Generation of RO create failed

HrishiDhondge · June 18, 2023, 7:45am

Hello,

I am trying to create the RO create for my workflow. To do so, I am following this talk. According to this talk, I can generate the RO create from the provenance information with the help of runcrate tool.

I installed runcrate as per the instructions.

Now coming to the actual part, when I run my CWL workflow to save provenance information I get a warning as follows:
research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7ff8e3e73dc0>

Then, when I tried to generate the RO crate from the saved provenance using runcrate I get the following error:
Entity wf:main not found in Provenance<urn:uuid:669d5067-67a4-47f6-8744-29a1e9d93690 from /path/to/Provenance/metadata/provenance/primary.cwlprov.xml>

I am not sure, how to address this. The command I used to generate RO crate from provenance information was:
runcrate convert Test_latest/Prov1/ -o Test_lates/ROcrate

I also tried to runcrate report Test_lates/Prov1/ and the output of this command gives following error:
raise ValueError(f"Not a valid RO-Crate: missing {Metadata.BASENAME}") ValueError: Not a valid RO-Crate: missing ro-crate-metadata.json

How can I solve this issue and generate the RO crate successfully?
Is it a good practice to add either Provenance info or RO crate to workflowhub with the code?

mrc · June 19, 2023, 1:40pm

Is your workflow public? If not, can you post the entire log?

What is your cwltool version?

HrishiDhondge · June 19, 2023, 1:53pm

Yes, the workflow is public and registered on WorkflowHub here.
I am using the latest version of cwltool==3.1.20230601100705.
Below is the entire log:

