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NCBI Prokaryotic Genome Annotation Pipeline
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Help needed with Python related issues #255

Closed tarunaaggarwal closed 1 year ago

tarunaaggarwal commented 1 year ago

Hello,

I installed PGAP and ran it on the test genomes successfully. But now I'm having Python-related issues when trying to run PGAP on my own data using a script. Might you please help me resolve the errors below? Thank you!

Traceback (most recent call last):
  File "/home/taruna/miniconda3/lib/python3.8/urllib/request.py", line 1354, in do_open
    h.request(req.get_method(), req.selector, req.data, headers,
  File "/home/taruna/miniconda3/lib/python3.8/http/client.py", line 1252, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "/home/taruna/miniconda3/lib/python3.8/http/client.py", line 1298, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "/home/taruna/miniconda3/lib/python3.8/http/client.py", line 1247, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "/home/taruna/miniconda3/lib/python3.8/http/client.py", line 1007, in _send_output
    self.send(msg)
  File "/home/taruna/miniconda3/lib/python3.8/http/client.py", line 947, in send
    self.connect()
  File "/home/taruna/miniconda3/lib/python3.8/http/client.py", line 1414, in connect
    super().connect()
  File "/home/taruna/miniconda3/lib/python3.8/http/client.py", line 918, in connect
    self.sock = self._create_connection(
  File "/home/taruna/miniconda3/lib/python3.8/socket.py", line 808, in create_connection
    raise err
  File "/home/taruna/miniconda3/lib/python3.8/socket.py", line 796, in create_connection
    sock.connect(sa)
OSError: [Errno 113] No route to host

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/taruna/pkgs/pgap/pgap.py", line 917, in main
    params = Setup(args)
  File "/home/taruna/pkgs/pgap/pgap.py", line 521, in __init__
    self.remote_versions = self.get_remote_versions()
  File "/home/taruna/pkgs/pgap/pgap.py", line 595, in get_remote_versions
    response = urlopen('https://api.github.com/repos/ncbi/pgap/releases/latest')
  File "/home/taruna/miniconda3/lib/python3.8/urllib/request.py", line 222, in urlopen
    return opener.open(url, data, timeout)
  File "/home/taruna/miniconda3/lib/python3.8/urllib/request.py", line 525, in open
    response = self._open(req, data)
  File "/home/taruna/miniconda3/lib/python3.8/urllib/request.py", line 542, in _open
    result = self._call_chain(self.handle_open, protocol, protocol +
  File "/home/taruna/miniconda3/lib/python3.8/urllib/request.py", line 502, in _call_chain
    result = func(*args)
  File "/home/taruna/miniconda3/lib/python3.8/urllib/request.py", line 1397, in https_open
    return self.do_open(http.client.HTTPSConnection, req,
  File "/home/taruna/miniconda3/lib/python3.8/urllib/request.py", line 1357, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 113] No route to host>

Contents of my script:

#!/bin/bash
#SBATCH --job-name=pgapTest
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
#SBATCH --partition=largemem
#SBATCH --time=30-00:00:00
#SBATCH --mail-user=taruna@ucsb.edu
#SBATCH --mail-type=BEGIN,END,FAIL
#SBATCH -e slurm-%x.err-%N
#SBATCH -o slurm-%x.out-%N

/home/taruna/pkgs/pgap/pgap.py -r \
-o /home/taruna/sargassum/metagenomes/clean_data/pgap-v2022-12-13.build6494-results/OA \
/home/taruna/sargassum/metagenomes/clean_data/pgap-v2022-12-13.build6494-results/yamlFiles/OAbin3.yaml
azat-badretdin commented 1 year ago

Thank you for your report, Taruna! It looks like you do not have internet connection, you might try it with /home/taruna/pkgs/pgap/pgap.py --no-internet option added

tarunaaggarwal commented 1 year ago

Ah okay thank you. I tried to run it with --no-internet but it fails again. I think it's failing because I don't have a specific taxa...the most specific I can get is at the class level. I got the following error today.

