking_workflow
job_report.html 0000644 0000000 0000000 00013371742 15027232134 012630 0 ustar root root
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'massqlFilterSpectra (1)'
Caused by:
Process `massqlFilterSpectra (1)` terminated with an error exit status (1)
Command executed:
python /app/workflows_user/classical_networking_workflow/bin/scripts/massql_filter_spectra.py specs_ms.mgf specs_ms_filtered.mgf --massql "QUERY scaninfo(MS2DATA) WHERE MS2PROD=85.029"
Command exit status:
1
Command output:
TOTAL QUERIES 1
scan precmz ms1scan rt ... i i_norm mslevel i_norm_ms1
0 19 0 0 0 ... 259258.753173 1.0 2 NaN
1 53 0 0 0 ... 128093.913087 1.0 2 NaN
2 55 0 0 0 ... 130342.528810 1.0 2 NaN
3 58 0 0 0 ... 168111.955080 1.0 2 NaN
4 60 0 0 0 ... 196663.588135 1.0 2 NaN
... ... ... ... .. ... ... ... ... ...
1144 7194 0 0 0 ... 34216.473389 1.0 2 NaN
1145 7210 0 0 0 ... 36651.197021 1.0 2 NaN
1146 7227 0 0 0 ... 35813.869629 1.0 2 NaN
1147 7230 0 0 0 ... 45010.175293 1.0 2 NaN
1148 7245 0 0 0 ... 16586.342773 1.0 2 NaN
[1149 rows x 9 columns]
Command error:
0%| | 0/1 [00:00
main()
File "/app/workflows_user/classical_networking_workflow/bin/scripts/massql_filter_spectra.py", line 30, in main
ms1_df, ms2_df = msql_fileloading.load_data(args.input_mgf)
NameError: name 'msql_fileloading' is not defined
Work dir:
/data/nf_data/server/nf_work/2e83f115114a4a9c97caa28384cd5f55/20/c7e8765a5eb758a0b19e1b01e040eb
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
nextflow run /app/workflows_user/classical_networking_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/2e83f115114a4a9c97caa28384cd5f55/job_parameters.yaml -w /data/nf_data/server/nf_work/2e83f115114a4a9c97caa28384cd5f55 -with-report /data/nf_data/server/nf_tasks/2e83f115114a4a9c97caa28384cd5f55/job_report.html -with-timeline /data/nf_data/server/nf_tasks/2e83f115114a4a9c97caa28384cd5f55/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/2e83f115114a4a9c97caa28384cd5f55/job_dag.html -with-weblog 'http://localhost:4000/nf_weblog/2e83f115114a4a9c97caa28384cd5f55' -c /app/launchserver/nextflow_slurm.config8613f3614a81b9f8e54d2d26ac0f5fe8fbcc6692-2145-46d0-9035-d66121d43563These plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.
Launch time:
Elapsed time:
Legend: job wall time / memory usage (RAM)