Functional annotation of protein sequences - Workflow

[rlibouba]

Hello, I'd like to suggest this new protein sequence annotation workflow, using eggNOG Mapper and Interproscan.

At the same time, I'd like to tell you about a problem I'm having with interproscan testing. I get this error
Failed to find output [interproscan xml] in invocation outputs [{'eggNOG Mapper annotations': {'src': 'hda', 'id': '4bafbd75dc760dfd', 'workflow_step_id': '6a2bc09b040f62c5'}, 'eggNOG Mapper seed_orthologs': {'src': 'hda', 'id': '2e6846bf7c441bd6', 'workflow_step_id': '6a2bc09b040f62c5'}}]

Have a nice day!

[bgruening]

@rlibouba we need a .dockstore.yml file here.

[bgruening]

Ok, now the CI is properly running :)

[mvdbeek]

Hey @rlibouba, this is the error message:

The reference data is coming from cvmfs, do you know where we can get 5.59-91.0 from ?

[rlibouba]

Hi @mvdbeek, thanks for your feedback. Sorry for my late reply.

Checking with @abretaud , it should be linked to the data manager. Do you think we should use idc (https://github.com/galaxyproject/idc) to manage the problem?

[abretaud]

Yep, it uses this DM: https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_interproscan
It's a few tens of Gb IIRC, if it could be managed by IDC it would great, but not sure if it's ready to handle non-genome data

[mvdbeek]

I think the problem was that we don't have a great way to publish large datasets, but we can always rsync this onto cvmfs from a site that has the data available

[abretaud]

Ok, the DM mostly downloads a big archive but also makes a few file indexing and .properties file writing

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Functional_annotation_of_protein_sequences.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input:

      • step_state: scheduled

    • Step 2: InterProScan:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7f541560911b11efa0bb6fbe6244f820"
            applications	["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"]
            chromInfo	"/tmp/tmpglv3_kjp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"5.59-91.0"
            dbkey	"?"
            goterms	true
            iprlookup	false
            licensed	{"__current_case__": 1, "applications_licensed": ["Phobius", "SignalP_EUK", "TMHMM"], "use": "true"}
            oformat	["TSV", "XML"]
            pathways	true
            seqtype	"p"

    • Step 3: eggNOG Mapper:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"7f541560911b11efa0bb6fbe6244f820"
            annotation_options	{"__current_case__": 0, "go_evidence": "non-electronic", "no_annot": "", "seed_ortholog_evalue": "0.001", "seed_ortholog_score": null, "target_orthologs": "all", "tax_scope": null}
            chromInfo	"/tmp/tmpglv3_kjp/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            eggnog_data	"5.0.2"
            ortho_method	{"__current_case__": 0, "dmnd_ignore_warnings": false, "dmnd_iterate": false, "evalue": null, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_trans": {"__current_case__": 0, "itype": "proteins"}, "m": "diamond", "matrix_gapcosts": {"__current_case__": 2, "gap_costs": "--gapopen 11 --gapextend 1", "matrix": "BLOSUM62"}, "pident": null, "query_cover": null, "score": "0.001", "sensmode": "sensitive", "subject_cover": null}
            output_options	{"md5": false, "no_file_comments": false, "report_orthologs": false}

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • a75ad98d0072565b

    • history_state

      • error

    • invocation_id

      • a75ad98d0072565b

    • invocation_state

      • scheduled

    • workflow_id

      • a75ad98d0072565b

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Functional_annotation_of_protein_sequences.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input:

      • step_state: scheduled

    • Step 2: InterProScan:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"981cf6669d1411efb86a952a98c6485c"
            applications	["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"]
            chromInfo	"/tmp/tmpv6ekc37k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"5.59-91.0"
            dbkey	"?"
            goterms	true
            iprlookup	false
            licensed	{"__current_case__": 1, "applications_licensed": ["Phobius", "SignalP_EUK", "TMHMM"], "use": "true"}
            oformat	["TSV", "XML"]
            pathways	true
            seqtype	"p"