PGAP version 2022-12-13.build6494 is up to date.
Output will be placed in: /home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/results
WARNING: open files is less than the recommended value of 8000
PGAP failed, docker exited with rc = 1
Printing log starting from failed job:

[2023-04-19 15:22:54] DEBUG [step pgapx_yaml_ctl] job input {
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/ignore_all_errors": null,
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input": {
        "location": "file:///tmp/n37tqmrd/submol.json",
        "basename": "submol.json",
        "nameroot": "submol",
        "nameext": ".json",
        "class": "File",
        "checksum": "sha1$671a0c2166cbe26d5313169b8ebfbee313b532d6",
        "size": 1082,
        "http://commonwl.org/cwltool#generation": 0
    },
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input_fasta": {
        "class": "File",
        "location": "file:///home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/with_coverage.3.fa",
        "size": 3376319,
        "basename": "with_coverage.3.fa",
        "nameroot": "with_coverage.3",
        "nameext": ".fa"
    },
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/no_internet": null,
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/taxon_db": {
        "class": "File",
        "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3",
        "basename": "taxonomy.sqlite3",
        "size": 1083080704,
        "nameroot": "taxonomy",
        "nameext": ".sqlite3"
    }
}
[2023-04-19 15:22:54] DEBUG [step pgapx_yaml_ctl] evaluated job input to {
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/ignore_all_errors": null,
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input": {
        "location": "file:///tmp/n37tqmrd/submol.json",
        "basename": "submol.json",
        "nameroot": "submol",
        "nameext": ".json",
        "class": "File",
        "checksum": "sha1$671a0c2166cbe26d5313169b8ebfbee313b532d6",
        "size": 1082,
        "http://commonwl.org/cwltool#generation": 0
    },
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input_fasta": {
        "class": "File",
        "location": "file:///home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/with_coverage.3.fa",
        "size": 3376319,
        "basename": "with_coverage.3.fa",
        "nameroot": "with_coverage.3",
        "nameext": ".fa"
    },
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/no_internet": null,
    "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/taxon_db": {
        "class": "File",
        "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3",
        "basename": "taxonomy.sqlite3",
        "size": 1083080704,
        "nameroot": "taxonomy",
        "nameext": ".sqlite3"
    }
}
[2023-04-19 15:22:54] INFO [step pgapx_yaml_ctl] start
[2023-04-19 15:22:54] DEBUG [job pgapx_yaml_ctl] initializing from file:///pgap/pgap/progs/pgapx_yaml_ctl.cwl as part of step pgapx_yaml
_ctl
[2023-04-19 15:22:54] DEBUG [job pgapx_yaml_ctl] {
    "ignore_all_errors": null,
    "input": {
        "location": "file:///tmp/n37tqmrd/submol.json",
        "basename": "submol.json",
        "nameroot": "submol",
        "nameext": ".json",
        "class": "File",
        "checksum": "sha1$671a0c2166cbe26d5313169b8ebfbee313b532d6",