Entire Log

[2023-06-19 13:33:13] INFO /users/hdhondge/miniconda3/envs/CroMaSt/bin/cwltool 3.1.20230601100705
[2023-06-19 13:33:13] INFO [cwltool] /users/hdhondge/miniconda3/envs/CroMaSt/bin/cwltool --parallel --timestamps --provenance Run_prov --leave-tmpdir --outdir=/data2/hdhondge/CroMaSt/Results2/ CroMaSt.cwl Results1/new_param.yml
[2023-06-19 13:33:13] INFO Resolved 'CroMaSt.cwl' to 'file:///local/data2/hdhondge/CroMaSt/CroMaSt.cwl'
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
[2023-06-19 13:33:29] WARNING Workflow checker warning:
Tools/resmapping_cath_instances_subwf.cwl:89:12: Source 'resmapped_domains' of type ["null",
                                                 "File"] may be incompatible
Tools/resmapping_cath_instances_subwf.cwl:104:5:   with sink 'cath_domain_posi_file' of type
                                                   "File"
Tools/resmapping_cath_instances_subwf.cwl:103:5:   Source is from conditional step and may
                                                   produce `null`
Tools/resmapping_cath_instances_subwf.cwl:89:12: Source 'resmapped_domains' of type ["null",
                                                 "File"] may be incompatible
Tools/resmapping_cath_instances_subwf.cwl:104:5:   with sink 'cath_domain_posi_file' of type
                                                   "File"
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
Tools/align_compute_avg.cwl:44:7: Warning: Field 'location' contains undefined reference to
                                  'file:///local/data2/hdhondge/CroMaSt/Tools/split_PDB'
[2023-06-19 13:33:45] WARNING Workflow checker warning:
CroMaSt.cwl:226:12: Source 'averaged_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:325:7:    with sink 'core_struct' of type "File"
                      source has linkMerge method merge_nested
                      Source is from conditional step, but pickValue is not used
CroMaSt.cwl:226:12: Source 'averaged_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:379:7:    with sink 'core_domain_struct' of type ["File", {"type": "array", "items":
                      "File"}]
                      source has linkMerge method merge_nested
                      Source is from conditional step, but pickValue is not used
CroMaSt.cwl:287:55: Source 'cath_crossmap_passed' of type ["null", "File"] may be incompatible
CroMaSt.cwl:389:7:    with sink 'crossmap_cath' of type "File"
CroMaSt.cwl:287:11: Source 'pfam_crossmap_passed' of type ["null", "File"] may be incompatible
CroMaSt.cwl:388:7:    with sink 'crossmap_pfam' of type "File"
CroMaSt.cwl:226:12: Source 'averaged_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:299:7:    with sink 'core_struct' of type "File"
                      source has linkMerge method merge_nested
                      Source is from conditional step, but pickValue is not used
CroMaSt.cwl:226:12: Source 'averaged_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:261:7:    with sink 'core_avg' of type [{"type": "array", "items": "File"}, "File"]
                      source has linkMerge method merge_nested
                      Source is from conditional step, but pickValue is not used
CroMaSt.cwl:148:25: Source 'cath_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:159:7:    with sink 'resmapped_cath' of type "File"
                      source has linkMerge method merge_nested
                      Source is from conditional step, but pickValue is not used
CroMaSt.cwl:148:11: Source 'pfam_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:168:7:    with sink 'resmapped_pfam' of type "File"
                      source has linkMerge method merge_nested
                      Source is from conditional step, but pickValue is not used
CroMaSt.cwl:340:12: Source 'unmapped_aligned_results' of type ["null", "File"] may be incompatible
CroMaSt.cwl:551:5:    with sink 'align_unmap_cath' of type "File"
CroMaSt.cwl:550:5:    Source is from conditional step and may produce `null`
CroMaSt.cwl:340:12: Source 'unmapped_aligned_results' of type ["null", "File"] may be incompatible
CroMaSt.cwl:551:5:    with sink 'align_unmap_cath' of type "File"
CroMaSt.cwl:314:12: Source 'unmapped_aligned_results' of type ["null", "File"] may be incompatible
CroMaSt.cwl:533:5:    with sink 'align_unmap_pfam' of type "File"
CroMaSt.cwl:532:5:    Source is from conditional step and may produce `null`
CroMaSt.cwl:314:12: Source 'unmapped_aligned_results' of type ["null", "File"] may be incompatible
CroMaSt.cwl:533:5:    with sink 'align_unmap_pfam' of type "File"
CroMaSt.cwl:287:55: Source 'cath_crossmap_passed' of type ["null", "File"] may be incompatible
CroMaSt.cwl:463:5:    with sink 'crossmapped_cath_passed' of type "File"
CroMaSt.cwl:287:11: Source 'pfam_crossmap_passed' of type ["null", "File"] may be incompatible
CroMaSt.cwl:457:5:    with sink 'crossmapped_pfam_passed' of type "File"
CroMaSt.cwl:148:25: Source 'cath_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:475:5:    with sink 'crossres_mappedcath' of type "File"
CroMaSt.cwl:474:5:    Source is from conditional step and may produce `null`
CroMaSt.cwl:148:25: Source 'cath_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:475:5:    with sink 'crossres_mappedcath' of type "File"
CroMaSt.cwl:148:11: Source 'pfam_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:469:5:    with sink 'crossres_mappedpfam' of type "File"
CroMaSt.cwl:468:5:    Source is from conditional step and may produce `null`
CroMaSt.cwl:148:11: Source 'pfam_structs' of type ["null", "File"] may be incompatible
CroMaSt.cwl:469:5:    with sink 'crossres_mappedpfam' of type "File"
CroMaSt.cwl:340:56: Source 'failed_domains_list' of type ["null", "File"] may be incompatible
CroMaSt.cwl:563:5:    with sink 'unmap_cath_failed' of type "File"
CroMaSt.cwl:562:5:    Source is from conditional step and may produce `null`
CroMaSt.cwl:340:56: Source 'failed_domains_list' of type ["null", "File"] may be incompatible
CroMaSt.cwl:563:5:    with sink 'unmap_cath_failed' of type "File"
CroMaSt.cwl:340:38: Source 'domain_like_list' of type ["null", "File"] may be incompatible
CroMaSt.cwl:557:5:    with sink 'unmap_cath_passed' of type "File"
CroMaSt.cwl:556:5:    Source is from conditional step and may produce `null`
CroMaSt.cwl:340:38: Source 'domain_like_list' of type ["null", "File"] may be incompatible
CroMaSt.cwl:557:5:    with sink 'unmap_cath_passed' of type "File"
CroMaSt.cwl:314:56: Source 'failed_domains_list' of type ["null", "File"] may be incompatible
CroMaSt.cwl:545:5:    with sink 'unmap_pfam_failed' of type "File"
CroMaSt.cwl:544:5:    Source is from conditional step and may produce `null`
CroMaSt.cwl:314:56: Source 'failed_domains_list' of type ["null", "File"] may be incompatible
CroMaSt.cwl:545:5:    with sink 'unmap_pfam_failed' of type "File"
CroMaSt.cwl:314:38: Source 'domain_like_list' of type ["null", "File"] may be incompatible
CroMaSt.cwl:539:5:    with sink 'unmap_pfam_passed' of type "File"
CroMaSt.cwl:538:5:    Source is from conditional step and may produce `null`
CroMaSt.cwl:314:38: Source 'domain_like_list' of type ["null", "File"] may be incompatible
CroMaSt.cwl:539:5:    with sink 'unmap_pfam_passed' of type "File"
[2023-06-19 13:33:45] INFO [provenance] Adding to RO file:///data2/hdhondge/CroMaSt/Results1/core_avgStruct.pdb
[2023-06-19 13:33:45] INFO [provenance] Adding to RO file:///data2/hdhondge/CroMaSt/Results1/domain_like_structures.json