    • Step 3: eggNOG Mapper:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"981cf6669d1411efb86a952a98c6485c"
            annotation_options	{"__current_case__": 0, "go_evidence": "non-electronic", "no_annot": "", "seed_ortholog_evalue": "0.001", "seed_ortholog_score": null, "target_orthologs": "all", "tax_scope": null}
            chromInfo	"/tmp/tmpv6ekc37k/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            eggnog_data	"5.0.2"
            ortho_method	{"__current_case__": 0, "dmnd_ignore_warnings": false, "dmnd_iterate": false, "evalue": null, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_trans": {"__current_case__": 0, "itype": "proteins"}, "m": "diamond", "matrix_gapcosts": {"__current_case__": 2, "gap_costs": "--gapopen 11 --gapextend 1", "matrix": "BLOSUM62"}, "pident": null, "query_cover": null, "score": "0.001", "sensmode": "sensitive", "subject_cover": null}
            output_options	{"md5": false, "no_file_comments": false, "report_orthologs": false}

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 32d241b6562b0252

    • history_state

      • error

    • invocation_id

      • 32d241b6562b0252

    • invocation_state

      • scheduled

    • workflow_id

      • 32d241b6562b0252

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Functional_annotation_of_protein_sequences.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input:

      • step_state: scheduled

    • Step 2: InterProScan:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"f260d004a73f11ef98d565f464fb6b9d"
            applications	["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"]
            chromInfo	"/tmp/tmpgu23bwdj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"5.59-91.0"
            dbkey	"?"
            goterms	true
            iprlookup	false
            licensed	{"__current_case__": 1, "applications_licensed": ["Phobius", "SignalP_EUK", "TMHMM"], "use": "true"}
            oformat	["TSV", "XML"]
            pathways	true
            seqtype	"p"

    • Step 3: eggNOG Mapper:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • emapper.py  --data_dir '/data/db/data_managers/eggnog_data/5.0.2'   -m 'diamond' -i '/tmp/tmpgu23bwdj/files/7/8/f/dataset_78f87717-518c-4697-8e2f-d43cf6764bf1.dat' --itype 'proteins'   --matrix 'BLOSUM62' --gapopen 11 --gapextend 1 --sensmode sensitive --dmnd_iterate no   --score 0.001   --seed_ortholog_evalue 0.001 --target_orthologs=all --go_evidence=non-electronic $EGGNOG_DBMEM     --output='results' --cpu "${GALAXY_SLOTS:-4}" --scratch_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --temp_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR}

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"f260d004a73f11ef98d565f464fb6b9d"
            annotation_options	{"__current_case__": 0, "go_evidence": "non-electronic", "no_annot": "", "seed_ortholog_evalue": "0.001", "seed_ortholog_score": null, "target_orthologs": "all", "tax_scope": null}
            chromInfo	"/tmp/tmpgu23bwdj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            eggnog_data	"5.0.2"
            ortho_method	{"__current_case__": 0, "dmnd_ignore_warnings": false, "dmnd_iterate": false, "evalue": null, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_trans": {"__current_case__": 0, "itype": "proteins"}, "m": "diamond", "matrix_gapcosts": {"__current_case__": 2, "gap_costs": "--gapopen 11 --gapextend 1", "matrix": "BLOSUM62"}, "pident": null, "query_cover": null, "score": "0.001", "sensmode": "sensitive", "subject_cover": null}
            output_options	{"md5": false, "no_file_comments": false, "report_orthologs": false}

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 84a218bda92fbd60

    • history_state

      • error

    • invocation_id

      • 84a218bda92fbd60

    • invocation_state

      • scheduled

    • workflow_id

      • 84a218bda92fbd60

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Functional_annotation_of_protein_sequences.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input:

