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NCBI Prokaryotic Genome Annotation Pipeline
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[BUG] <PGAP failed with lengthy output> #176

Closed brittonstrickland closed 2 years ago

brittonstrickland commented 3 years ago

Running PGAP on a SPADES-assembled bacterial genome using my HPC (local option is an M1 MacBook, but it seems to not be supported). I ran the MG37 test successfully with no warnings or errors.

To ensure this isn't an issue with my YAML files, I copied them directly from the MG37 test file and filled them in with my data. My OS also runs Singularity, so I'm not sure if that is an issue since it's trying to run docker (I can't figure out how to flag it to run singularity instead, if that is the issue). It runs with no issue for a few minutes and returns a lengthy report:

Log files attached

tmp-outdir.zip

$PGAP/pgap.py -D singularity -n --debug -o lactoreuteri_out 

/data/das_lab/Data_analysis/LactoGenomes/PGAP/lacto.reuteri/input.yaml
PGAP version 2021-07-01.build5508 is up to date.
Output will be placed in: /gpfs52/data/das_lab/Data_analysis/LactoGenomes/PGAP/lacto.reuteri/lactoreuteri_out.2
INFO:    Using cached SIF image
WARNING: open files is less than the recommended value of 8000
PGAP failed, docker exited with rc = 1
Printing log starting from failed job:

