flow_filelinking.yaml 0000644 0000000 0000000 00000001611 14540151521 013757 0 ustar root root - parameter: spectra_path
target: input_spectra/dummy_spectra.mgf
- parameter: library_path
target: input_library/ms2query_random_forest_model.onnx
- parameter: library_path
target: input_library/ms2ds_model_GNPS_15_12_2021.hdf5
- parameter: library_path
target: input_library/ms2query_library.sqlite
- parameter: library_path
target: input_library/spec2vec_model_GNPS_15_12_2021.model.wv.vectors.npy
- parameter: library_path
target: input_library/ALL_GNPS_210409_positive_processed_annotated_CF_NPC_classes.txt
- parameter: library_path
target: input_library/library_GNPS_15_12_2021_s2v_embeddings.pickle
- parameter: library_path
target: input_library/library_GNPS_15_12_2021_ms2ds_embeddings.pickle
- parameter: library_path
target: input_library/spec2vec_model_GNPS_15_12_2021.model
- parameter: library_path
target: input_library/spec2vec_model_GNPS_15_12_2021.model.syn1neg.npy
input_library/ 0000755 0000000 0000000 00000000000 14540151521 012435 5 ustar root root input_library/ms2query_library.sqlite 0000777 0000000 0000000 00000000000 14540151521 037265 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/ms2query_library.sqlite ustar root root input_library/ms2query_random_forest_model.onnx 0000777 0000000 0000000 00000000000 14540151521 043363 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/ms2query_random_forest_model.onnx ustar root root ././@LongLink 0000644 0000000 0000000 00000000157 00000000000 011605 K ustar root root /data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model.wv.vectors.npy input_library/spec2vec_model_GNPS_15_12_2021.model.wv.vectors.npy 0000777 0000000 0000000 00000000000 14540151521 045650 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model.wv.vustar root root input_library/spec2vec_model_GNPS_15_12_2021.model 0000777 0000000 0000000 00000000000 14540151521 042025 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model ustar root root ././@LongLink 0000644 0000000 0000000 00000000154 00000000000 011602 K ustar root root /data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model.syn1neg.npy input_library/spec2vec_model_GNPS_15_12_2021.model.syn1neg.npy 0000777 0000000 0000000 00000000000 14540151521 045106 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/spec2vec_model_GNPS_15_12_2021.model.syn1ustar root root ././@LongLink 0000644 0000000 0000000 00000000151 00000000000 011577 K ustar root root /data/nf_data/useruploads/shared/ms2query/positiveim_model/library_GNPS_15_12_2021_s2v_embeddings.pickle input_library/library_GNPS_15_12_2021_s2v_embeddings.pickle 0000777 0000000 0000000 00000000000 14540151521 044756 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/library_GNPS_15_12_2021_s2v_embeddings.piustar root root ././@LongLink 0000644 0000000 0000000 00000000173 00000000000 011603 K ustar root root /data/nf_data/useruploads/shared/ms2query/positiveim_model/ALL_GNPS_210409_positive_processed_annotated_CF_NPC_classes.txt input_library/ALL_GNPS_210409_positive_processed_annotated_CF_NPC_classes.txt 0000777 0000000 0000000 00000000000 14540151521 050755 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/ALL_GNPS_210409_positive_processed_annotaustar root root input_library/ms2ds_model_GNPS_15_12_2021.hdf5 0000777 0000000 0000000 00000000000 14540151521 040135 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/ms2ds_model_GNPS_15_12_2021.hdf5 ustar root root ././@LongLink 0000644 0000000 0000000 00000000153 00000000000 011601 K ustar root root /data/nf_data/useruploads/shared/ms2query/positiveim_model/library_GNPS_15_12_2021_ms2ds_embeddings.pickle input_library/library_GNPS_15_12_2021_ms2ds_embeddings.pickle 0000777 0000000 0000000 00000000000 14540151521 045261 2/data/nf_data/useruploads/shared/ms2query/positiveim_model/library_GNPS_15_12_2021_ms2ds_embeddings.ustar root root input_spectra/ 0000755 0000000 0000000 00000000000 14540151521 012432 5 ustar root root input_spectra/dummy_spectra.mgf 0000777 0000000 0000000 00000000000 14540151521 031516 2/data/nf_data/useruploads/alberto/ms2query/dummy_spectra.mgf ustar root root job_dag.html 0000644 0000000 0000000 00000012172 14540152246 012035 0 ustar root root
Nextflow Cytoscape.js with Dagre
Nextflow Cytoscape.js with Dagre
job_parameters.yaml 0000644 0000000 0000000 00000001327 14540151521 013436 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: 8979365f96f8468d98ad7ba919b4e4af
OMETAUSER: alberto
additional_metadata: retention_time feature_id
create_time: 2023-12-18 15:17:27 PST-0800
description: ''
ion_mode: positive
library_path: /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/input_library
outdir: /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af
spectra_path: /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/input_spectra
task: 8979365f96f8468d98ad7ba919b4e4af
workflow_version: SERVER:0.1.2;WORKFLOW:0.2
workflowname: ms2query_nextflow_workflow
job_report.html 0000644 0000000 0000000 00013115515 14540152245 012625 0 ustar root root
[festering_lavoisier] Nextflow Workflow Report
Nextflow Report
Nextflow workflow report
[festering_lavoisier]
Workflow execution completed successfully!