      • step_state: scheduled

    • Step 2: InterProScan:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"f260d004a73f11ef98d565f464fb6b9d"
            applications	["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"]
            chromInfo	"/tmp/tmpgu23bwdj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"5.59-91.0"
            dbkey	"?"
            goterms	true
            iprlookup	false
            licensed	{"__current_case__": 1, "applications_licensed": ["Phobius", "SignalP_EUK", "TMHMM"], "use": "true"}
            oformat	["TSV", "XML"]
            pathways	true
            seqtype	"p"

    • Step 3: eggNOG Mapper:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • emapper.py  --data_dir '/data/db/data_managers/eggnog_data/5.0.2'   -m 'diamond' -i '/tmp/tmpgu23bwdj/files/7/8/f/dataset_78f87717-518c-4697-8e2f-d43cf6764bf1.dat' --itype 'proteins'   --matrix 'BLOSUM62' --gapopen 11 --gapextend 1 --sensmode sensitive --dmnd_iterate no   --score 0.001   --seed_ortholog_evalue 0.001 --target_orthologs=all --go_evidence=non-electronic $EGGNOG_DBMEM     --output='results' --cpu "${GALAXY_SLOTS:-4}" --scratch_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --temp_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR}

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"f260d004a73f11ef98d565f464fb6b9d"
            annotation_options	{"__current_case__": 0, "go_evidence": "non-electronic", "no_annot": "", "seed_ortholog_evalue": "0.001", "seed_ortholog_score": null, "target_orthologs": "all", "tax_scope": null}
            chromInfo	"/tmp/tmpgu23bwdj/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            eggnog_data	"5.0.2"
            ortho_method	{"__current_case__": 0, "dmnd_ignore_warnings": false, "dmnd_iterate": false, "evalue": null, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_trans": {"__current_case__": 0, "itype": "proteins"}, "m": "diamond", "matrix_gapcosts": {"__current_case__": 2, "gap_costs": "--gapopen 11 --gapextend 1", "matrix": "BLOSUM62"}, "pident": null, "query_cover": null, "score": "0.001", "sensmode": "sensitive", "subject_cover": null}
            output_options	{"md5": false, "no_file_comments": false, "report_orthologs": false}

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 84a218bda92fbd60

    • history_state

      • error

    • invocation_id

      • 84a218bda92fbd60

    • invocation_state

      • scheduled

    • workflow_id

      • 84a218bda92fbd60

[mvdbeek]

We'll also need the interproscan database. I did see this in the tool:

I guess we at least need to make that a workflow parameter, and then also mention how that license can be gotten ?

Is there an alternative we could use with a more open license ?

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Functional_annotation_of_protein_sequences.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input:

      • step_state: scheduled

    • Step 2: InterProScan:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8c22039ea8c011ef829f6108412c6c96"
            applications	["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"]
            chromInfo	"/tmp/tmp59gsvdmb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"5.59-91.0"
            dbkey	"?"
            goterms	true
            iprlookup	false
            licensed	{"__current_case__": 1, "applications_licensed": ["Phobius", "SignalP_EUK", "TMHMM"], "use": "true"}
            oformat	["TSV", "XML"]
            pathways	true
            seqtype	"p"

    • Step 3: eggNOG Mapper:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • emapper.py  --data_dir '/data/db/data_managers/eggnog_data/5.0.2'   -m 'diamond' -i '/tmp/tmp59gsvdmb/files/7/a/e/dataset_7ae45ad2-dd48-42a0-934f-8233a1df599b.dat' --itype 'proteins'   --matrix 'BLOSUM62' --gapopen 11 --gapextend 1 --sensmode sensitive --dmnd_iterate no   --score 0.001   --seed_ortholog_evalue 0.001 --target_orthologs=all --go_evidence=non-electronic $EGGNOG_DBMEM     --output='results' --cpu "${GALAXY_SLOTS:-4}" --scratch_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --temp_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR}