        "size": 1082,
        "http://commonwl.org/cwltool#generation": 0
    },
    "input_fasta": {
        "class": "File",
        "location": "file:///home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/with_coverage.3.fa",
        "size": 3376319,
        "basename": "with_coverage.3.fa",
        "nameroot": "with_coverage.3",
        "nameext": ".fa"
    },
    "no_internet": null,
    "taxon_db": {
        "class": "File",
        "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3",
        "basename": "taxonomy.sqlite3",
        "size": 1083080704,
        "nameroot": "taxonomy",
        "nameext": ".sqlite3"
    },
    "ifmt": "JSON",
    "ofmt": "JSON",
    "output_annotation_name": "input.asn",
    "output_input_asn_type_name": "input_asn_type.txt",
    "output_ltp_name": "genome.ltp.txt",
    "output_taxid_name": "taxid.txt"
}
[2023-04-19 15:22:54] DEBUG [job pgapx_yaml_ctl] path mappings is {
    "file:///tmp/n37tqmrd/submol.json": [
        "/tmp/n37tqmrd/submol.json",
        "/tmp/gnkc2aez/stg57b95de1-faea-4142-90f6-b2e15e148801/submol.json",
        "File",
        true
    ],
    "file:///home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/with_coverage.3.fa": [
        "/home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/with_coverage.3.fa",
        "/tmp/gnkc2aez/stg151904f6-e0f3-4a2d-9d65-b7f51a6cdc9b/with_coverage.3.fa",
        "File",
        true
    ],
    "file:///pgap/input/uniColl_path/taxonomy.sqlite3": [
        "/pgap/input/uniColl_path/taxonomy.sqlite3",
        "/tmp/gnkc2aez/stg3c44c53a-a4da-4a25-a101-390a1b9af642/taxonomy.sqlite3",
        "File",
        true
    ]
}
[2023-04-19 15:22:54] DEBUG [job pgapx_yaml_ctl] command line bindings is [
    {
        "position": [
            -1000000,
            0
        ],
        "datum": "pgapx_yaml_ctl"
    },
    {
        "prefix": "-ifmt",
        "position": [
            0,
            "ifmt"
        ],
        "datum": "JSON"
    },
    {
        "prefix": "-input",
        "position": [
            0,
            "input"
        ],
        "datum": {
            "location": "file:///tmp/n37tqmrd/submol.json",
            "basename": "submol.json",
            "nameroot": "submol",
            "nameext": ".json",
            "class": "File",
            "checksum": "sha1$671a0c2166cbe26d5313169b8ebfbee313b532d6",
            "size": 1082,
            "http://commonwl.org/cwltool#generation": 0,
            "path": "/tmp/gnkc2aez/stg57b95de1-faea-4142-90f6-b2e15e148801/submol.json",
            "dirname": "/tmp/gnkc2aez/stg57b95de1-faea-4142-90f6-b2e15e148801"
        }
    },
    {
        "prefix": "-input-fasta",
        "position": [
            0,
            "input_fasta"
        ],
        "datum": {
            "class": "File",
            "location": "file:///home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/with_coverage.3.fa",
            "size": 3376319,
            "basename": "with_coverage.3.fa",
            "nameroot": "with_coverage.3",
            "nameext": ".fa",
            "path": "/tmp/gnkc2aez/stg151904f6-e0f3-4a2d-9d65-b7f51a6cdc9b/with_coverage.3.fa",
            "dirname": "/tmp/gnkc2aez/stg151904f6-e0f3-4a2d-9d65-b7f51a6cdc9b"
        }
    },
    {
        "prefix": "-ofmt",
        "position": [
            0,