Run times
18-Dec-2023 23:17:59 - 18-Dec-2023 23:23:01
( duration: 5m 2s )
1 succeeded
0 cached
0 ignored
0 failed
Nextflow command
nextflow run /app/workflows_user/ms2query_nextflow_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_parameters.yaml -w /data/nf_data/server/nf_work/8979365f96f8468d98ad7ba919b4e4af -with-report /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_report.html -with-timeline /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_dag.html -with-weblog 'http://localhost:4000/nf_weblog/8979365f96f8468d98ad7ba919b4e4af' -c /app/launchserver/nextflow.config
CPU-Hours
0.1
Launch directory
/data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af
Work directory
/data/nf_data/server/nf_work/8979365f96f8468d98ad7ba919b4e4af
Project directory
/app/workflows_user/ms2query_nextflow_workflow
Script name
nf_workflow.nf
Script ID
05d0f9bfbd6d4117d83a84fa0ed552d1
Workflow session
5e855e67-600e-402d-b044-39d8f4b4cfa6
Workflow profile
standard
Nextflow version
version 21.10.0, build 5640 (11-11-2021 18:27 UTC)
Resource Usage
These plots give an overview of the distribution of resource usage for each process.
CPU
Memory
Tasks
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.
(tasks table omitted because the dataset is too big)
job_timeline.html 0000644 0000000 0000000 00000753741 14540152245 013125 0 ustar root root
Processes execution timeline
Launch time:
Elapsed time:
Legend: job wall time / memory usage (RAM)
nextflow_stdout.log 0000644 0000000 0000000 00000001213 14540152247 013530 0 ustar root root N E X T F L O W ~ version 21.10.0
Launching `/app/workflows_user/ms2query_nextflow_workflow/nf_workflow.nf` [festering_lavoisier] - revision: 05d0f9bfbd
[- ] process > processMS2query -
[- ] process > processMS2query [ 0%] 0 of 1
executor > local (1)
[b3/61469f] process > processMS2query [ 0%] 0 of 1
executor > local (1)
[b3/61469f] process > processMS2query [ 0%] 0 of 1 ✔
executor > local (1)
[b3/61469f] process > processMS2query [100%] 1 of 1 ✔
executor > local (1)
[b3/61469f] process > processMS2query [100%] 1 of 1 ✔
Completed at: 18-Dec-2023 23:23:08
Duration : 5m 7s
CPU hours : 0.1
Succeeded : 1
nf_cmd.sh 0000644 0000000 0000000 00000001160 14540151521 011332 0 ustar root root nextflow run /app/workflows_user/ms2query_nextflow_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_parameters.yaml -w /data/nf_data/server/nf_work/8979365f96f8468d98ad7ba919b4e4af -with-report /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_report.html -with-timeline /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_dag.html -with-weblog http://localhost:4000/nf_weblog/8979365f96f8468d98ad7ba919b4e4af -c /app/launchserver/nextflow.config nf_output/ 0000755 0000000 0000000 00000000000 14540152237 011602 5 ustar root root nf_output/results/ 0000755 0000000 0000000 00000000000 14540152237 013303 5 ustar root root nf_output/results/dummy_spectra.csv 0000644 0000000 0000000 00000004202 14540152237 016672 0 ustar root root query_spectrum_nr,ms2query_model_prediction,precursor_mz_difference,precursor_mz_query_spectrum,precursor_mz_analog,inchikey,analog_compound_name,smiles,retention_time,feature_id,cf_kingdom,cf_superclass,cf_class,cf_subclass,cf_direct_parent,npc_class_results,npc_superclass_results,npc_pathway_results
1,0.9323,0.0000,667.1150,667.1150,USXIYWCPCGVOKF,Hectochlorin,C[C@H]1[C@@H](OC(C2=CSC([C@H](C(C)(OC(C3=CSC([C@H](C(C)(O)C)OC1=O)=N3)=O)C)OC(C)=O)=N2)=O)CCCC([37Cl])(Cl)C,,,Organic compounds,Organic acids and derivatives,Peptidomimetics,Depsipeptides,Cyclic depsipeptides,Cyclic peptides; Depsipeptides,Oligopeptides,Amino acids and Peptides; Polyketides