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8c22039ea8c011ef829f6108412c6c96"
            annotation_options	{"__current_case__": 0, "go_evidence": "non-electronic", "no_annot": "", "seed_ortholog_evalue": "0.001", "seed_ortholog_score": null, "target_orthologs": "all", "tax_scope": null}
            chromInfo	"/tmp/tmp59gsvdmb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            eggnog_data	"5.0.2"
            ortho_method	{"__current_case__": 0, "dmnd_ignore_warnings": false, "dmnd_iterate": false, "evalue": null, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_trans": {"__current_case__": 0, "itype": "proteins"}, "m": "diamond", "matrix_gapcosts": {"__current_case__": 2, "gap_costs": "--gapopen 11 --gapextend 1", "matrix": "BLOSUM62"}, "pident": null, "query_cover": null, "score": "0.001", "sensmode": "sensitive", "subject_cover": null}
            output_options	{"md5": false, "no_file_comments": false, "report_orthologs": false}

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 843f5186ea97db5f

    • history_state

      • error

    • invocation_id

      • 843f5186ea97db5f

    • invocation_state

      • scheduled

    • workflow_id

      • 843f5186ea97db5f

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Functional_annotation_of_protein_sequences.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input:

      • step_state: scheduled

    • Step 2: InterProScan:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8c22039ea8c011ef829f6108412c6c96"
            applications	["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"]
            chromInfo	"/tmp/tmp59gsvdmb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"5.59-91.0"
            dbkey	"?"
            goterms	true
            iprlookup	false
            licensed	{"__current_case__": 1, "applications_licensed": ["Phobius", "SignalP_EUK", "TMHMM"], "use": "true"}
            oformat	["TSV", "XML"]
            pathways	true
            seqtype	"p"

    • Step 3: eggNOG Mapper:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is queued

          Command Line:

          • emapper.py  --data_dir '/data/db/data_managers/eggnog_data/5.0.2'   -m 'diamond' -i '/tmp/tmp59gsvdmb/files/7/a/e/dataset_7ae45ad2-dd48-42a0-934f-8233a1df599b.dat' --itype 'proteins'   --matrix 'BLOSUM62' --gapopen 11 --gapextend 1 --sensmode sensitive --dmnd_iterate no   --score 0.001   --seed_ortholog_evalue 0.001 --target_orthologs=all --go_evidence=non-electronic $EGGNOG_DBMEM     --output='results' --cpu "${GALAXY_SLOTS:-4}" --scratch_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --temp_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR}

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"8c22039ea8c011ef829f6108412c6c96"
            annotation_options	{"__current_case__": 0, "go_evidence": "non-electronic", "no_annot": "", "seed_ortholog_evalue": "0.001", "seed_ortholog_score": null, "target_orthologs": "all", "tax_scope": null}
            chromInfo	"/tmp/tmp59gsvdmb/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            eggnog_data	"5.0.2"
            ortho_method	{"__current_case__": 0, "dmnd_ignore_warnings": false, "dmnd_iterate": false, "evalue": null, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_trans": {"__current_case__": 0, "itype": "proteins"}, "m": "diamond", "matrix_gapcosts": {"__current_case__": 2, "gap_costs": "--gapopen 11 --gapextend 1", "matrix": "BLOSUM62"}, "pident": null, "query_cover": null, "score": "0.001", "sensmode": "sensitive", "subject_cover": null}
            output_options	{"md5": false, "no_file_comments": false, "report_orthologs": false}

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 843f5186ea97db5f

    • history_state

      • error

    • invocation_id

      • 843f5186ea97db5f

    • invocation_state

      • scheduled

    • workflow_id

      • 843f5186ea97db5f

[mvdbeek]

Oops, failed to change the actual data location in the eggnog data table, doing that now.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	1
Failure	0
Skipped	0

Errored Tests

• ❌ Functional_annotation_of_protein_sequences.ga_0

  Execution Problem:

  • Failed to run workflow, at least one job is in [error] state.
    

