Annotate CRAVAT error - Githubissues

[1-ERROR]

CMD: annotate_with_cravat: oc run \~/Pipline/Hematological_Disease/Fastqs/NDX551335/20240802_E200019755_BeiJingDiAnT7_C_1/00.mergeRawFq/E2/varcalling.outdir_38/cromwell-executions/ctat_mutations/61f6d8cb-04c3-4610-974e-afe077b6004a/call-AnnotateVariants/annotate_variants_wf/99ca4f62-b8ac-4e6b-8bcd-94a56b786999/call-open_cravat/inputs/-1742349461/E2.annot_cosmic.vcf.gz --module-option vcfreporter.type=separate --system-option modules_dir=~/Resource/Site/data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat -t vcf -l hg38 -d \~/Pipline/Hematological_Disease/Fastqs/NDX551335/20240802_E200019755_BeiJingDiAnT7_C_1/00.mergeRawFq/E2/varcalling.outdir_38/cromwell-executions/ctat_mutations/61f6d8cb-04c3-4610-974e-afe077b6004a/call-AnnotateVariants/annotate_variants_wf/99ca4f62-b8ac-4e6b-8bcd-94a56b786999/call-open_cravat/execution -n E2.cravat.tmp

+ /usr/local/src/ctat-mutations/src/groom_vcf.py E2.cravat.tmp.vcf E2.cravat.groom.vcf Traceback (most recent call last): File "/usr/local/src/ctat-mutations/src/groom_vcf.py", line 43, in with ctat_util.open_file_for_reading(args.str_input_file) as hndl_vcf: File "/usr/local/src/ctat-mutations/src/ctat_util.py", line 10, in open_file_for_reading return open(filename, 'rt', encoding="utf-8", errors='ignore') # regular text file FileNotFoundError: [Errno 2] No such file or directory: 'E2.cravat.tmp.vcf'

[2-TRACE]

File "/usr/local/bin/miniconda3/lib/python3.10/site-packages/cravat/cravat_class.py", line 460, in main self.result_path = self.run_aggregator() File "/usr/local/bin/miniconda3/lib/python3.10/site-packages/cravat/cravat_class.py", line 1131, in run_aggregator s_aggregator.run() File "/usr/local/bin/miniconda3/lib/python3.10/site-packages/cravat/aggregator.py", line 114, in run for lnum, line, rd in self.base_reader.loop_data(): File "/usr/local/bin/miniconda3/lib/python3.10/site-packages/cravat/inout.py", line 157, in loop_data tok = json.loads(tok) File "/usr/local/bin/miniconda3/lib/python3.10/json/init.py", line 346, in loads return _default_decoder.decode(s) File "/usr/local/bin/miniconda3/lib/python3.10/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/bin/miniconda3/lib/python3.10/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

[3-TRACE]

/usr/local/bin/miniconda3/lib/python3.10/json/decoder.py

    try:
        obj, end = self.scan_once(s, idx)
    except StopIteration as err:
        raise JSONDecodeError("Expecting value", s, err.value) from None
    return obj, end

so, I add print command in decoder.py print(obj, end) shows some invalid key, value pair, ... nan 0 0 ...

Hi,

open cravat is a 3rd party tool that we use. If it's giving trouble, you can disable it with --no_cravat when running ctat mutations.

hope this helps

On Wed, Aug 7, 2024 at 10:00 PM QifengSun @.***> wrote:

[1-ERROR]

CMD: annotate_with_cravat: oc run ~/Pipline/Hematological_Disease/Fastqs/NDX551335/20240802_E200019755_BeiJingDiAnT7_C_1/00.mergeRawFq/E2/varcalling.outdir_38/cromwell-executions/ctat_mutations/61f6d8cb-04c3-4610-974e-afe077b6004a/call-AnnotateVariants/annotate_variants_wf/99ca4f62-b8ac-4e6b-8bcd-94a56b786999/call-open_cravat/inputs/-1742349461/ E2.annot_cosmic.vcf.gz --module-option vcfreporter.type=separate --system-option modules_dir=~/Resource/Site/ data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v44_CTAT_lib_Oct292023.plug-n-play/ctat_genome_lib_build_dir/ctat_mutation_lib/cravat -t vcf -l hg38 -d ~/Pipline/Hematological_Disease/Fastqs/NDX551335/20240802_E200019755_BeiJingDiAnT7_C_1/00.mergeRawFq/E2/varcalling.outdir_38/cromwell-executions/ctat_mutations/61f6d8cb-04c3-4610-974e-afe077b6004a/call-AnnotateVariants/annotate_variants_wf/99ca4f62-b8ac-4e6b-8bcd-94a56b786999/call-open_cravat/execution -n E2.cravat.tmp

/usr/local/src/ctat-mutations/src/groom_vcf.py E2.cravat.tmp.vcf E2.cravat.groom.vcf Traceback (most recent call last): File "/usr/local/src/ctat-mutations/src/groom_vcf.py", line 43, in with ctat_util.open_file_for_reading(args.str_input_file) as hndl_vcf: File "/usr/local/src/ctat-mutations/src/ctat_util.py", line 10, in open_file_for_reading return open(filename, 'rt', encoding="utf-8", errors='ignore') # regular text file FileNotFoundError: [Errno 2] No such file or directory: 'E2.cravat.tmp.vcf'

[2-TRACE]

File "/usr/local/bin/miniconda3/lib/python3.10/site-packages/cravat/ cravat_class.py", line 460, in main self.result_path = self.run_aggregator() File "/usr/local/bin/miniconda3/lib/python3.10/site-packages/cravat/cravat_class.py", line 1131, in run_aggregator s_aggregator.run() File "/usr/local/bin/miniconda3/lib/python3.10/site-packages/cravat/ aggregator.py", line 114, in run for lnum, line, rd in self.base_reader.loop_data(): File "/usr/local/bin/miniconda3/lib/python3.10/site-packages/cravat/ inout.py", line 157, in loop_data tok = json.loads(tok) File "/usr/local/bin/miniconda3/lib/python3.10/json/init.py", line 346, in loads return _default_decoder.decode(s) File "/usr/local/bin/miniconda3/lib/python3.10/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/usr/local/bin/miniconda3/lib/python3.10/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

[3-TRACE]

/usr/local/bin/miniconda3/lib/python3.10/json/decoder.py
try:
    obj, end = self.scan_once(s, idx)
except StopIteration as err:
    raise JSONDecodeError("Expecting value", s, err.value) from None
return obj, end
so, I add print command in decoder.py print(obj, end) shows some invalid key, value pair, ... nan 0 0 ...

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas

TrinityCTAT / ctat-mutations

Annotate CRAVAT error #137

[1-ERROR]

[2-TRACE]

/usr/local/bin/miniconda3/lib/python3.10/json/decoder.py

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