[2021-11-24 13:57:56] DEBUG [step fastaval] job input {
    "file:///pgap/pgap/pgap.cwl#fastaval/check_internal_ns": true,
    "file:///pgap/pgap/pgap.cwl#fastaval/check_min_seqlen": 200,
    "file:///pgap/pgap/pgap.cwl#fastaval/ignore_all_errors": null,
    "file:///pgap/pgap/pgap.cwl#fastaval/in": {
        "class": "File",
        "location": "file:///pgap/user_input/2817_AM_25_scaffolds.fasta",
        "size": 4239707,
        "basename": "2817_AM_25_scaffolds.fasta",
        "nameroot": "2817_AM_25_scaffolds",
        "nameext": ".fasta"
    }
}
[2021-11-24 13:57:56] DEBUG [step fastaval] evaluated job input to {
    "file:///pgap/pgap/pgap.cwl#fastaval/check_internal_ns": true,
    "file:///pgap/pgap/pgap.cwl#fastaval/check_min_seqlen": 200,
    "file:///pgap/pgap/pgap.cwl#fastaval/ignore_all_errors": null,
    "file:///pgap/pgap/pgap.cwl#fastaval/in": {
        "class": "File",
        "location": "file:///pgap/user_input/2817_AM_25_scaffolds.fasta",
        "size": 4239707,
        "basename": "2817_AM_25_scaffolds.fasta",
        "nameroot": "2817_AM_25_scaffolds",
        "nameext": ".fasta"
    }
}
[2021-11-24 13:57:56] INFO [step fastaval] start
[2021-11-24 13:57:56] DEBUG [job fastaval] initializing from file:///pgap/pgap/progs/fastaval.cwl as part of step fastaval
[2021-11-24 13:57:56] DEBUG [job fastaval] {
    "check_internal_ns": true,
    "check_min_seqlen": 200,
    "ignore_all_errors": null,
    "in": {
        "class": "File",
        "location": "file:///pgap/user_input/2817_AM_25_scaffolds.fasta",
        "size": 4239707,
        "basename": "2817_AM_25_scaffolds.fasta",
        "nameroot": "2817_AM_25_scaffolds",
        "nameext": ".fasta"
    },
    "allow_implicit_gnl": null,
    "disallow_seqid_type": null,
    "input": null,
    "max_seqid_count": null,
    "outname": "fastaval.xml"
}
[2021-11-24 13:57:56] DEBUG [job fastaval] path mappings is {
    "file:///pgap/user_input/2817_AM_25_scaffolds.fasta": [
        "/pgap/user_input/2817_AM_25_scaffolds.fasta",
        "/pgap/output/debug/tmpdir/wtbxs203/stgec7604a2-95db-49e3-8885-b35e52648dab/2817_AM_25_scaffolds.fasta",
        "File",
        true
    ]
}
[2021-11-24 13:57:56] DEBUG [job fastaval] command line bindings is [
    {
        "position": [
            -1000000,
            0
        ],
        "datum": "fastaval.sh"
    },
    {
        "prefix": "-check_internal_ns",
        "position": [
            0,
            "check_internal_ns"
        ],
        "datum": true
    },
    {
        "prefix": "-check_min_seqlen",
        "position": [
            0,
            "check_min_seqlen"
        ],
        "datum": 200
    },
    {
        "prefix": "-in",
        "position": [
            0,
            "in"
        ],
        "datum": {
            "class": "File",
            "location": "file:///pgap/user_input/2817_AM_25_scaffolds.fasta",
            "size": 4239707,
            "basename": "2817_AM_25_scaffolds.fasta",
            "nameroot": "2817_AM_25_scaffolds",
            "nameext": ".fasta",
            "path": "/pgap/output/debug/tmpdir/wtbxs203/stgec7604a2-95db-49e3-8885-b35e52648dab/2817_AM_25_scaffolds.fasta",
            "dirname": "/pgap/output/debug/tmpdir/wtbxs203/stgec7604a2-95db-49e3-8885-b35e52648dab"
        }
    },
    {
        "prefix": "-out",
        "position": [
            0,
            "outname"
        ],
        "datum": "fastaval.xml"
    }
]
[2021-11-24 13:57:56] DEBUG [job fastaval] initial work dir {}
[2021-11-24 13:57:56] INFO [job fastaval] /pgap/output/debug/tmp-outdir/2oeym91p$ fastaval.sh \
    -check_internal_ns \
    -check_min_seqlen \
    200 \
    -in \
    /pgap/output/debug/tmpdir/wtbxs203/stgec7604a2-95db-49e3-8885-b35e52648dab/2817_AM_25_scaffolds.fasta \
    -out \
    fastaval.xml
+ POSITIONAL=()
+ ignore_all_errors=false
+ [[ 7 -gt 0 ]]
+ key=-check_internal_ns
+ case "$key" in
+ POSITIONAL+=("$key")
+ shift
+ [[ 6 -gt 0 ]]
+ key=-check_min_seqlen
+ case "$key" in
+ POSITIONAL+=("$key")
+ shift