[2023-06-19 13:33:45] INFO [provenance] Adding to RO file:///data2/hdhondge/CroMaSt/Results1/failed_domains_list.json
[2023-06-19 13:33:45] INFO [provenance] Adding to RO file:///data2/hdhondge/CroMaSt/Results1/family_ids.json
[2023-06-19 13:33:45] INFO [provenance] Adding to RO file:///data2/hdhondge/CroMaSt/Results1/CroMaSt_input.yml
[2023-06-19 13:33:45] INFO [provenance] Adding to RO file:///data2/hdhondge/CroMaSt/Results1/crossmapped_cath_passed.json
[2023-06-19 13:33:45] INFO [provenance] Adding to RO file:///data2/hdhondge/CroMaSt/Results1/crossmapped_pfam_passed.json
[2023-06-19 13:33:45] INFO [provenance] Adding to RO file:///data2/hdhondge/CroMaSt/Results1/true_domains.json
[2023-06-19 13:33:45] INFO [workflow ] starting step get_family_ids
[2023-06-19 13:33:45] INFO [workflow ] start
[2023-06-19 13:33:45] INFO [step get_family_ids] start
[2023-06-19 13:33:45] INFO [job get_family_ids] /tmp/u9f97b3d$ python3 \
    get_family_ids.py \
    -p \
    PF03467 \
    PF03880 \
    PF04847 \
    PF05172 \
    PF08675 \
    PF08777 \
    PF08952 \
    PF09162 \
    PF11608 \
    PF11835 \
    PF13893 \
    PF16367 \
    PF16842 \
    PF17774 \
    -n \
    1 \
    -f \
    /tmp/u9f97b3d/family_ids.json
[2023-06-19 13:33:45] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:33:45] INFO [job get_family_ids] completed success
[2023-06-19 13:33:45] INFO [step get_family_ids] completed success
[2023-06-19 13:33:45] INFO [workflow ] starting step cath_domain_instances
[2023-06-19 13:33:45] INFO [step cath_domain_instances] start
[2023-06-19 13:33:45] INFO [workflow cath_domain_instances] starting step filter_cath_structures
[2023-06-19 13:33:45] INFO [workflow cath_domain_instances] start
[2023-06-19 13:33:45] INFO [step filter_cath_structures] start
[2023-06-19 13:33:45] INFO [workflow ] starting step pfam_domain_instances
[2023-06-19 13:33:45] INFO [step pfam_domain_instances] start
[2023-06-19 13:33:45] INFO [workflow pfam_domain_instances] start
[2023-06-19 13:33:45] INFO [workflow pfam_domain_instances] starting step filter_pfam_structures
[2023-06-19 13:33:45] INFO [step filter_pfam_structures] start
[2023-06-19 13:33:45] INFO [job filter_cath_structures] /tmp/kk_tecl6$ python3 \
    separate_cath.py \
    -l \
    31 \
    -d \
    /tmp/kk_tecl6/obsolete_PDB_entry_ids.txt \
    -o \
    obsolete_cath.txt \
    -c \
    /tmp/kk_tecl6/cath-domain-description-file.txt \
    -n \
    Filtered_CATH.csv \
    -s \
    part.csv \
    -f \
    /tmp/fadlj2ia/stgeff70189-3142-41fb-a5fa-4443ddae0016/family_ids.json
[2023-06-19 13:33:45] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:33:45] INFO [job filter_pfam_structures] /tmp/v65wak31$ python3 \
    separate_pfam.py \
    -l \
    31 \
    -d \
    /tmp/v65wak31/obsolete_PDB_entry_ids.txt \
    -o \
    obsolete_pfam.txt \
    -p \
    /tmp/v65wak31/pdbmap \
    -n \
    Filtered_Pfam.csv \
    -s \
    part.csv \
    -f \
    /tmp/msoym7xl/stg9327731c-da08-4b5d-8ad6-7363e40a4b17/family_ids.json
[2023-06-19 13:33:45] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:33:48] INFO [job filter_pfam_structures] Max memory used: 61MiB
[2023-06-19 13:33:49] INFO [job filter_pfam_structures] completed success
[2023-06-19 13:33:49] INFO [step filter_pfam_structures] completed success
[2023-06-19 13:33:49] INFO [workflow pfam_domain_instances] starting step resmapping_pfam_structs
[2023-06-19 13:33:49] INFO [step resmapping_pfam_structs] start
[2023-06-19 13:33:49] INFO [workflow resmapping_pfam_structs] starting step resmapping_for_Pfam_UP2PDB
[2023-06-19 13:33:49] INFO [workflow resmapping_pfam_structs] start
[2023-06-19 13:33:49] INFO [step resmapping_for_Pfam_UP2PDB] start
[2023-06-19 13:33:49] INFO [job resmapping_for_Pfam_UP2PDB] /tmp/a7tz2mcq$ python3 \
    resmapping_pfam2pdb.py \
    -f \
    /tmp/yopz756i/stg0894283c-86cb-4034-a279-f65d7896420f/0_part.csv \
    -s \
    /tmp/yopz756i/stg3a87b5c4-d857-4fdc-9844-0fb5026bd856/SIFTS \
    -m \
    pfam_resMapped.csv \
    -l \
    lost_pfam.txt
[2023-06-19 13:33:49] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:33:56] INFO [job filter_cath_structures] Max memory used: 60MiB
[2023-06-19 13:33:56] INFO [job filter_cath_structures] completed success
[2023-06-19 13:33:56] INFO [step filter_cath_structures] completed success
[2023-06-19 13:33:56] INFO [workflow cath_domain_instances] starting step resmapping_cath_structs
[2023-06-19 13:33:56] WARNING [job step resmapping_cath_structs] Notice: scattering over empty input in 'flt_files'.  All outputs will be empty.
[2023-06-19 13:33:56] INFO [step resmapping_cath_structs] completed success
[2023-06-19 13:33:56] INFO [workflow cath_domain_instances] starting step collect_lost_instances
[2023-06-19 13:33:56] INFO [step collect_lost_instances] start
[2023-06-19 13:33:56] INFO [workflow cath_domain_instances] starting step add_domain_positions
[2023-06-19 13:33:56] INFO [step add_domain_positions] will be skipped
[2023-06-19 13:33:56] INFO [step add_domain_positions] completed skipped
[2023-06-19 13:33:56] INFO [job collect_lost_instances] /tmp/89aoormj$ python3 \
    collect_lost_instances.py \
    cath_lost_resmap_domain_StIs.json
[2023-06-19 13:33:56] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:33:56] INFO [job collect_lost_instances] completed success
[2023-06-19 13:33:56] INFO [step collect_lost_instances] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:33:56] INFO [workflow cath_domain_instances] completed success
[2023-06-19 13:33:56] INFO [step cath_domain_instances] completed success
[2023-06-19 13:36:05] INFO [job resmapping_for_Pfam_UP2PDB] Max memory used: 92MiB
[2023-06-19 13:36:06] INFO [job resmapping_for_Pfam_UP2PDB] completed success
[2023-06-19 13:36:06] INFO [step resmapping_for_Pfam_UP2PDB] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:36:06] INFO [workflow resmapping_pfam_structs] completed success
[2023-06-19 13:36:06] INFO [step resmapping_pfam_structs] completed success
[2023-06-19 13:36:06] INFO [workflow pfam_domain_instances] starting step add_domain_positions_2
[2023-06-19 13:36:06] INFO [step add_domain_positions_2] start
[2023-06-19 13:36:06] INFO [workflow pfam_domain_instances] starting step collect_lost_instances_2
[2023-06-19 13:36:06] INFO [step collect_lost_instances_2] start
[2023-06-19 13:36:06] INFO [job add_domain_positions] /tmp/oskxpuaa$ python3 \
    add_domain_num.py \
    -i \
    /tmp/8andmar0/stg152329b2-b9b7-4a97-9b8a-5df6ef72b078/pfam_resMapped.csv \
    -o \
    pfam_resmapped_domain_StIs.csv
[2023-06-19 13:36:06] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:36:06] INFO [job collect_lost_instances_2] /tmp/b_wxjed8$ python3 \
    collect_lost_instances.py \
    pfam_lost_resmap_domain_StIs.json
[2023-06-19 13:36:06] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:36:06] INFO [job collect_lost_instances_2] completed success
[2023-06-19 13:36:06] INFO [step collect_lost_instances_2] completed success
[2023-06-19 13:36:07] INFO [job add_domain_positions] completed success
[2023-06-19 13:36:07] INFO [step add_domain_positions_2] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:36:07] INFO [workflow pfam_domain_instances] completed success
[2023-06-19 13:36:07] INFO [step pfam_domain_instances] completed success
[2023-06-19 13:36:07] INFO [workflow ] starting step add_crossmapped_to_resmapped
[2023-06-19 13:36:07] INFO [step add_crossmapped_to_resmapped] start