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input:

      • step_state: scheduled

    • Step 2: InterProScan:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is error

          Command Line:

          • mkdir -p $HOME/.interproscan-5 && sed 's|^\(data.directory=\).*$|\1/cvmfs/data.galaxyproject.org/byhand/interproscan/5.59-91.0/data|' $(dirname $(readlink -f $(command -v interproscan.sh)))/interproscan.properties > $HOME/.interproscan-5/interproscan.properties && export _JAVA_OPTIONS=-Duser.home=$HOME &&  interproscan.sh  -dp --input '/tmp/tmp2k6jlp1y/files/d/2/7/dataset_d27e9c6c-f288-4a6a-9b62-ff0a449757c8.dat' --seqtype p -f TSV,XML  --applications TIGRFAM,FunFam,SFLD,SUPERFAMILY,PANTHER,Gene3D,Hamap,PrositeProfiles,Coils,SMART,CDD,PRINTS,PIRSR,PrositePatterns,AntiFam,Pfam,MobiDBLite,PIRSF,Phobius,SignalP_EUK,TMHMM --tempdir ${TEMP:-$_GALAXY_JOB_TMP_DIR}  --pathways --goterms   --cpu ${GALAXY_SLOTS:-4}  --output-file-base 'output'

          Exit Code:

          • 1

          Standard Error:

          • Picked up _JAVA_OPTIONS: -Duser.home=/tmp/tmp2k6jlp1y/job_working_directory/000/2/home
            

          Standard Output:

          • 25/11/2024 11:35:51:740 Welcome to InterProScan-5.59-91.0
            25/11/2024 11:35:51:741 Running InterProScan v5 in STANDALONE mode... on Linux
            Invalid input specified for -appl/--applications parameter:
            Analysis Phobius does not exist or is deactivated.
            Analysis TMHMM does not exist or is deactivated.
            Analysis SignalP_EUK does not exist or is deactivated.
            
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"4a6d9e1eab2111efa444510c20e813f0"
            applications	["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"]
            chromInfo	"/tmp/tmp2k6jlp1y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"5.59-91.0"
            dbkey	"?"
            goterms	true
            iprlookup	false
            licensed	{"__current_case__": 1, "applications_licensed": ["Phobius", "SignalP_EUK", "TMHMM"], "use": "true"}
            oformat	["TSV", "XML"]
            pathways	true
            seqtype	"p"

    • Step 3: eggNOG Mapper:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is running

          Command Line:

          • emapper.py  --data_dir '/cvmfs/data.galaxyproject.org/byhand/eggnog_data/5.0.2'   -m 'diamond' -i '/tmp/tmp2k6jlp1y/files/d/2/7/dataset_d27e9c6c-f288-4a6a-9b62-ff0a449757c8.dat' --itype 'proteins'   --matrix 'BLOSUM62' --gapopen 11 --gapextend 1 --sensmode sensitive --dmnd_iterate no   --score 0.001   --seed_ortholog_evalue 0.001 --target_orthologs=all --go_evidence=non-electronic $EGGNOG_DBMEM     --output='results' --cpu "${GALAXY_SLOTS:-4}" --scratch_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --temp_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR}

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"4a6d9e1eab2111efa444510c20e813f0"
            annotation_options	{"__current_case__": 0, "go_evidence": "non-electronic", "no_annot": "", "seed_ortholog_evalue": "0.001", "seed_ortholog_score": null, "target_orthologs": "all", "tax_scope": null}
            chromInfo	"/tmp/tmp2k6jlp1y/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            eggnog_data	"5.0.2"
            ortho_method	{"__current_case__": 0, "dmnd_ignore_warnings": false, "dmnd_iterate": false, "evalue": null, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_trans": {"__current_case__": 0, "itype": "proteins"}, "m": "diamond", "matrix_gapcosts": {"__current_case__": 2, "gap_costs": "--gapopen 11 --gapextend 1", "matrix": "BLOSUM62"}, "pident": null, "query_cover": null, "score": "0.001", "sensmode": "sensitive", "subject_cover": null}
            output_options	{"md5": false, "no_file_comments": false, "report_orthologs": false}

  • Other invocation details

    • error_message

      • Failed to run workflow, at least one job is in [error] state.