+ [[ 5 -gt 0 ]]
+ key=200
+ case "$key" in
+ POSITIONAL+=("$key")
+ shift
+ [[ 4 -gt 0 ]]
+ key=-in
+ case "$key" in
+ POSITIONAL+=("$key")
+ shift
+ [[ 3 -gt 0 ]]
+ key=/pgap/output/debug/tmpdir/wtbxs203/stgec7604a2-95db-49e3-8885-b35e52648dab/2817_AM_25_scaffolds.fasta
+ case "$key" in
+ POSITIONAL+=("$key")
+ shift
+ [[ 2 -gt 0 ]]
+ key=-out
+ case "$key" in
+ POSITIONAL+=("$key")
+ shift
+ [[ 1 -gt 0 ]]
+ key=fastaval.xml
+ case "$key" in
+ POSITIONAL+=("$key")
+ shift
+ [[ 0 -gt 0 ]]
+ set -- -check_internal_ns -check_min_seqlen 200 -in /pgap/output/debug/tmpdir/wtbxs203/stgec7604a2-95db-49e3-8885-b35e52648dab/2817_AM_25_scaffolds.fasta -out fastaval.xml
+ set +e
+ fastaval -check_internal_ns -check_min_seqlen 200 -in /pgap/output/debug/tmpdir/wtbxs203/stgec7604a2-95db-49e3-8885-b35e52648dab/2817_AM_25_scaffolds.fasta -out fastaval.xml
+ result=255
+ set -e
+ false
+ exit 255
[2021-11-24 13:57:57] DEBUG Could not collect memory usage, job ended before monitoring began.
[2021-11-24 13:57:57] WARNING [job fastaval] completed permanentFail
[2021-11-24 13:57:57] DEBUG [job fastaval] outputs {
    "out": {
        "location": "file:///pgap/output/debug/tmp-outdir/2oeym91p/fastaval.xml",
        "basename": "fastaval.xml",
        "nameroot": "fastaval",
        "nameext": ".xml",
        "class": "File",
        "checksum": "sha1$c51491b5eb9d1501023447cf76f803430b220f13",
        "size": 574158,
        "http://commonwl.org/cwltool#generation": 0
    },
    "success": true
}
[2021-11-24 13:57:57] DEBUG [step fastaval] produced output {
    "file:///pgap/pgap/pgap.cwl#fastaval/success": true
}
[2021-11-24 13:57:57] WARNING [step fastaval] completed permanentFail
[2021-11-24 13:57:57] DEBUG [job fastaval] Removing input staging directory /pgap/output/debug/tmpdir/wtbxs203
[2021-11-24 13:57:57] INFO [workflow ] completed permanentFail
[2021-11-24 13:57:57] DEBUG [workflow ] outputs {
    "calls": null,
    "final_asndisc_error_diag": null,
    "final_asnval_error_diag": null,
    "gbk": null,
    "gff": null,
    "initial_asndisc_error_diag": null,
    "initial_asnval_error_diag": null,
    "input_fasta": {
        "class": "File",
        "location": "file:///pgap/user_input/2817_AM_25_scaffolds.fasta",
        "size": 4239707,
        "basename": "2817_AM_25_scaffolds.fasta",
        "nameroot": "2817_AM_25_scaffolds",
        "nameext": ".fasta"
    },
    "input_submol": {
        "class": "File",
        "location": "file:///pgap/user_input/pgap_submol_kin56d9w.yaml",
        "size": 1583,
        "basename": "pgap_submol_kin56d9w.yaml",
        "nameroot": "pgap_submol_kin56d9w",
        "nameext": ".yaml"
    },
    "nucleotide_fasta": null,
    "protein_fasta": null,
    "sqn": null
}
[2021-11-24 13:57:57] DEBUG Copying /pgap/user_input/2817_AM_25_scaffolds.fasta to /pgap/output/2817_AM_25_scaffolds.fasta
[2021-11-24 13:57:57] DEBUG Copying /pgap/user_input/pgap_submol_kin56d9w.yaml to /pgap/output/pgap_submol_kin56d9w.yaml
{
    "calls": null,
    "final_asndisc_error_diag": null,
    "final_asnval_error_diag": null,
    "gbk": null,
    "gff": null,
    "initial_asndisc_error_diag": null,
    "initial_asnval_error_diag": null,
    "input_fasta": {
        "class": "File",
        "location": "file:///pgap/output/2817_AM_25_scaffolds.fasta",
        "size": 4239707,
        "basename": "2817_AM_25_scaffolds.fasta",
        "checksum": "sha1$ca7a9d30ae496a2e07e1a2db54a9f4a95a442c02",
        "path": "/pgap/output/2817_AM_25_scaffolds.fasta"
    },
    "input_submol": {
        "class": "File",
        "location": "file:///pgap/output/pgap_submol_kin56d9w.yaml",
        "size": 1583,
        "basename": "pgap_submol_kin56d9w.yaml",
        "checksum": "sha1$db7356b0f1aff244d2930aa5fe6765d46ac67489",
        "path": "/pgap/output/pgap_submol_kin56d9w.yaml"
    },
    "nucleotide_fasta": null,
    "protein_fasta": null,
    "sqn": null
}
[2021-11-24 13:57:58] WARNING Final process status is permanentFail
azat-badretdin commented 3 years ago