[2023-06-19 13:36:07] INFO [job add_crossmapped_to_resmapped] /tmp/1c9nhrjh$ python3 \
    add_crossmapped2resmapped.py \
    -p \
    /tmp/m7u_2moc/stgc0b9e5ce-6838-402d-8da3-ba22cb3ced91/pfam_resmapped_domain_StIs.csv \
    -px \
    /tmp/m7u_2moc/stge75002b9-a239-4074-a759-b9be2faca38c/crossmapped_pfam_passed.json \
    -cx \
    /tmp/m7u_2moc/stg611f1bed-afd4-4ea3-bfc0-f8771c467dc0/crossmapped_cath_passed.json \
    -pr \
    pfam_res_crossMapped.csv \
    -cr \
    cath_res_crossMapped.csv
[2023-06-19 13:36:07] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:36:07] INFO [job add_crossmapped_to_resmapped] completed success
[2023-06-19 13:36:07] INFO [step add_crossmapped_to_resmapped] completed success
[2023-06-19 13:36:07] INFO [workflow ] starting step compare_instances_CATH_Pfam
[2023-06-19 13:36:07] INFO [step compare_instances_CATH_Pfam] start
[2023-06-19 13:36:07] INFO [job compare_instances_CATH_Pfam] /tmp/51a73ev0$ python3 \
    compare_cath_pfam.py \
    -l \
    31 \
    -c \
    /tmp/wiubg70o/stg6191943c-6107-4b39-8267-4ff23c7c9d21/cath_res_crossMapped.csv \
    -p \
    /tmp/wiubg70o/stg5b1ab25a-96d9-4782-95a7-9de2e4d95c47/pfam_res_crossMapped.csv \
    -f \
    /tmp/51a73ev0/true_domains.json \
    -uq_pf \
    unique_pfam.csv \
    -uq_ca \
    unique_cath.csv
[2023-06-19 13:36:07] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:36:08] INFO [job compare_instances_CATH_Pfam] completed success
[2023-06-19 13:36:08] INFO [step compare_instances_CATH_Pfam] completed success
[2023-06-19 13:36:08] INFO [workflow ] starting step crossmapping_Pfam2CATH
[2023-06-19 13:36:08] INFO [step crossmapping_Pfam2CATH] start
[2023-06-19 13:36:08] INFO [workflow ] starting step format_core_list
[2023-06-19 13:36:08] INFO [step format_core_list] start
[2023-06-19 13:36:08] INFO [workflow ] starting step crossmapping_CATH2Pfam
[2023-06-19 13:36:08] INFO [step crossmapping_CATH2Pfam] start
[2023-06-19 13:36:08] INFO [job crossmapping_Pfam2CATH] /tmp/4mtel3mt$ python3 \
    map_unique_struct_pfam2cath.py \
    -c \
    /tmp/_qfq79rc/stg9e7b5ea3-cf77-4177-9fcf-d189d5cfe17b/cath-domain-description-file.txt \
    -x \
    pfam_crossMapped_cath.jsonx \
    -l \
    31 \
    -u \
    pfam_unq_unmapped.jsonx \
    -p \
    /tmp/_qfq79rc/stg98b7c529-4d10-4e58-99b1-2677e350f761/unique_pfam.csv
[2023-06-19 13:36:08] INFO [job format_core_list] /tmp/tr8p7lta$ python3 \
    list_true_domains.py
[2023-06-19 13:36:08] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:36:08] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:36:08] INFO [job crossmapping_CATH2Pfam] /tmp/u1alckm8$ python3 \
    map_unique_struct_cath2pfam.py \
    -x \
    cath_crossMapped_pfam.jsonx \
    -l \
    31 \
    -u \
    cath_unq_unmapped.jsonx \
    -p \
    /tmp/br56pq7z/stg6a228f02-e1fd-44fb-8358-ded924000e04/pdbmap \
    -c \
    /tmp/br56pq7z/stg8062ff82-25bf-4040-99f6-b69a6db90659/unique_cath.csv
[2023-06-19 13:36:08] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:36:08] INFO [job format_core_list] completed success
[2023-06-19 13:36:08] INFO [step format_core_list] completed success
[2023-06-19 13:36:08] INFO [workflow ] starting step chop_and_avg_for_core
[2023-06-19 13:36:08] INFO [step chop_and_avg_for_core] will be skipped
[2023-06-19 13:36:08] INFO [step chop_and_avg_for_core] completed skipped
[2023-06-19 13:36:09] INFO [job crossmapping_CATH2Pfam] completed success
[2023-06-19 13:36:09] INFO [step crossmapping_CATH2Pfam] completed success
[2023-06-19 13:36:09] INFO [workflow ] starting step unmapped_from_cath
[2023-06-19 13:36:09] INFO [step unmapped_from_cath] will be skipped
[2023-06-19 13:36:09] INFO [step unmapped_from_cath] completed skipped
[2023-06-19 13:36:09] INFO [workflow ] starting step chop_and_avg_for_CATH2Pfam
[2023-06-19 13:36:09] INFO [step chop_and_avg_for_CATH2Pfam] start
[2023-06-19 13:36:09] INFO [workflow chop_and_avg_for_CATH2Pfam] starting step chop_and_avg_from_list
[2023-06-19 13:36:09] INFO [workflow chop_and_avg_for_CATH2Pfam] start
[2023-06-19 13:36:09] WARNING [job step chop_and_avg_from_list] Notice: scattering over empty input in 'in_file'.  All outputs will be empty.
[2023-06-19 13:36:09] INFO [step chop_and_avg_from_list] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:36:09] INFO [workflow chop_and_avg_for_CATH2Pfam] completed success
[2023-06-19 13:36:09] INFO [step chop_and_avg_for_CATH2Pfam] completed success
[2023-06-19 13:37:57] INFO [job crossmapping_Pfam2CATH] Max memory used: 1633MiB
[2023-06-19 13:37:57] INFO [job crossmapping_Pfam2CATH] completed success
[2023-06-19 13:37:57] INFO [step crossmapping_Pfam2CATH] completed success
[2023-06-19 13:37:57] INFO [workflow ] starting step chop_and_avg_for_Pfam2CATH
[2023-06-19 13:37:57] INFO [step chop_and_avg_for_Pfam2CATH] start
[2023-06-19 13:37:57] INFO [workflow chop_and_avg_for_Pfam2CATH] starting step chop_and_avg_from_list_2
[2023-06-19 13:37:57] INFO [workflow chop_and_avg_for_Pfam2CATH] start
[2023-06-19 13:37:57] WARNING [job step chop_and_avg_from_list_2] Notice: scattering over empty input in 'in_file'.  All outputs will be empty.
[2023-06-19 13:37:57] INFO [step chop_and_avg_from_list_2] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:37:57] INFO [workflow chop_and_avg_for_Pfam2CATH] completed success
[2023-06-19 13:37:57] INFO [step chop_and_avg_for_Pfam2CATH] completed success
[2023-06-19 13:37:57] INFO [workflow ] starting step unmapped_from_pfam
[2023-06-19 13:37:57] INFO [step unmapped_from_pfam] start
[2023-06-19 13:37:57] INFO [workflow unmapped_from_pfam] start
[2023-06-19 13:37:57] INFO [workflow unmapped_from_pfam] starting step per_unp_dom_instance
[2023-06-19 13:37:57] INFO [step per_unp_dom_instance] start
[2023-06-19 13:37:57] INFO [workflow ] starting step align_avg_structs_pairwise
[2023-06-19 13:37:57] INFO [step align_avg_structs_pairwise] start
[2023-06-19 13:37:57] INFO [job per_unp_dom_instance] /tmp/i8076r4i$ python3 \
    crossmapped_per_unp_dom.py \
    -f \
    /tmp/qxxv1f5n/stgea00de1c-7406-4ffd-b1a5-668ae8a2e2c7/pfam_unq_unmapped.jsonx > /tmp/i8076r4i/5a0b5b0ee8819feece292f4af464b2ccbffcead7
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [job align_avg_structs_pairwise] /tmp/6k4obnu6$ python3 \
    pairwise_aligner.py \
    -t \
    /tmp/i_f8nxc2/stg6b0813eb-025b-436b-9ae3-aa13422a1f7b/core_avgStruct.pdb \
    -r \
    align_Struct_analysis.csv
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [job per_unp_dom_instance] completed success
[2023-06-19 13:37:57] INFO [step per_unp_dom_instance] completed success
[2023-06-19 13:37:57] INFO [workflow unmapped_from_pfam] starting step avg_unp_domains
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains] starting step chop_structs
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains] start
[2023-06-19 13:37:57] INFO [step chop_structs] start
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_2] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_2] starting step chop_structs_2
[2023-06-19 13:37:57] INFO [step chop_structs_2] start
[2023-06-19 13:37:57] INFO [job chop_structs] /tmp/knkvijgl$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/2puoo18c/stgd8991b78-f390-42f8-bff2-15b858be8183/unmapped_domain_1_A0A6A5Q318.json \
    -p \
    /tmp/2puoo18c/stge8492157-02db-4490-bf6a-a0182a13663a/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/knkvijgl/99a4dda21068e1076bcbc268ceeef8242974f012