    • history_id

      • 583fc7a87169bf5a

    • history_state

      • error

    • invocation_id

      • 583fc7a87169bf5a

    • invocation_state

      • scheduled

    • workflow_id

      • 583fc7a87169bf5a

[mvdbeek]

I think we've got everything on cvmfs now and the interproscan run fails with

25/11/2024 11:35:51:740 Welcome to InterProScan-5.59-91.0
25/11/2024 11:35:51:741 Running InterProScan v5 in STANDALONE mode... on Linux
Invalid input specified for -appl/--applications parameter:
Analysis Phobius does not exist or is deactivated.
Analysis TMHMM does not exist or is deactivated.
Analysis SignalP_EUK does not exist or is deactivated.

I assume these are the modules that require manual installation and a license change ?
Is there any use in setting applications_licensed to a free subset ?

[rlibouba]

Thanks for your feedback @mvdbeek
It might be interesting to update interproscan and fix the licensing issue. What do you think?
(ping @abretaud)

[mvdbeek]

Very cool and timely, thanks @rlibouba and @abretaud! I've just edited some minor things in the last commit, if it still looks good I'm happy to merge this.

[github-actions]

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	1
Error	0
Failure	0
Skipped	0

Passed Tests

• ✅ Functional_annotation_of_protein_sequences.ga_0

  Workflow invocation details

  • Invocation Messages

  • Steps

    • Step 1: input:

      • step_state: scheduled

    • Step 2: InterProScan:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • mkdir -p $HOME/.interproscan-5 && sed 's|^\(data.directory=\).*$|\1/cvmfs/data.galaxyproject.org/byhand/interproscan/5.59-91.0/data|' $(dirname $(readlink -f $(command -v interproscan.sh)))/interproscan.properties > $HOME/.interproscan-5/interproscan.properties && export _JAVA_OPTIONS=-Duser.home=$HOME &&  interproscan.sh  -dp --input '/tmp/tmpu3yxq8a1/files/0/c/8/dataset_0c8bdf11-2196-45c8-8874-9e8ab5d47aed.dat' --seqtype p -f TSV,XML  --applications TIGRFAM,FunFam,SFLD,SUPERFAMILY,PANTHER,Gene3D,Hamap,PrositeProfiles,Coils,SMART,CDD,PRINTS,PIRSR,PrositePatterns,AntiFam,Pfam,MobiDBLite,PIRSF --tempdir ${TEMP:-$_GALAXY_JOB_TMP_DIR}  --pathways --goterms   --cpu ${GALAXY_SLOTS:-4}  --output-file-base 'output'

          Exit Code:

          • 0

          Standard Error:

          • Picked up _JAVA_OPTIONS: -Duser.home=/tmp/tmpu3yxq8a1/job_working_directory/000/2/home
            

          Standard Output:

          • 03/12/2024 17:42:01:064 Welcome to InterProScan-5.59-91.0
            03/12/2024 17:42:01:066 Running InterProScan v5 in STANDALONE mode... on Linux
            03/12/2024 17:42:16:978 RunID: 2f40f6204fc9_20241203_174216689_a8sj
            03/12/2024 17:42:36:848 Loading file /tmp/tmpu3yxq8a1/files/0/c/8/dataset_0c8bdf11-2196-45c8-8874-9e8ab5d47aed.dat
            03/12/2024 17:42:36:849 Running the following analyses:
            [AntiFam-7.0,CDD-3.18,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2021_04,MobiDBLite-2.0,PANTHER-17.0,Pfam-35.0,PIRSF-3.10,PIRSR-2021_05,PRINTS-42.0,ProSitePatterns-2022_01,ProSiteProfiles-2022_01,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0]
            Pre-calculated match lookup service DISABLED.  Please wait for match calculations to complete...
            03/12/2024 17:47:49:552 25% completed
            03/12/2024 18:03:37:483 50% completed
            03/12/2024 18:05:39:094 75% completed
            03/12/2024 18:08:09:329 91% completed
            03/12/2024 18:08:26:165 100% done:  InterProScan analyses completed 
            