            "ofmt"
        ],
        "datum": "JSON"
    },
    {
        "prefix": "-output-annotation",
        "position": [
            0,
            "output_annotation_name"
        ],
        "datum": "input.asn"
    },
    {
        "prefix": "-output-asn-type",
        "position": [
            0,
            "output_input_asn_type_name"
        ],
        "datum": "input_asn_type.txt"
    },
    {
        "prefix": "-output-ltp",
        "position": [
            0,
            "output_ltp_name"
        ],
        "datum": "genome.ltp.txt"
    },
    {
        "prefix": "-output-taxid",
        "position": [
            0,
            "output_taxid_name"
        ],
        "datum": "taxid.txt"
    },
    {
        "prefix": "-taxon-db",
        "position": [
            0,
            "taxon_db"
        ],
        "datum": {
            "class": "File",
            "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3",
            "basename": "taxonomy.sqlite3",
            "size": 1083080704,
            "nameroot": "taxonomy",
            "nameext": ".sqlite3",
            "path": "/tmp/gnkc2aez/stg3c44c53a-a4da-4a25-a101-390a1b9af642/taxonomy.sqlite3",
            "dirname": "/tmp/gnkc2aez/stg3c44c53a-a4da-4a25-a101-390a1b9af642"
        }
    }
]
[2023-04-19 15:22:54] DEBUG [job pgapx_yaml_ctl] initial work dir {}
[2023-04-19 15:22:54] INFO [job pgapx_yaml_ctl] /tmp/pi0nsvfh$ pgapx_yaml_ctl \
    -ifmt \
    JSON \
    -input \
    /tmp/gnkc2aez/stg57b95de1-faea-4142-90f6-b2e15e148801/submol.json \
    -input-fasta \
    /tmp/gnkc2aez/stg151904f6-e0f3-4a2d-9d65-b7f51a6cdc9b/with_coverage.3.fa \
    -ofmt \
    JSON \
    -output-annotation \
    input.asn \
    -output-asn-type \
    input_asn_type.txt \
    -output-ltp \
    genome.ltp.txt \
    -output-taxid \
    taxid.txt \
    -taxon-db \
    /tmp/gnkc2aez/stg3c44c53a-a4da-4a25-a101-390a1b9af642/taxonomy.sqlite3
ignoring failure of pgapx_yaml_input.GetFasta
terminate called after throwing an instance of 'ncbi::CException'
  what():  NCBI C++ Exception:
    Error: CWL(CException::eUnknown) "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/app/cloud/cwl
/pgapx_yaml_ctl.cpp", line 246: CPgapxYamlCtlApplication::Run() --- Unknown organism Gammaproteobacteria OAbin3
     Stack trace:
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/pgapx_yaml_ctl :0  offset=
0x0 addr=0x41a83e
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libxncbi.so /export/home/g
pipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp:702 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStrea
m, char const*, int*, bool*) offset=0x0 addr=0x7fbe173d7472
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/lib/libxncbi.so /export/home/g
pipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp:1014 ncbi::CNcbiApplicationAPI::AppMain(int, char const* con
st*, char const* const*, ncbi::EAppDiagStream, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char
> > const&) offset=0x0 addr=0x7fbe173daa3c
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/pgapx_yaml_ctl :0  offset=
0x0 addr=0x40ca49
      /usr/lib64/libc-2.17.so :0  offset=0x0 addr=0x7fbe15e03554
      /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/pgapx_yaml_ctl :0  offset=
0x0 addr=0x40cc19
       :0  offset=0x0 addr=0xffffffffffffffff