I removed the pandas warning from one of the tools to keep it relatively short.

HrishiDhondge · June 19, 2023, 1:55pm

Second part of the log

[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_3] starting step chop_structs_3
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_3] start
[2023-06-19 13:37:57] INFO [step chop_structs_3] start
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_4] starting step chop_structs_4
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_4] start
[2023-06-19 13:37:57] INFO [step chop_structs_4] start
[2023-06-19 13:37:57] INFO [job chop_structs_2] /tmp/d_pe67_n$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/_gilevj2/stgb6990e4f-ebd7-45fc-bba7-a143307172c7/unmapped_domain_1_P0A9P6.json \
    -p \
    /tmp/_gilevj2/stgd1491899-895c-4f95-8bdf-33ed098e1363/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/d_pe67_n/99a4dda21068e1076bcbc268ceeef8242974f012
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [job chop_structs_3] /tmp/8obiuj5w$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/59f125cu/stg72a7eb10-5387-4ad4-8f11-c62adca26492/unmapped_domain_1_P21693.json \
    -p \
    /tmp/59f125cu/stgdc71e63d-8e35-4cc6-a8bf-0895dfb4e6f6/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/8obiuj5w/99a4dda21068e1076bcbc268ceeef8242974f012
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_5] starting step chop_structs_5
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_5] start
[2023-06-19 13:37:57] INFO [step chop_structs_5] start
[2023-06-19 13:37:57] INFO [job chop_structs_4] /tmp/fnm_81tm$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/c1lwczc8/stg8a784610-722b-4bda-97f4-3b02d7ec8686/unmapped_domain_1_P40567.json \
    -p \
    /tmp/c1lwczc8/stg0699b957-5bce-4867-a063-93994c2e291e/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/fnm_81tm/99a4dda21068e1076bcbc268ceeef8242974f012
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_6] starting step chop_structs_6
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_6] start
[2023-06-19 13:37:57] INFO [step chop_structs_6] start
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_7] starting step chop_structs_7
[2023-06-19 13:37:57] INFO [job chop_structs_5] /tmp/azsbjhlt$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/ujxr5t1s/stgada7885b-7272-4f8c-aca8-687ea495a548/unmapped_domain_1_P49960.json \
    -p \
    /tmp/ujxr5t1s/stgc7e58974-733d-4318-881f-88490933c94f/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/azsbjhlt/99a4dda21068e1076bcbc268ceeef8242974f012
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_7] start
[2023-06-19 13:37:57] INFO [step chop_structs_7] start
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [job chop_structs_6] /tmp/pfna9l3i$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/sby8gw5b/stg90f1d5a6-d1dd-42c6-845c-e7c99adce8ea/unmapped_domain_1_Q17RY0.json \
    -p \
    /tmp/sby8gw5b/stg192d82da-e5eb-4a97-a9dc-dd554618c9b6/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/pfna9l3i/99a4dda21068e1076bcbc268ceeef8242974f012
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_8] starting step chop_structs_8
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_8] start
[2023-06-19 13:37:57] INFO [step chop_structs_8] start
[2023-06-19 13:37:57] INFO [job chop_structs_7] /tmp/9zb160n4$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/opwywd6n/stg1453f640-2d96-4da5-881a-fddb5a3b5571/unmapped_domain_1_Q4G0J3.json \
    -p \
    /tmp/opwywd6n/stg65757dbd-cff6-428b-a6c6-ffac55137860/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/9zb160n4/99a4dda21068e1076bcbc268ceeef8242974f012
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [step avg_unp_domains] start
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_9] starting step chop_structs_9
[2023-06-19 13:37:57] INFO [workflow avg_unp_domains_9] start
[2023-06-19 13:37:57] INFO [step chop_structs_9] start
[2023-06-19 13:37:57] INFO [job chop_structs_8] /tmp/ern5y6m4$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/7rrb3ies/stgbca36e17-7959-4836-b3a1-259dbacad8f3/unmapped_domain_1_Q8VDG3.json \
    -p \
    /tmp/7rrb3ies/stgb83672e9-ed6d-4334-8492-79063c0f95c3/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/ern5y6m4/99a4dda21068e1076bcbc268ceeef8242974f012
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:57] INFO [job chop_structs_9] /tmp/dxo87uab$ python3 \
    chop_struct2domains.py \
    -f \
    /tmp/9p_jmoxl/stg3abe8f3c-e5c1-4a22-9729-583c91171527/unmapped_domain_1_Q9BZB8.json \
    -p \
    /tmp/9p_jmoxl/stgdbc83757-0cb4-4da4-b3ea-5bea178429fb/PDB_files \
    -s \
    split_PDB \
    -k \
    KPAX_RESULTS > /tmp/dxo87uab/99a4dda21068e1076bcbc268ceeef8242974f012
[2023-06-19 13:37:57] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:58] INFO [job chop_structs_2] Max memory used: 93MiB
[2023-06-19 13:37:58] INFO [job chop_structs_2] completed success
[2023-06-19 13:37:58] INFO [step chop_structs_2] completed success
[2023-06-19 13:37:58] INFO [workflow avg_unp_domains_2] starting step avg_chopped_structs_unp_domains_2
[2023-06-19 13:37:58] INFO [step avg_chopped_structs_unp_domains_2] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:37:58] INFO [job avg_chopped_structs_unp_domains] /tmp/1sarkp9w$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/ylz_b1tn/stg703fe899-995e-42bc-a2f2-a1f214ae6569/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/ylz_b1tn/stg6eede303-f8ea-4269-85c6-ec923be45c7e/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:37:58] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
/tmp/6k4obnu6/pairwise_aligner.py:88: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  kaln_df = kaln_df.append(one, ignore_index=True)
/tmp/6k4obnu6/pairwise_aligner.py:88: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  kaln_df = kaln_df.append(one, ignore_index=True)
[2023-06-19 13:37:59] INFO [job chop_structs_5] Max memory used: 82MiB
[2023-06-19 13:37:59] INFO [job chop_structs_5] completed success
[2023-06-19 13:37:59] INFO [step chop_structs_5] completed success
[2023-06-19 13:37:59] INFO [workflow avg_unp_domains_5] starting step avg_chopped_structs_unp_domains_5
[2023-06-19 13:37:59] INFO [step avg_chopped_structs_unp_domains_5] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:37:59] INFO [job avg_chopped_structs_unp_domains_2] /tmp/2vtd79tl$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/4tqimjfw/stg492c51f4-dfba-4785-a804-bb032cce8f7c/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/4tqimjfw/stga20b73e6-e846-4620-8229-c1165adb506e/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:37:59] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:59] INFO [job align_avg_structs_pairwise] Max memory used: 79MiB
[2023-06-19 13:37:59] INFO [job chop_structs_8] Max memory used: 81MiB
[2023-06-19 13:37:59] INFO [job chop_structs_8] completed success
[2023-06-19 13:37:59] INFO [step chop_structs_8] completed success
[2023-06-19 13:37:59] INFO [workflow avg_unp_domains_8] starting step avg_chopped_structs_unp_domains_8
[2023-06-19 13:37:59] INFO [step avg_chopped_structs_unp_domains_8] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:37:59] INFO [job avg_chopped_structs_unp_domains_3] /tmp/g188qd7n$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/6sm4opu4/stgff6f541c-5dda-4f3c-b81f-cfcc0e2ab72d/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/6sm4opu4/stgaf0cf259-a260-41ff-961e-52c49d32dd80/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:37:59] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:59] INFO [job chop_structs_7] Max memory used: 84MiB
[2023-06-19 13:37:59] INFO [job chop_structs_7] completed success
[2023-06-19 13:37:59] INFO [step chop_structs_7] completed success
[2023-06-19 13:37:59] INFO [workflow avg_unp_domains_7] starting step avg_chopped_structs_unp_domains_7
[2023-06-19 13:37:59] INFO [step avg_chopped_structs_unp_domains_7] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:37:59] INFO [job avg_chopped_structs_unp_domains_4] /tmp/ugf3i2vx$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/69_e6m9s/stg2dd3c52a-8d3c-458c-9ca7-0a91e0714303/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/69_e6m9s/stg9919d2c1-272a-4628-894e-c219c1662a8f/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:37:59] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:37:59] INFO [job align_avg_structs_pairwise] completed success
[2023-06-19 13:37:59] INFO [step align_avg_structs_pairwise] completed success
[2023-06-19 13:37:59] INFO [workflow ] starting step check_alignment_scores
[2023-06-19 13:37:59] INFO [step check_alignment_scores] start
[2023-06-19 13:37:59] INFO [job check_alignment_scores] /tmp/qpspckfl$ python3 \
    check_threshold.py \
    -a \
    /tmp/1o4v9wcz/stg88d1302e-80f9-4263-b9b4-39ad6956e1ec/align_Struct_analysis.csv \
    -f \
    /tmp/1o4v9wcz/stg35049313-0c3b-4c93-b83d-b845cd75c342/family_ids.json \
    -s \
    Mscore \
    -t \
    0.6 \
    -px \
    /tmp/1o4v9wcz/stg6c1bedd7-5687-4a60-96ba-d33ce517e828/pfam_crossMapped_cath.jsonx \
    -cx \
    /tmp/1o4v9wcz/stg6811ecdf-4a45-4339-a44f-5504935dddc4/cath_crossMapped_pfam.jsonx
[2023-06-19 13:37:59] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:38:00] INFO [job avg_chopped_structs_unp_domains] Max memory used: 85MiB
[2023-06-19 13:38:00] INFO [job avg_chopped_structs_unp_domains] completed success
[2023-06-19 13:38:00] INFO [step avg_chopped_structs_unp_domains_2] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:38:00] INFO [workflow avg_unp_domains_2] completed success
[2023-06-19 13:38:00] INFO [job chop_structs_3] Max memory used: 82MiB
[2023-06-19 13:38:00] INFO [job chop_structs_3] completed success
[2023-06-19 13:38:00] INFO [step chop_structs_3] completed success
[2023-06-19 13:38:00] INFO [workflow avg_unp_domains_3] starting step avg_chopped_structs_unp_domains_3
[2023-06-19 13:38:00] INFO [step avg_chopped_structs_unp_domains_3] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:38:00] INFO [job avg_chopped_structs_unp_domains_5] /tmp/ngmtvunp$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/0yopn99a/stg0df48036-cc59-4644-ad07-69d78719eb81/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/0yopn99a/stgc4d23acb-f796-49f1-9689-6ae535439702/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:38:00] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:38:00] INFO [job check_alignment_scores] completed success
[2023-06-19 13:38:00] INFO [step check_alignment_scores] completed success
[2023-06-19 13:38:00] INFO [job chop_structs_9] Max memory used: 96MiB
[2023-06-19 13:38:00] INFO [job chop_structs_9] completed success
[2023-06-19 13:38:00] INFO [step chop_structs_9] completed success
[2023-06-19 13:38:00] INFO [workflow avg_unp_domains_9] starting step avg_chopped_structs_unp_domains_9