2,0.9453,0.0000,553.1300,553.1300,DJXURFUTIYZESV,1-Caffeoyl-5-feruloylquinic acid,COC1=C(C=CC(=C1)/C=C/C(=O)O[C@@H]2C[C@](C[C@H]([C@@H]2O)O)(C(=O)O)OC(=O)/C=C/C3=CC(=C(C=C3)O)O)O,,,Organic compounds,Organic oxygen compounds,Organooxygen compounds,Alcohols and polyols,Quinic acids and derivatives,Cinnamic acids and derivatives,Phenylpropanoids (C6-C3),Shikimates and Phenylpropanoids
3,0.8810,0.0000,212.0820,212.0820,APVQOOKHDZVJEX,Mirapex,CCCN[C@H]1CCC2=C(C1)SC(=N2)N.O.Cl.Cl,,,Organic compounds,Organic nitrogen compounds,Organonitrogen compounds,Amines,Aralkylamines,,,Alkaloids
4,0.9453,0.0000,850.6360,850.6360,VCAGNEUDNVLWPT,Halovir C,CCCCCCCCCCCCCC(=O)NC(C)(C)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(=O)NC(CCC(N)=O)C(=O)N[C@H](CO)CC(C)C,,,Organic compounds,Organic acids and derivatives,Carboxylic acids and derivatives,"Amino acids, peptides, and analogues",Oligopeptides,Linear peptides; Lipopeptides,Oligopeptides,Amino acids and Peptides
5,0.8820,0.0000,431.2080,431.2080,QFKOZHNKLSMVDN,,C[C@H](N1C(=O)N2CCc3c([nH]c4ccccc34)[C@@]2(C)C1=O)C(=O)NCc5ccc(C)cc5,,,Organic compounds,Organic acids and derivatives,Carboxylic acids and derivatives,"Amino acids, peptides, and analogues",Dipeptides,Carboline alkaloids,Tryptophan alkaloids,Alkaloids
6,0.8763,0.0000,236.0110,236.0110,PZXOQEXFMJCDPG,Pesticide1_Omethoate_C5H12NO4PS_,CNC(=O)CSP(=O)(OC)OC,,,Organic compounds,Organic acids and derivatives,Carboxylic acids and derivatives,Carboxylic acid derivatives,Secondary carboxylic acid amides,,,
nf_output/ms2query_results.zip 0000644 0000000 0000000 00000002346 14540152237 015703 0 ustar root root PK
W results/UT ӀeӀeux PK W#y results/dummy_spectra.csvUT ԀeӀeux Umo8ί@H.KB92mپ$Ѳl*:.X8v$']N:U<33ste).HjdsE&*f"J59 -tti&)6IZ!.oXj;*IU!H,eHIsls`"#m\*10+R Yfd>"R#:,,+DU6{tJR?\Dži F}Zn+"~ ǼH]+JVQFlunε*oV?>TIAos \3YT3=<:OFs=m_ cN MKt5IO) 1Pj%y{j0drJ)-2nkh
#w|rM`]l.U~ۋV B\w1&T %$~UtSTݷ`هB1nUO?,WӤе`7g̿_/>vǞU gtHp1jٍzRpjfK*v.ѭ.\k"[k\ǣ&]wvtyv}9t4gG4쵂7?aC3B=ߜQ%c.=
PK
W A results/UT Ӏeux PK W#y B results/dummy_spectra.csvUT Ԁeux PK # nf_resume_cmd.sh 0000644 0000000 0000000 00000001170 14540151521 012713 0 ustar root root nextflow run /app/workflows_user/ms2query_nextflow_workflow/nf_workflow.nf -params-file /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_parameters.yaml -w /data/nf_data/server/nf_work/8979365f96f8468d98ad7ba919b4e4af -with-report /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_report.html -with-timeline /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_timeline.html -with-dag /data/nf_data/server/nf_tasks/8979365f96f8468d98ad7ba919b4e4af/job_dag.html -resume -with-weblog http://localhost:4000/nf_weblog/8979365f96f8468d98ad7ba919b4e4af -c /app/launchserver/nextflow.config submission_parameters.yaml 0000644 0000000 0000000 00000000556 14540151521 015062 0 ustar root root additional_metadata: retention_time feature_id
create_time: 2023-12-18 15:17:27 PST-0800
description: ''
ion_mode: positive
library_path: USERUPLOAD/shared/ms2query/positiveim_model
spectra_path: USERUPLOAD/alberto/ms2query/dummy_spectra.mgf
task: 8979365f96f8468d98ad7ba919b4e4af
workflow_version: SERVER:0.1.2;WORKFLOW:0.2
workflowname: ms2query_nextflow_workflow
workflowdisplay.yaml 0000644 0000000 0000000 00000000373 14540151521 013701 0 ustar root root name: ms2query_nextflow_workflow
displayname: results
Views:
- name: MS2Query results zip
displayname: MS2Query results zip
viewname: ms2query_zip_file
displaytype: download
parameters:
filename: nf_output/ms2query_results.zip