            2024-12-03 18:08:26,681 [main] [uk.ac.ebi.interpro.scan.jms.main.Run:1801] WARN - deleteWorkingDirectoryOnCompletion : false
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c1fb8b44b19d11ef8cd15f2b55b1640d"
            applications	["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"]
            chromInfo	"/tmp/tmpu3yxq8a1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            database	"5.59-91.0"
            dbkey	"?"
            goterms	true
            iprlookup	false
            licensed	{"__current_case__": 0, "use": "false"}
            oformat	["TSV", "XML"]
            pathways	true
            seqtype	"p"

    • Step 3: eggNOG Mapper:

      • step_state: scheduled

      • Jobs

        • Job 1:

          • Job state is ok

          Command Line:

          • emapper.py  --data_dir '/cvmfs/data.galaxyproject.org/byhand/eggnog_data/5.0.2'   -m 'diamond' -i '/tmp/tmpu3yxq8a1/files/0/c/8/dataset_0c8bdf11-2196-45c8-8874-9e8ab5d47aed.dat' --itype 'proteins'   --matrix 'BLOSUM62' --gapopen 11 --gapextend 1 --sensmode sensitive --dmnd_iterate no   --score 0.001   --seed_ortholog_evalue 0.001 --target_orthologs=all --go_evidence=non-electronic $EGGNOG_DBMEM     --output='results' --cpu "${GALAXY_SLOTS:-4}" --scratch_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --temp_dir ${TEMP:-$_GALAXY_JOB_TMP_DIR}

          Exit Code:

          • 0

          Standard Error:

          • �[1;32mFunctional annotation of hits...�[0m
            0 0.0003800392150878906 0.00 q/s (% mem usage: 8.00, % mem avail: 91.99)
            24 178.59459018707275 0.13 q/s (% mem usage: 8.20, % mem avail: 91.81)
            

          Standard Output:

          • #  emapper-2.1.8
            # emapper.py  --data_dir /cvmfs/data.galaxyproject.org/byhand/eggnog_data/5.0.2 -m diamond -i /tmp/tmpu3yxq8a1/files/0/c/8/dataset_0c8bdf11-2196-45c8-8874-9e8ab5d47aed.dat --itype proteins --matrix BLOSUM62 --gapopen 11 --gapextend 1 --sensmode sensitive --dmnd_iterate no --score 0.001 --seed_ortholog_evalue 0.001 --target_orthologs=all --go_evidence=non-electronic --output=results --cpu 1 --scratch_dir /tmp/tmpu3yxq8a1/tmp --temp_dir /tmp/tmpu3yxq8a1/tmp
            �[1;33m  /usr/local/bin/diamond blastp -d /cvmfs/data.galaxyproject.org/byhand/eggnog_data/5.0.2/eggnog_proteins.dmnd -q /tmp/tmpu3yxq8a1/files/0/c/8/dataset_0c8bdf11-2196-45c8-8874-9e8ab5d47aed.dat --threads 1 -o /tmp/tmpu3yxq8a1/tmp/results.emapper.hits --tmpdir /tmp/tmpu3yxq8a1/tmp/emappertmp_dmdn_qygb_zoj --sensitive -e 0.001 --min-score 0.001 --matrix BLOSUM62 --gapopen 11 --gapextend 1 --top 3  --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp�[0m
             Copying result file /tmp/tmpu3yxq8a1/tmp/results.emapper.hits from scratch to /tmp/tmpu3yxq8a1/job_working_directory/000/3/working
             Copying result file /tmp/tmpu3yxq8a1/tmp/results.emapper.seed_orthologs from scratch to /tmp/tmpu3yxq8a1/job_working_directory/000/3/working
             Copying result file /tmp/tmpu3yxq8a1/tmp/results.emapper.annotations from scratch to /tmp/tmpu3yxq8a1/job_working_directory/000/3/working
            �[31mData in /tmp/tmpu3yxq8a1/tmp will be not removed. Please, clear it manually.�[0m
            �[32mDone�[0m
            �[1;33mResult files:�[0m
               /tmp/tmpu3yxq8a1/job_working_directory/000/3/working/results.emapper.hits
               /tmp/tmpu3yxq8a1/job_working_directory/000/3/working/results.emapper.seed_orthologs
               /tmp/tmpu3yxq8a1/job_working_directory/000/3/working/results.emapper.annotations
            