Stack trace (most recent call last):
#12   Object "", at 0xffffffffffffffff, in
#11   Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/pgapx_yaml_ctl", a
t 0x40cc19, in _start
#10   Object "/usr/lib64/libc-2.17.so", at 0x7fbe15e03554, in __libc_start_main
#9    Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/pgapx_yaml_ctl", a
t 0x40ca49, in main
#8    Source "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 1014, in AppMain [0x7fbe1
73daa3c]
#7    Source "/export/home/gpipe/TeamCity/Agent2/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 702, in x_TryMain [0x7fbe
173d7472]
#6    Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2022-12-13.build6494/arch/x86_64/bin/pgapx_yaml_ctl", a
t 0x41a8ae, in CPgapxYamlCtlApplication::Run()
#5    Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_throw.cc", line 93, in __cxa_throw [0x7fbe16985222]
#4    Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 57, in terminate [0x7fbe16984fe0]
#3    Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 47, in __cxa_begin_catch [0x7fbe16984f95]
#2    Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/vterminate.cc", line 95, in __verbose_terminate_handler [0x7fbe169871a4]
#1    Object "/usr/lib64/libc-2.17.so", at 0x7fbe15e18a77, in abort
#0    Object "/usr/lib64/libc-2.17.so", at 0x7fbe15e17387, in raise
Aborted (Signal sent by tkill() 94298 2660)
[2023-04-19 15:23:41] INFO [job pgapx_yaml_ctl] Max memory used: 0MiB
[2023-04-19 15:23:41] WARNING [job pgapx_yaml_ctl] was terminated by signal: SIGABRT
[2023-04-19 15:23:41] ERROR [job pgapx_yaml_ctl] Job error:
("Error collecting output for parameter 'input_asn_type': pgap/progs/pgapx_yaml_ctl.cwl:75:13: Did not find output file with glob patter
n: '['input_asn_type.txt']'.", {})
[2023-04-19 15:23:41] WARNING [job pgapx_yaml_ctl] completed permanentFail
[2023-04-19 15:23:41] DEBUG [job pgapx_yaml_ctl] outputs {}
[2023-04-19 15:23:41] ERROR [step pgapx_yaml_ctl] Output is missing expected field file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_
ctl/output_annotation
[2023-04-19 15:23:41] ERROR [step pgapx_yaml_ctl] Output is missing expected field file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_
ctl/output_ltp
[2023-04-19 15:23:41] ERROR [step pgapx_yaml_ctl] Output is missing expected field file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_
ctl/input_asn_type
[2023-04-19 15:23:41] ERROR [step pgapx_yaml_ctl] Output is missing expected field file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_
ctl/taxid
[2023-04-19 15:23:41] DEBUG [step pgapx_yaml_ctl] produced output {}
[2023-04-19 15:23:41] WARNING [step pgapx_yaml_ctl] completed permanentFail
[2023-04-19 15:23:41] DEBUG [job pgapx_yaml_ctl] Removing input staging directory /tmp/gnkc2aez
[2023-04-19 15:23:41] DEBUG [job pgapx_yaml_ctl] Removing temporary directory /tmp/fr5lmrk_
[2023-04-19 15:23:41] INFO [workflow prepare_input_template] completed permanentFail
[2023-04-19 15:23:41] DEBUG [workflow prepare_input_template] outputs {
    "input_asn_type": null,
    "locus_tag_prefix": null,
    "output_entries": null,
    "output_seq_submit": null,
    "submol_block_json": {
        "location": "file:///tmp/n37tqmrd/submol.json",
        "basename": "submol.json",
        "nameroot": "submol",
        "nameext": ".json",
        "class": "File",
        "checksum": "sha1$671a0c2166cbe26d5313169b8ebfbee313b532d6",
        "size": 1082,
        "http://commonwl.org/cwltool#generation": 0
    },
    "taxid": null
}
[2023-04-19 15:23:41] DEBUG [step prepare_input_template] produced output {
    "file:///pgap/pgap/pgap.cwl#prepare_input_template/output_seq_submit": null,
    "file:///pgap/pgap/pgap.cwl#prepare_input_template/output_entries": null,
    "file:///pgap/pgap/pgap.cwl#prepare_input_template/locus_tag_prefix": null,
    "file:///pgap/pgap/pgap.cwl#prepare_input_template/submol_block_json": {
        "location": "file:///tmp/n37tqmrd/submol.json",
        "basename": "submol.json",