The fastaval.xml file inside your output .zip has diagnostics, please look for severity=ERROR XML records.

brittonstrickland commented 3 years ago

I was able to find the error which was due to a contig being less than 200bp. I ran again, but it failed again. The fastaval.xml reported no more errors.

/data/das_lab/Data_analysis/LactoGenomes/PGAP/pgap.py -D singularity -n -d --no-internet -o lactoreuteri_out /data/das_lab/Data_analysis/LactoGenomes/PGAP/lacto.reuteri/input.yaml
--no-internet flag enabled, not checking remote versions.
Output will be placed in: /gpfs52/data/das_lab/Data_analysis/LactoGenomes/PGAP/lacto.reuteri/lactoreuteri_out.1
INFO:    Using cached SIF image
WARNING: open files is less than the recommended value of 8000
PGAP failed, docker exited with rc = 1
Printing log starting from failed job:

[2021-11-24 18:24:28] DEBUG [step screen_evaluate] job input {
    "file:///pgap/pgap/vecscreen/vecscreen.cwl#screen_evaluate/ifmt": "seq-annot",
    "file:///pgap/pgap/vecscreen/vecscreen.cwl#screen_evaluate/ignore_all_errors": false,
    "file:///pgap/pgap/vecscreen/vecscreen.cwl#screen_evaluate/tab": {
        "location": "file:///pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab",
        "basename": "calls.tab",
        "nameroot": "calls",
        "nameext": ".tab",
        "class": "File",
        "checksum": "sha1$15888c8845e5cc1c92cc0dc50eda97c32e8785c4",
        "size": 1197,
        "http://commonwl.org/cwltool#generation": 0
    }
}
[2021-11-24 18:24:28] DEBUG [step screen_evaluate] evaluated job input to {
    "file:///pgap/pgap/vecscreen/vecscreen.cwl#screen_evaluate/ifmt": "seq-annot",
    "file:///pgap/pgap/vecscreen/vecscreen.cwl#screen_evaluate/ignore_all_errors": false,
    "file:///pgap/pgap/vecscreen/vecscreen.cwl#screen_evaluate/tab": {
        "location": "file:///pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab",
        "basename": "calls.tab",
        "nameroot": "calls",
        "nameext": ".tab",
        "class": "File",
        "checksum": "sha1$15888c8845e5cc1c92cc0dc50eda97c32e8785c4",
        "size": 1197,
        "http://commonwl.org/cwltool#generation": 0
    }
}
[2021-11-24 18:24:28] INFO [step screen_evaluate] start
[2021-11-24 18:24:28] DEBUG [job screen_evaluate] initializing from file:///pgap/pgap/progs/screen_evaluate.cwl as part of step screen_evaluate
[2021-11-24 18:24:28] DEBUG [job screen_evaluate] {
    "ifmt": "seq-annot",
    "ignore_all_errors": false,
    "tab": {
        "location": "file:///pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab",
        "basename": "calls.tab",
        "nameroot": "calls",
        "nameext": ".tab",
        "class": "File",
        "checksum": "sha1$15888c8845e5cc1c92cc0dc50eda97c32e8785c4",
        "size": 1197,
        "http://commonwl.org/cwltool#generation": 0
    },
    "asn": null,
    "it": false
}
[2021-11-24 18:24:28] DEBUG [job screen_evaluate] path mappings is {
    "file:///pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab": [
        "/pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab",
        "/pgap/output/debug/tmpdir/dk_kt0sf/stg3e8886d1-f626-4451-95ac-dca2fcebe289/calls.tab",
        "File",
        true
    ]
}
[2021-11-24 18:24:28] DEBUG [job screen_evaluate] command line bindings is [
    {
        "position": [
            -1000000,
            0
        ],
        "datum": "screen_evaluate"
    },
    {
        "prefix": "-ifmt",
        "position": [
            0,
            "ifmt"
        ],
        "datum": "seq-annot"
    },
    {
        "prefix": "-ignore-all-errors",
        "position": [
            0,
            "ignore_all_errors"
        ],
        "datum": false
    },
    {
        "prefix": "-it",
        "position": [
            0,
            "it"
        ],
        "datum": false
    },
    {
        "prefix": "-tab",
        "position": [
            0,
            "tab"
        ],