            ================================================================================
            CITATION:
            If you use this software, please cite:
            
            [1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain 
                  prediction at the metagenomic scale. Carlos P. Cantalapiedra, 
                  Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
                  Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293
            
            [2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
                  orthology resource based on 5090 organisms and 2502 viruses. Jaime
                  Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernandez-Plaza,
                  Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas
                  Rattei, Lars J Jensen, Christian von Mering and Peer Bork. Nucleic Acids
                  Research, Volume 47, Issue D1, 8 January 2019, Pages D309-D314,
                  https://doi.org/10.1093/nar/gky1085 
            
            [3] Sensitive protein alignments at tree-of-life scale using DIAMOND.
                   Buchfink B, Reuter K, Drost HG. 2021.
                   Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x
            
            e.g. Functional annotation was performed using emapper-2.1.8 [1]
             based on eggNOG orthology data [2]. Sequence searches were performed using [3].
            
            
            ================================================================================
            
            Total hits processed: 24
            Total time: 2301 secs
            FINISHED
            

          Traceback:

          Job Parameters:

          • Job parameter	Parameter value
            __input_ext	"input"
            __workflow_invocation_uuid__	"c1fb8b44b19d11ef8cd15f2b55b1640d"
            annotation_options	{"__current_case__": 0, "go_evidence": "non-electronic", "no_annot": "", "seed_ortholog_evalue": "0.001", "seed_ortholog_score": null, "target_orthologs": "all", "tax_scope": null}
            chromInfo	"/tmp/tmpu3yxq8a1/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"
            dbkey	"?"
            eggnog_data	"5.0.2"
            ortho_method	{"__current_case__": 0, "dmnd_ignore_warnings": false, "dmnd_iterate": false, "evalue": null, "input": {"values": [{"id": 1, "src": "hda"}]}, "input_trans": {"__current_case__": 0, "itype": "proteins"}, "m": "diamond", "matrix_gapcosts": {"__current_case__": 2, "gap_costs": "--gapopen 11 --gapextend 1", "matrix": "BLOSUM62"}, "pident": null, "query_cover": null, "score": "0.001", "sensmode": "sensitive", "subject_cover": null}
            output_options	{"md5": false, "no_file_comments": false, "report_orthologs": false}

  • Other invocation details

    • history_id

      • bb0c4fc373c5ac99

    • history_state

      • ok

    • invocation_id

      • bb0c4fc373c5ac99

    • invocation_state

      • scheduled

    • workflow_id

      • bb0c4fc373c5ac99

[abretaud]

Ah cool to see this being ready :) Just 2 typos on my email address
For licensing: yep the warnings are coming from these manual-only components, so that's the best we can do I think.
And yep, we should update interproscan soon, but it's always been tricky :D We ca merge this version for now

[rlibouba]

Hi @mvdbeek ! Do you think everything is good and can be merged?