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NCBI-Hackathons / Virus_Detection_SRA

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Use of uninitialized value $rlen in division (/) #9

Open sean-la opened 7 years ago

sean-la commented 7 years ago

I’m getting the following error with SIDEARM:

(sidearm) bash-4.2$ cwl-runner --preserve-environment BLASTDB --preserve-environment PERL5LIB /Software/sidearm/bin/cwl-runner 1.0.20170413194156
Resolved 'sidearm.cwl' to '/Software/Virus_Detection_SRA/cwl/tools/sidearm.cwl'
[job alignsrr] /tmp/tmpwrkHIE$ align_SRR_to_references.pl \
    -b \
    bacteria \
    -s \
    ERR1301508 \
    -t \
    24
Running command: magicblast -db bacteria -sra ERR1301508 -num_threads 24 | samtools view -bS - | samtools sort -o ERR1301508.bacteria.bam
[bam_sort_core] merging from 6 files...

real    3160m12.524s
user    55314m21.432s
sys     2314m54.336s
[job alignsrr] completed success
[step alignsrr] completed success
[job bam2seqs] /tmp/tmp_oa6d1$ bam2seqs.pl \
    -b \
    /tmp/tmp0a8Jxn/stgbd8aab1c-18d8-4229-854c-91ce1720408a/ERR1301508.bacteria.bam \
    --nopaired \
    -f \
    fasta
[job bam2seqs] completed success
[step bam2seqs] completed success
[job summarizebam] /tmp/tmpxRixsj$ summarize_bam_by_ref.pl \
    -v \
    -f \
    /tmp/tmpdk6zi5/stga83b2467-03d7-473f-975d-5b8908d1f76f/ERR1301508.bacteria.bam \
    -g \
    /tmp/tmpdk6zi5/stg0697d797-439c-4a2a-b79e-65d5de9853bc/bacteria.fasta
Use of uninitialized value $rlen in division (/) at /Software/Virus_Detection_SRA/bin/summarize_bam_by_ref.pl line 73.
Illegal division by zero at /Software/Virus_Detection_SRA/bin/summarize_bam_by_ref.pl line 73.
[job summarizebam] completed permanentFail
[step summarizebam] completed permanentFail
[workflow sidearm.cwl] outdir is /tmp/tmpTwfjF3
{   
    "report_tsv": {
        "checksum": "sha1$b9e27ea41ef657c53a719eb630b045c013ab0c5a",
        "basename": "ERR1301508.bacteria.bam.summarize.tsv",
        "location": "file:///Software/Virus_Detection_SRA/cwl/tools/ERR1301508.bacteria.bam.summarize.tsv",
        "path": "/Software/Virus_Detection_SRA/cwl/tools/ERR1301508.bacteria.bam.summarize.tsv",
        "class": "File",
        "size": 66
    },
    "bamfile": {
        "checksum": "sha1$cefe33d6e2cfe77cf7145ebb8e89d5de7e58f49e",
        "basename": "ERR1301508.bacteria.bam",
        "location": "file:///Software/Virus_Detection_SRA/cwl/tools/ERR1301508.bacteria.bam",
        "path": "/Software/Virus_Detection_SRA/cwl/tools/ERR1301508.bacteria.bam",
        "class": "File",
        "size": 681364564
    }
}
Final process status is permanentFail
pcantalupo commented 7 years ago

Please post your input yml file on Gist. Also, what is the format of your bacterial identifiers in the fasta file? Please send me several identifiers.