        "datum": {
            "location": "file:///pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab",
            "basename": "calls.tab",
            "nameroot": "calls",
            "nameext": ".tab",
            "class": "File",
            "checksum": "sha1$15888c8845e5cc1c92cc0dc50eda97c32e8785c4",
            "size": 1197,
            "http://commonwl.org/cwltool#generation": 0,
            "path": "/pgap/output/debug/tmpdir/dk_kt0sf/stg3e8886d1-f626-4451-95ac-dca2fcebe289/calls.tab",
            "dirname": "/pgap/output/debug/tmpdir/dk_kt0sf/stg3e8886d1-f626-4451-95ac-dca2fcebe289"
        }
    }
]
[2021-11-24 18:24:28] DEBUG [job screen_evaluate] initial work dir {}
[2021-11-24 18:24:28] INFO [job screen_evaluate] /pgap/output/debug/tmp-outdir/h1o1mpxv$ screen_evaluate \
    -ifmt \
    seq-annot \
    -tab \
    /pgap/output/debug/tmpdir/dk_kt0sf/stg3e8886d1-f626-4451-95ac-dca2fcebe289/calls.tab
[2021-11-24 18:24:29] DEBUG Could not collect memory usage, job ended before monitoring began.
[2021-11-24 18:24:29] WARNING [job screen_evaluate] completed permanentFail
[2021-11-24 18:24:29] DEBUG [job screen_evaluate] outputs {
    "success": true
}
[2021-11-24 18:24:29] DEBUG [step screen_evaluate] produced output {
    "file:///pgap/pgap/vecscreen/vecscreen.cwl#screen_evaluate/success": true
}
[2021-11-24 18:24:29] WARNING [step screen_evaluate] completed permanentFail
[2021-11-24 18:24:29] INFO [workflow vecscreen] completed permanentFail
[2021-11-24 18:24:29] DEBUG [workflow vecscreen] outputs {
    "adaptor_blastdb_dir": {
        "location": "file:///pgap/output/debug/tmp-outdir/zz3728de/blastdir",
        "basename": "blastdir",
        "nameroot": "blastdir",
        "nameext": "",
        "class": "Directory"
    },
    "blast_align": {
        "location": "file:///pgap/output/debug/tmp-outdir/vm14cslg/blast.1.asn",
        "basename": "blast.1.asn",
        "nameroot": "blast.1",
        "nameext": ".asn",
        "class": "File",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "size": 0,
        "http://commonwl.org/cwltool#generation": 0
    },
    "calls": {
        "location": "file:///pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab",
        "basename": "calls.tab",
        "nameroot": "calls",
        "nameext": ".tab",
        "class": "File",
        "checksum": "sha1$15888c8845e5cc1c92cc0dc50eda97c32e8785c4",
        "size": 1197,
        "http://commonwl.org/cwltool#generation": 0
    },
    "contamination_feats": {
        "location": "file:///pgap/output/debug/tmp-outdir/pmtlyxsl/feats.asn",
        "basename": "feats.asn",
        "nameroot": "feats",
        "nameext": ".asn",
        "class": "File",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "size": 0,
        "http://commonwl.org/cwltool#generation": 0
    },
    "filtered_align": {
        "location": "file:///pgap/output/debug/tmp-outdir/jojdviwj/align.asn",
        "basename": "align.asn",
        "nameroot": "align",
        "nameext": ".asn",
        "class": "File",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "size": 0,
        "http://commonwl.org/cwltool#generation": 0
    },
    "foreign_feats": {
        "location": "file:///pgap/output/debug/tmp-outdir/91bhinl4/fscr_feats.asn",
        "basename": "fscr_feats.asn",
        "nameroot": "fscr_feats",
        "nameext": ".asn",
        "class": "File",
        "checksum": "sha1$4218f2cf54234e488985175cefe21e838bf7a117",
        "size": 10198,
        "http://commonwl.org/cwltool#generation": 0
    },
    "hits": {
        "location": "file:///pgap/output/debug/tmp-outdir/ixduf3_t/output.asn",
        "basename": "output.asn",
        "nameroot": "output",
        "nameext": ".asn",
        "class": "File",
        "checksum": "sha1$37dc5c8094b08a79d50ae45f4aea63857a5e1b63",
        "size": 22096,
        "http://commonwl.org/cwltool#generation": 0
    },
    "out_cache_dir": {