        "nameroot": "submol",
        "nameext": ".json",
        "class": "File",
        "checksum": "sha1$671a0c2166cbe26d5313169b8ebfbee313b532d6",
        "size": 1082,
        "http://commonwl.org/cwltool#generation": 0
    },
    "file:///pgap/pgap/pgap.cwl#prepare_input_template/taxid": null
}
[2023-04-19 15:23:41] WARNING [step prepare_input_template] completed permanentFail
[2023-04-19 15:23:41] INFO [workflow ] completed permanentFail
[2023-04-19 15:23:41] DEBUG [workflow ] outputs {
    "calls": null,
    "cds_nucleotide_fasta": null,
    "cds_protein_fasta": null,
    "checkm_raw": null,
    "final_asndisc_error_diag": null,
    "final_asnval_error_diag": null,
    "gbk": null,
    "gff": null,
    "gff_enhanced": null,
    "initial_asndisc_error_diag": null,
    "initial_asnval_error_diag": null,
    "input_fasta": {
        "class": "File",
        "location": "file:///home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/with_coverage.3.fa",
        "size": 3376319,
        "basename": "with_coverage.3.fa",
        "nameroot": "with_coverage.3",
        "nameext": ".fa"
    },
    "input_submol": {
        "class": "File",
        "location": "file:///pgap/user_input/pgap_submol_9g_om9e1.yaml",
        "size": 1211,
        "basename": "pgap_submol_9g_om9e1.yaml",
        "nameroot": "pgap_submol_9g_om9e1",
        "nameext": ".yaml"
    },
    "nucleotide_fasta": null,
    "protein_fasta": null,
    "sqn": null
}
[2023-04-19 15:23:41] DEBUG Copying /home/taruna/sargassum/metagenomes/clean_data/pgap/OA/3/with_coverage.3.fa to /pgap/output/with_cove
rage.3.fa
[2023-04-19 15:23:41] DEBUG Copying /pgap/user_input/pgap_submol_9g_om9e1.yaml to /pgap/output/pgap_submol_9g_om9e1.yaml
[2023-04-19 15:23:41] DEBUG Removing intermediate output directory /tmp/01mhm4hz
[2023-04-19 15:23:41] DEBUG Removing intermediate output directory /tmp/pi0nsvfh
[2023-04-19 15:23:41] DEBUG Removing intermediate output directory /tmp/n37tqmrd
[2023-04-19 15:23:41] DEBUG Removing intermediate output directory /tmp/i_hn51ln
[2023-04-19 15:23:41] DEBUG Removing intermediate output directory /tmp/cqxw_ubv
{
    "calls": null,
    "cds_nucleotide_fasta": null,
    "cds_protein_fasta": null,
    "checkm_raw": null,
    "final_asndisc_error_diag": null,
    "final_asnval_error_diag": null,
    "gbk": null,
    "gff": null,
    "gff_enhanced": null,
    "initial_asndisc_error_diag": null,
    "initial_asnval_error_diag": null,
    "input_fasta": {
        "class": "File",
        "location": "file:///pgap/output/with_coverage.3.fa",
        "size": 3376319,
        "basename": "with_coverage.3.fa",
        "checksum": "sha1$68213496aa7ca8f53bbc94c986b01f02bf6079b8",
        "path": "/pgap/output/with_coverage.3.fa"
    },
    "input_submol": {
        "class": "File",
        "location": "file:///pgap/output/pgap_submol_9g_om9e1.yaml",
        "size": 1211,
        "basename": "pgap_submol_9g_om9e1.yaml",
        "checksum": "sha1$f29598be95c9f12e597829d6c915bf36d473b2e8",
        "path": "/pgap/output/pgap_submol_9g_om9e1.yaml"
    },
    "nucleotide_fasta": null,
    "protein_fasta": null,
    "sqn": null
}
[2023-04-19 15:23:41] WARNING Final process status is permanentFail
azat-badretdin commented 1 year ago

I think it's failing because I don't have a specific taxa

Correct!

Gammaproteobacteria OAbin3

That's a strange looking taxname...

tarunaaggarwal commented 1 year ago

Hahaha, strange looking indeed! The OAbin3 is an identifier that I added. I'm working with MAGs so I don't have much taxonomic resolution. Does this mean I can't use PGAP for annotating my MAGs?

azat-badretdin commented 1 year ago

It needs to be a registered taxonomy

tarunaaggarwal commented 1 year ago

Gammaproteobacteria is in NCBI taxonomy list but it's just not specific enough for PGAP. I will try to blast marker genes from this MAG and see if I can get a more specific taxonomy. Thank you!

azat-badretdin commented 1 year ago

It needs to be a genus or below.