[2023-06-19 13:38:00] INFO [step avg_chopped_structs_unp_domains_9] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:38:00] INFO [job avg_chopped_structs_unp_domains_6] /tmp/j03tbsar$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/g7t8srpy/stgd81e49f3-e4de-4aa2-8dbf-cb1814dfd347/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/g7t8srpy/stgf3e4b27b-27db-4156-97da-d624d5ca7e63/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:38:00] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:38:01] INFO [job avg_chopped_structs_unp_domains_5] completed success
[2023-06-19 13:38:01] INFO [step avg_chopped_structs_unp_domains_3] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:38:01] INFO [workflow avg_unp_domains_3] completed success
[2023-06-19 13:38:01] INFO [job chop_structs_6] Max memory used: 94MiB
[2023-06-19 13:38:01] INFO [job chop_structs_6] completed success
[2023-06-19 13:38:01] INFO [step chop_structs_6] completed success
[2023-06-19 13:38:01] INFO [workflow avg_unp_domains_6] starting step avg_chopped_structs_unp_domains_6
[2023-06-19 13:38:01] INFO [step avg_chopped_structs_unp_domains_6] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:38:01] INFO [job avg_chopped_structs_unp_domains_7] /tmp/ll7pv5wy$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/5pwqh3lu/stg3c63165e-1782-4896-99b3-c78c3fba458d/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/5pwqh3lu/stgf12cdead-1f42-47d8-8633-05762560e2e6/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:38:01] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
unmapped_domain_1_P49960 2 unmapped_domain_1_P49960_avgStruct.pdb IF error happens
[2023-06-19 13:38:02] INFO [job avg_chopped_structs_unp_domains_2] Max memory used: 86MiB
[2023-06-19 13:38:02] INFO [job avg_chopped_structs_unp_domains_2] completed success
[2023-06-19 13:38:02] INFO [step avg_chopped_structs_unp_domains_5] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:38:02] INFO [workflow avg_unp_domains_5] completed success
unmapped_domain_1_Q8VDG3 3 unmapped_domain_1_Q8VDG3_avgStruct.pdb IF error happens
[2023-06-19 13:38:03] INFO [job avg_chopped_structs_unp_domains_3] Max memory used: 92MiB
[2023-06-19 13:38:03] INFO [job avg_chopped_structs_unp_domains_3] completed success
[2023-06-19 13:38:03] INFO [step avg_chopped_structs_unp_domains_8] completed success
[2023-06-19 13:38:03] INFO [workflow avg_unp_domains_8] completed success
unmapped_domain_1_Q17RY0 2 unmapped_domain_1_Q17RY0_avgStruct.pdb IF error happens
[2023-06-19 13:38:04] INFO [job avg_chopped_structs_unp_domains_7] Max memory used: 98MiB
[2023-06-19 13:38:04] INFO [job avg_chopped_structs_unp_domains_7] completed success
[2023-06-19 13:38:04] INFO [step avg_chopped_structs_unp_domains_6] completed success
[2023-06-19 13:38:04] INFO [workflow avg_unp_domains_6] completed success
unmapped_domain_1_Q9BZB8 2 unmapped_domain_1_Q9BZB8_avgStruct.pdb IF error happens
[2023-06-19 13:38:04] INFO [job avg_chopped_structs_unp_domains_6] Max memory used: 94MiB
[2023-06-19 13:38:04] INFO [job avg_chopped_structs_unp_domains_6] completed success
[2023-06-19 13:38:04] INFO [step avg_chopped_structs_unp_domains_9] completed success
[2023-06-19 13:38:04] INFO [workflow avg_unp_domains_9] completed success
unmapped_domain_1_Q4G0J3 3 unmapped_domain_1_Q4G0J3_avgStruct.pdb IF error happens
[2023-06-19 13:38:05] INFO [job avg_chopped_structs_unp_domains_4] Max memory used: 86MiB
[2023-06-19 13:38:05] INFO [job avg_chopped_structs_unp_domains_4] completed success
[2023-06-19 13:38:05] INFO [step avg_chopped_structs_unp_domains_7] completed success
[2023-06-19 13:38:05] INFO [workflow avg_unp_domains_7] completed success
[2023-06-19 13:38:10] INFO [job chop_structs] Max memory used: 67MiB
[2023-06-19 13:38:10] INFO [job chop_structs] completed success
[2023-06-19 13:38:10] INFO [step chop_structs] completed success
[2023-06-19 13:38:10] INFO [workflow avg_unp_domains] starting step avg_chopped_structs_unp_domains
[2023-06-19 13:38:10] INFO [step avg_chopped_structs_unp_domains] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:38:10] INFO [job avg_chopped_structs_unp_domains_8] /tmp/u0ay_u1u$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/w14i7c72/stg73efed26-7ed7-4def-8844-0191d559c710/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/w14i7c72/stg663c438e-2550-40a0-a2f6-6ac432f1c8a3/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:38:10] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
unmapped_domain_1_A0A6A5Q318 2 unmapped_domain_1_A0A6A5Q318_avgStruct.pdb IF error happens
[2023-06-19 13:38:12] INFO [job avg_chopped_structs_unp_domains_8] Max memory used: 101MiB
[2023-06-19 13:38:12] INFO [job avg_chopped_structs_unp_domains_8] completed success
[2023-06-19 13:38:12] INFO [step avg_chopped_structs_unp_domains] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:38:12] INFO [workflow avg_unp_domains] completed success
[2023-06-19 13:38:13] INFO [job chop_structs_4] Max memory used: 88MiB
[2023-06-19 13:38:13] INFO [job chop_structs_4] completed success
[2023-06-19 13:38:13] INFO [step chop_structs_4] completed success
[2023-06-19 13:38:13] INFO [workflow avg_unp_domains_4] starting step avg_chopped_structs_unp_domains_4
[2023-06-19 13:38:13] INFO [step avg_chopped_structs_unp_domains_4] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:38:13] INFO [job avg_chopped_structs_unp_domains_9] /tmp/yesd51wa$ python3 \
    align_compute_avg.py \
    -f \
    /tmp/q6bru3pe/stg7651e23c-915f-461f-aa27-f235c5bcd495/99a4dda21068e1076bcbc268ceeef8242974f012 \
    -s \
    /tmp/q6bru3pe/stg49cc0000-bbd9-4d1e-9970-39cdeb4183ee/split_PDB \
    -k \
    KPAX_RESULTS
[2023-06-19 13:38:13] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
unmapped_domain_1_P40567 5 unmapped_domain_1_P40567_avgStruct.pdb IF error happens
[2023-06-19 13:38:16] INFO [job avg_chopped_structs_unp_domains_9] Max memory used: 99MiB
[2023-06-19 13:38:16] INFO [job avg_chopped_structs_unp_domains_9] completed success
[2023-06-19 13:38:16] INFO [step avg_chopped_structs_unp_domains_4] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:38:16] INFO [workflow avg_unp_domains_4] completed success
[2023-06-19 13:38:16] INFO [step avg_unp_domains] completed success
[2023-06-19 13:38:16] INFO [workflow unmapped_from_pfam] starting step copy_avg_dom
[2023-06-19 13:38:16] INFO [step copy_avg_dom] start
[2023-06-19 13:38:16] INFO [job copy_avg_dom] /tmp/gjy7c1j9$ python \
    script.py
[2023-06-19 13:38:16] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:38:16] INFO [job copy_avg_dom] completed success
[2023-06-19 13:38:16] INFO [step copy_avg_dom] completed success
[2023-06-19 13:38:16] INFO [workflow unmapped_from_pfam] starting step pairwise_align_avg_structs
[2023-06-19 13:38:16] INFO [step pairwise_align_avg_structs] start
Warning: invalid field 'nameroot', expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field 'nameext', expected one of: 'class', 'location', 'path', 'basename', 'listing'
[2023-06-19 13:38:16] INFO [job pairwise_align_avg_structs] /tmp/sg5h986e$ python3 \
    pairwise_aligner.py \
    -d \
    /tmp/5_ww6ydm/stgf212598a-bb2f-4aef-ac61-17a140e2507c/avg_split_PDB \
    -t \
    /tmp/5_ww6ydm/stge310164b-0824-4ae1-9088-902e4da7e862/core_avgStruct.pdb \
    -r \
    align_Struct_analysis.csv
[2023-06-19 13:38:16] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:38:17] INFO [job pairwise_align_avg_structs] completed success
[2023-06-19 13:38:17] INFO [step pairwise_align_avg_structs] completed success
[2023-06-19 13:38:17] INFO [workflow unmapped_from_pfam] starting step check_threshold_step
[2023-06-19 13:38:17] INFO [step check_threshold_step] start
[2023-06-19 13:38:17] INFO [job check_threshold_step] /tmp/kwq3zd1o$ python3 \
    filter_align_scores.py \
    -s \
    Mscore \
    -f \
    pfam_unmapped_failed_structs.csv \
    -p \
    pfam_unmapped_passed_structs.csv \
    -t \
    0.6 \
    -i \
    /tmp/tojafpj5/stgbd8e2a5d-3614-4dc6-b933-9749bd217281/align_Struct_analysis.csv \
    -x \
    /tmp/tojafpj5/stg42d6c252-aad0-465e-a6d8-2ce59548d1f3/pfam_unq_unmapped.jsonx
[2023-06-19 13:38:17] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
/tmp/kwq3zd1o/filter_align_scores.py:44: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  final_df = final_df.append(tmp_group, ignore_index=True)
/tmp/kwq3zd1o/filter_align_scores.py:44: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  final_df = final_df.append(tmp_group, ignore_index=True)
[2023-06-19 13:38:18] INFO [job check_threshold_step] completed success
[2023-06-19 13:38:18] INFO [step check_threshold_step] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
[2023-06-19 13:38:18] INFO [workflow unmapped_from_pfam] completed success
[2023-06-19 13:38:18] INFO [step unmapped_from_pfam] completed success
[2023-06-19 13:38:18] INFO [workflow ] starting step gather_failed_domains
[2023-06-19 13:38:18] INFO [step gather_failed_domains] start
[2023-06-19 13:38:18] INFO [workflow ] starting step gather_domain_like
[2023-06-19 13:38:18] INFO [step gather_domain_like] start
[2023-06-19 13:38:18] INFO [job gather_failed_domains] /tmp/2da1zwkx$ python3 \
    merge_unmapped.py \
    -p \
    /tmp/opu_ecbw/stg8f2ebd9c-919c-4a84-90dd-1037f4a596ba/pfam_unmapped_failed_structs.csv \
    -px \
    /tmp/opu_ecbw/stgd32eb944-5c8d-4f59-a42f-86d88e311ca0/crossmapped_pfam_failed.json \
    -o \
    /tmp/2da1zwkx/failed_domains_list.json \
    -cx \
    /tmp/opu_ecbw/stg13df5bed-0e05-4fe8-90c2-91a108fef038/crossmapped_cath_failed.json
[2023-06-19 13:38:18] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:38:18] INFO [job gather_domain_like] /tmp/3sia3mqf$ python3 \
    merge_unmapped.py \
    -p \
    /tmp/0t6jrnj7/stgf0c4f059-ff36-47d3-8764-5bcdbb23be4e/pfam_unmapped_passed_structs.csv \
    -o \
    /tmp/3sia3mqf/domain_like_structures.json
[2023-06-19 13:38:18] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
[2023-06-19 13:38:18] INFO [job gather_failed_domains] completed success
[2023-06-19 13:38:18] INFO [step gather_failed_domains] completed success
[2023-06-19 13:38:18] INFO [job gather_domain_like] completed success
[2023-06-19 13:38:18] INFO [step gather_domain_like] completed success
[2023-06-19 13:38:18] INFO [workflow ] starting step create_new_parameters
[2023-06-19 13:38:18] INFO [step create_new_parameters] start
[2023-06-19 13:38:18] INFO [job create_new_parameters] /tmp/8ciw6370$ python3 \
    create_param.py \
    -i \
    /tmp/0ns_ouf1/stg44e2a912-db6a-4cc5-8e75-5e6d1b35323c/CroMaSt_input.yml \
    -o \
    new_param.yml \
    -px \
    /tmp/0ns_ouf1/stg1b4b9d23-d42f-4cae-b45a-9e65084c6ff3/crossmapped_pfam_passed.json \
    -cx \
    /tmp/0ns_ouf1/stg86c01cfd-dc5c-45ce-b1c7-4a771ff54560/crossmapped_cath_passed.json
[2023-06-19 13:38:18] WARNING research_obj set but one of process_run_id or prov_obj is missing from runtimeContext: <cwltool.context.RuntimeContext object at 0x7f7755d43a00>
new_param.yml
[2023-06-19 13:38:18] INFO [job create_new_parameters] completed success
[2023-06-19 13:38:18] INFO [step create_new_parameters] completed success
[2023-06-19 13:38:18] INFO [workflow ] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(