        "location": "file:///pgap/output/debug/tmp-outdir/eqx6gd_d/sequence_cache",
        "basename": "sequence_cache",
        "nameroot": "sequence_cache",
        "nameext": "",
        "class": "Directory"
    },
    "success": true
}
[2021-11-24 18:24:29] DEBUG [step vecscreen] produced output {
    "file:///pgap/pgap/pgap.cwl#vecscreen/success": true,
    "file:///pgap/pgap/pgap.cwl#vecscreen/calls": {
        "location": "file:///pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab",
        "basename": "calls.tab",
        "nameroot": "calls",
        "nameext": ".tab",
        "class": "File",
        "checksum": "sha1$15888c8845e5cc1c92cc0dc50eda97c32e8785c4",
        "size": 1197,
        "http://commonwl.org/cwltool#generation": 0
    }
}
[2021-11-24 18:24:29] WARNING [step vecscreen] completed permanentFail
[2021-11-24 18:24:29] DEBUG [job screen_evaluate] Removing input staging directory /pgap/output/debug/tmpdir/dk_kt0sf
[2021-11-24 18:24:29] INFO [workflow ] completed permanentFail
[2021-11-24 18:24:29] DEBUG [workflow ] outputs {
    "calls": {
        "location": "file:///pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab",
        "basename": "calls.tab",
        "nameroot": "calls",
        "nameext": ".tab",
        "class": "File",
        "checksum": "sha1$15888c8845e5cc1c92cc0dc50eda97c32e8785c4",
        "size": 1197,
        "http://commonwl.org/cwltool#generation": 0
    },
    "final_asndisc_error_diag": null,
    "final_asnval_error_diag": null,
    "gbk": null,
    "gff": null,
    "initial_asndisc_error_diag": null,
    "initial_asnval_error_diag": null,
    "input_fasta": {
        "class": "File",
        "location": "file:///pgap/user_input/2817_AM_25_scaffolds.200.fasta",
        "size": 4225230,
        "basename": "2817_AM_25_scaffolds.200.fasta",
        "nameroot": "2817_AM_25_scaffolds.200",
        "nameext": ".fasta"
    },
    "input_submol": {
        "class": "File",
        "location": "file:///pgap/user_input/pgap_submol_cg8rj68h.yaml",
        "size": 1583,
        "basename": "pgap_submol_cg8rj68h.yaml",
        "nameroot": "pgap_submol_cg8rj68h",
        "nameext": ".yaml"
    },
    "nucleotide_fasta": null,
    "protein_fasta": null,
    "sqn": null
}
[2021-11-24 18:24:29] DEBUG Copying /pgap/output/debug/tmp-outdir/ex0ujp5t/calls.tab to /pgap/output/calls.tab
[2021-11-24 18:24:29] DEBUG Copying /pgap/user_input/2817_AM_25_scaffolds.200.fasta to /pgap/output/2817_AM_25_scaffolds.200.fasta
[2021-11-24 18:24:29] DEBUG Copying /pgap/user_input/pgap_submol_cg8rj68h.yaml to /pgap/output/pgap_submol_cg8rj68h.yaml
{
    "calls": {
        "location": "file:///pgap/output/calls.tab",
        "basename": "calls.tab",
        "class": "File",
        "checksum": "sha1$15888c8845e5cc1c92cc0dc50eda97c32e8785c4",
        "size": 1197,
        "path": "/pgap/output/calls.tab"
    },
    "final_asndisc_error_diag": null,
    "final_asnval_error_diag": null,
    "gbk": null,
    "gff": null,
    "initial_asndisc_error_diag": null,
    "initial_asnval_error_diag": null,
    "input_fasta": {
        "class": "File",
        "location": "file:///pgap/output/2817_AM_25_scaffolds.200.fasta",
        "size": 4225230,
        "basename": "2817_AM_25_scaffolds.200.fasta",
        "checksum": "sha1$3d74957db170ec1159e7abdd5fb243fa450d0a17",
        "path": "/pgap/output/2817_AM_25_scaffolds.200.fasta"
    },
    "input_submol": {
        "class": "File",
        "location": "file:///pgap/output/pgap_submol_cg8rj68h.yaml",
        "size": 1583,
        "basename": "pgap_submol_cg8rj68h.yaml",
        "checksum": "sha1$db7356b0f1aff244d2930aa5fe6765d46ac67489",
        "path": "/pgap/output/pgap_submol_cg8rj68h.yaml"
    },
    "nucleotide_fasta": null,
    "protein_fasta": null,
    "sqn": null
}
[2021-11-24 18:24:29] WARNING Final process status is permanentFail
azat-badretdin commented 3 years ago 

[2021-11-24 18:24:28] INFO [job screen_evaluate] /pgap/output/debug/tmp-outdir/h1o1mpxv$ screen_evaluate \
    -ifmt \
    seq-annot \
    -tab \
    /pgap/output/debug/tmpdir/dk_kt0sf/stg3e8886d1-f626-4451-95ac-dca2fcebe289/calls.tab
[2021-11-24 18:24:29] DEBUG Could not collect memory usage, job ended before monitoring began.
[2021-11-24 18:24:29] WARNING [job screen_evaluate] completed permanentFail

see, now you have a problem in screening contamination. Please find the calls.tab under the same directory it will tell you what regions are contamination.

thibaudnis commented 2 years ago

@brittonstrickland: have you been able to remove the suspected adaptor contaminants from your genome? Alternatively you can run pgap.py with the flag ignore-all-errors.

brittonstrickland commented 2 years ago

I did remove adapter-contaminant contains, however I was met with another ERROR and no output annotation using --ignore-all-errors. See snippet of log below:

Wrong number of CDSs removed.  good_cdss.size(1) + feats_for_removal.size/2(0) = 1 != cdregions.size(2)
terminate called after throwing an instance of 'ncbi::CException'
  what():  NCBI C++ Exception:
    Error: BACTERIAL_PIPELINE(CException::eUnknown) "../../../../../../ncbi_cxx/src/internal/gpipe/app/bacterial_pipeline/bact_annot_filter.cpp", line 1131: CBactAnnotFilterApplication::x_CollectFeaturesNotInBestChain() --- Wrong number of CDSs removed.
     Stack trace:
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/bin/bact_annot_filter :0  offset=0x0 addr=0x417952
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/bin/bact_annot_filter :0  offset=0x0 addr=0x41989e
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/lib/libxncbi.so ../../../ncbi_cxx/src/corelib/ncbiapp.cpp:700 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x0 addr=0x2b057407b1f2
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/lib/libxncbi.so ../../../ncbi_cxx/src/corelib/ncbiapp.cpp:991 ncbi::CNcbiApplicationAPI::AppMain(int, char const* const*, char const* const*, ncbi::EAppDiagStream, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) offset=0x0 addr=0x2b057407e86c
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/bin/bact_annot_filter :0  offset=0x0 addr=0x40e747
      /usr/lib64/libc-2.17.so :0  offset=0x0 addr=0x2b0576d91554
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/bin/bact_annot_filter :0  offset=0x0 addr=0x40e8a9
       :0  offset=0x0 addr=0xffffffffffffffff

Stack trace (most recent call last):
#13   Object "", at 0xffffffffffffffff, in 
#12   Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/bin/bact_annot_filter", at 0x40e8a9, in _start
#11   Object "/usr/lib64/libc-2.17.so", at 0x2b0576d91554, in __libc_start_main
#10   Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/bin/bact_annot_filter", at 0x40e747, in main
#9    Source "../../../ncbi_cxx/src/corelib/ncbiapp.cpp", line 991, in AppMain [0x2b057407e86c]
#8    Source "../../../ncbi_cxx/src/corelib/ncbiapp.cpp", line 700, in x_TryMain [0x2b057407b1f2]
#7    Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/bin/bact_annot_filter", at 0x41989e, in CBactAnnotFilterApplication::Run()
#6    Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2021-07-01.build5508/arch/x86_64/bin/bact_annot_filter", at 0x41798a, in CBactAnnotFilterApplication::FeatureSelectionDP(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ncbi::CRef<ncbi::objects::CSeq_entry, ncbi::CObjectCounterLocker>, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, ncbi::CRef<ncbi::objects::CSeq_entry, ncbi::CObjectCounterLocker> > > >&)
#5    Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_throw.cc", line 93, in __cxa_throw [0x2b0576335262]
#4    Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 57, in terminate [0x2b0576335020]
#3    Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 47, in __cxa_begin_catch [0x2b0576334fd5]
#2    Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/vterminate.cc", line 95, in __verbose_terminate_handler [0x2b05763371e4]
#1    Object "/usr/lib64/libc-2.17.so", at 0x2b0576da6a77, in abort
#0    Object "/usr/lib64/libc-2.17.so", at 0x2b0576da5387, in raise
Aborted (Signal sent by tkill() 20727 660984)
[2021-12-06 22:40:43] INFO [job Bacterial_Annot_Filter] Max memory used: 45MiB
[2021-12-06 22:40:43] ERROR [job Bacterial_Annot_Filter] Job error:
("Error collecting output for parameter 'out_annotation':\npgap/progs/bact_annot_filter.cwl:63:13: Did not find output file with glob pattern: '['out-annotation.asn']'", {})
[2021-12-06 22:40:43] WARNING [job Bacterial_Annot_Filter] completed permanentFail
[2021-12-06 22:40:43] DEBUG [job Bacterial_Annot_Filter] outputs {}
[2021-12-06 22:40:43] ERROR [step Bacterial_Annot_Filter] Output is missing expected field file:///pgap/pgap/bacterial_annot/wf_bacterial_annot_pass4.cwl#Bacterial_Annot_Filter/out_annotation
[2021-12-06 22:40:43] DEBUG [step Bacterial_Annot_Filter] produced output {}
[2021-12-06 22:40:43] WARNING [step Bacterial_Annot_Filter] completed permanentFail
[2021-12-06 22:40:43] INFO [workflow bacterial_annot_4] completed permanentFail
[2021-12-06 22:40:43] DEBUG [workflow bacterial_annot_4] outputs {
    "out_annotation": null
}
azat-badretdin commented 2 years ago

Britton, what is the version of software you ran the last case? It should be in the header of the cwltool.log

azat-badretdin commented 2 years ago

Actually, I see that it is the July version. Would you mind trying our new version that we just release please?