[2023-06-19 13:38:19] INFO Final process status is success
[2023-06-19 13:38:19] INFO [provenance] Finalizing Research Object
[2023-06-19 13:38:19] INFO [provenance] Deleting existing /local/data2/hdhondge/CroMaSt/Run_prov
[2023-06-19 13:38:21] INFO [provenance] Research Object saved to /local/data2/hdhondge/CroMaSt/Run_prov

HrishiDhondge · June 19, 2023, 1:56pm

Outputs info from Workflow log

{
“align_unmap_cath”: null,
“align_unmap_pfam”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/align_Struct_analysis.csv”,
“basename”: “align_Struct_analysis.csv”,
“class”: “File”,
“checksum”: “sha1$a6078f3b267d3d91daddb3a12f7c616f576c8e21”,
“size”: 2291,
“format”: “http://edamontology.org/format_3752”,
“path”: “/data2/hdhondge/CroMaSt/Results2/align_Struct_analysis.csv”
},
“all_domain_like”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/domain_like_structures.json”,
“basename”: “domain_like_structures.json”,
“class”: “File”,
“checksum”: “sha1$e191e6e3abca6c918c63ade666a2a17a81121403”,
“size”: 31693,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/domain_like_structures.json”
},
“all_failed_domains”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/failed_domains_list.json”,
“basename”: “failed_domains_list.json”,
“class”: “File”,
“checksum”: “sha1$b15cca0131877e09d2414c448cf0f62f459b14b4”,
“size”: 9616,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/failed_domains_list.json”
},
“allmap_cath”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/cath_crossMapped_pfam.jsonx”,
“basename”: “cath_crossMapped_pfam.jsonx”,
“class”: “File”,
“checksum”: “sha1$bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f”,
“size”: 2,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/cath_crossMapped_pfam.jsonx”
},
“allmap_pfam”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/pfam_crossMapped_cath.jsonx”,
“basename”: “pfam_crossMapped_cath.jsonx”,
“class”: “File”,
“checksum”: “sha1$bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f”,
“size”: 2,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/pfam_crossMapped_cath.jsonx”
},
“avg_alignment_result”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/align_Struct_analysis.csv_2”,
“basename”: “align_Struct_analysis.csv”,
“class”: “File”,
“checksum”: “sha1$dba86745697ceeb3e546e4eb218eb58a703a184e”,
“size”: 630,
“format”: “http://edamontology.org/format_3752”,
“path”: “/data2/hdhondge/CroMaSt/Results2/align_Struct_analysis.csv_2”
},
“cath_crossmap_pfam_avg”: ,
“core_domains_list”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/coreDomains.json”,
“basename”: “coreDomains.json”,
“class”: “File”,
“checksum”: “sha1$8e9686a3cb95b4c0423cdf0d9538fb0db09572f0”,
“size”: 51040,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/coreDomains.json”
},
“core_structure”: null,
“crossmap_cath”: ,
“crossmap_pfam”: ,
“crossmapped_cath_passed”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/crossmapped_cath_passed.json”,
“basename”: “crossmapped_cath_passed.json”,
“class”: “File”,
“checksum”: “sha1$bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f”,
“size”: 2,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/crossmapped_cath_passed.json”
},
“crossmapped_pfam_passed”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/crossmapped_pfam_passed.json”,
“basename”: “crossmapped_pfam_passed.json”,
“class”: “File”,
“checksum”: “sha1$bf21a9e8fbc5a3846fb05b4fa0859e0917b2202f”,
“size”: 2,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/crossmapped_pfam_passed.json”
},
“crossres_mappedcath”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/cath_res_crossMapped.csv”,
“basename”: “cath_res_crossMapped.csv”,
“class”: “File”,
“checksum”: “sha1$1e6f28b9b3a46bf26bcc1b5db72b9af30b99bf64”,
“size”: 4209,
“format”: “http://edamontology.org/format_3752”,
“path”: “/data2/hdhondge/CroMaSt/Results2/cath_res_crossMapped.csv”
},
“crossres_mappedpfam”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/pfam_res_crossMapped.csv”,
“basename”: “pfam_res_crossMapped.csv”,
“class”: “File”,
“checksum”: “sha1$e94de2557620c3aca8954ca10613e4832cc31fa8”,
“size”: 5526,
“format”: “http://edamontology.org/format_3752”,
“path”: “/data2/hdhondge/CroMaSt/Results2/pfam_res_crossMapped.csv”
},
“family_ids_x”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/family_ids.json”,
“basename”: “family_ids.json”,
“class”: “File”,
“checksum”: “sha1$3d12faf52957d5247dd74c31d41a96a6fbe1f7f8”,
“size”: 380,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/family_ids.json”
},
“next_parmfile”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/new_param.yml”,
“basename”: “new_param.yml”,
“class”: “File”,
“checksum”: “sha1$77d6f1be66b9250a28b22839437e1f19bc308ead”,
“size”: 2209,
“format”: “EDAM - Bioscientific data analysis ontology - YAML - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/new_param.yml”
},
“pfam_crossmap_cath_avg”: ,
“reslost_cath”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/cath_lost_resmap_domain_StIs.json”,
“basename”: “cath_lost_resmap_domain_StIs.json”,
“class”: “File”,
“checksum”: “sha1$d51cbfa7d4c3dc2549c684225aa38c9591462499”,
“size”: 59,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/cath_lost_resmap_domain_StIs.json”
},
“reslost_pfam”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/pfam_lost_resmap_domain_StIs.json”,
“basename”: “pfam_lost_resmap_domain_StIs.json”,
“class”: “File”,
“checksum”: “sha1$d51cbfa7d4c3dc2549c684225aa38c9591462499”,
“size”: 59,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/pfam_lost_resmap_domain_StIs.json”
},
“resmapped_cath”: null,
“resmapped_pfam”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/pfam_resmapped_domain_StIs.csv”,
“basename”: “pfam_resmapped_domain_StIs.csv”,
“class”: “File”,
“checksum”: “sha1$d681f02920a46b8a822c697688e77f5304f918d0”,
“size”: 5527,
“format”: “http://edamontology.org/format_3752”,
“path”: “/data2/hdhondge/CroMaSt/Results2/pfam_resmapped_domain_StIs.csv”
},
“true_domains”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/true_domains.json”,
“basename”: “true_domains.json”,
“class”: “File”,
“checksum”: “sha1$be55bc64e52d35333280cca4e82f5f9e58262d8f”,
“size”: 149282,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/true_domains.json”
},
“unmap_cath”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/cath_unq_unmapped.jsonx”,
“basename”: “cath_unq_unmapped.jsonx”,
“class”: “File”,
“checksum”: “sha1$c99352b290c7b0b80192d494f88a3b55608d6694”,
“size”: 30,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/cath_unq_unmapped.jsonx”
},
“unmap_cath_failed”: null,
“unmap_cath_passed”: null,
“unmap_pfam”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/pfam_unq_unmapped.jsonx”,
“basename”: “pfam_unq_unmapped.jsonx”,
“class”: “File”,
“checksum”: “sha1$27687398f6c69d082b333f6b57fcd1c11353184e”,
“size”: 1295,
“format”: “EDAM - Bioscientific data analysis ontology - JSON - Classes | NCBO BioPortal”,
“path”: “/data2/hdhondge/CroMaSt/Results2/pfam_unq_unmapped.jsonx”
},
“unmap_pfam_failed”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/pfam_unmapped_failed_structs.csv”,
“basename”: “pfam_unmapped_failed_structs.csv”,
“class”: “File”,
“checksum”: “sha1$af68f8216c7deaf47642eddaf7ad407f09a7d2f8”,
“size”: 139,
“format”: “http://edamontology.org/format_3752”,
“path”: “/data2/hdhondge/CroMaSt/Results2/pfam_unmapped_failed_structs.csv”
},
“unmap_pfam_passed”: {
“location”: “file:///data2/hdhondge/CroMaSt/Results2/pfam_unmapped_passed_structs.csv”,
“basename”: “pfam_unmapped_passed_structs.csv”,
“class”: “File”,
“checksum”: “sha1$87923f1963875f5d228799c7aef3cb00e1d50ad2”,
“size”: 1161,
“format”: “http://edamontology.org/format_3752”,
“path”: “/data2/hdhondge/CroMaSt/Results2/pfam_unmapped_passed_structs.csv”
}
}

The log was quite long so had to divide it into parts.

HrishiDhondge · June 19, 2023, 2:35pm

Update:

I tried --provenance option with a single tool from the same workflow followed by runcrate convert command for generating RO crate and it worked! So might be something fishy with the workflow?

Tool Name: separate_pfam.cwl

Log for Tool

[2023-06-19 16:10:25] INFO /users/hdhondge/miniconda3/envs/CroMaSt/bin/cwltool 3.1.20230601100705
[2023-06-19 16:10:25] INFO [cwltool] /users/hdhondge/miniconda3/envs/CroMaSt/bin/cwltool --timestamps --provenance Run_prov2/ --outdir=/data2/hdhondge/CroMaSt/Results2/ Tools/separate_pfam.cwl yml/CroMaSt_input.yml
[2023-06-19 16:10:25] INFO Resolved 'Tools/separate_pfam.cwl' to 'file:///local/data2/hdhondge/CroMaSt/Tools/separate_pfam.cwl'
[2023-06-19 16:12:27] INFO [job separate_pfam.cwl] /tmp/n3ogdty0$ python3 \
    separate_pfam.py \
    -l \
    31 \
    -d \
    /tmp/n3ogdty0/obsolete_PDB_entry_ids.txt \
    -o \
    obsolete_pfam.txt \
    -p \
    /tmp/n3ogdty0/pdbmap \
    -n \
    Filtered_Pfam.csv \
    -s \
    part.csv \
    -f \
    /tmp/8bcctq_k/stg55b78be9-0ce6-43d6-874c-e910e905b71c/fam_ids.json
/tmp/n3ogdty0/separate_pfam.py:73: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  pfam_df = pfam_df.append({'PDB_id': line[0], 'Chain_id': line[1], \
/tmp/n3ogdty0/separate_pfam.py:73: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  pfam_df = pfam_df.append({'PDB_id': line[0], 'Chain_id': line[1], \
/tmp/n3ogdty0/separate_pfam.py:73: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  pfam_df = pfam_df.append({'PDB_id': line[0], 'Chain_id': line[1], \
/tmp/n3ogdty0/separate_pfam.py:73: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
  pfam_df = pfam_df.append({'PDB_id': line[0], 'Chain_id': line[1], \
[2023-06-19 16:14:13] INFO [job separate_pfam.cwl] Max memory used: 53MiB
[2023-06-19 16:14:13] INFO [job separate_pfam.cwl] completed success
/users/hdhondge/miniconda3/envs/CroMaSt/lib/python3.10/site-packages/rdflib/plugins/serializers/nt.py:40: UserWarning: NTSerializer always uses UTF-8 encoding. Given encoding was: None
  warnings.warn(
{
    "pfam_obs": {
        "location": "file:///data2/hdhondge/CroMaSt/Results2/obsolete_pfam.txt",
        "basename": "obsolete_pfam.txt",
        "class": "File",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "size": 0,
        "format": "http://edamontology.org/format_2330",
        "path": "/data2/hdhondge/CroMaSt/Results2/obsolete_pfam.txt"
    },
    "pfam_structs": {
        "location": "file:///data2/hdhondge/CroMaSt/Results2/Filtered_Pfam.csv",
        "basename": "Filtered_Pfam.csv",
        "class": "File",
        "checksum": "sha1$8fe3f0b3c50a03ee572f1da19afca2e809a99f69",
        "size": 194,
        "format": "http://edamontology.org/format_3752",
        "path": "/data2/hdhondge/CroMaSt/Results2/Filtered_Pfam.csv"
    },
    "splitted_pfam_sep": [
        {
            "location": "file:///data2/hdhondge/CroMaSt/Results2/0_part.csv",
            "basename": "0_part.csv",
            "class": "File",
            "checksum": "sha1$8fe3f0b3c50a03ee572f1da19afca2e809a99f69",
            "size": 194,
            "format": "http://edamontology.org/format_3752",
            "path": "/data2/hdhondge/CroMaSt/Results2/0_part.csv"
        }
    ]
}[2023-06-19 16:14:36] INFO Final process status is success
[2023-06-19 16:14:36] INFO [provenance] Finalizing Research Object
[2023-06-19 16:14:37] INFO [provenance] Deleting existing /local/data2/hdhondge/CroMaSt/Run_prov2
[2023-06-19 16:16:25] INFO [provenance] Research Object saved to /local/data2/hdhondge/CroMaSt/Run_prov2

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Generation of RO create failed

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