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hivlab / quantify-virome

quantify-virome: identify and quantify viruses from metagenomic shotgun sequences
MIT License
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RepeatMasker parseTagData error #19

Closed tpall closed 5 years ago

tpall commented 5 years ago

Problem with loading RM database

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       repeatmasker
        1

[Sun Dec  2 09:29:30 2018]
rule repeatmasker:
    input: mask/SRR5579964_repeatmasker_3.fa
    output: mask/SRR5579964_repeatmasker_3.fa.masked, mask/SRR5579964_repeatmasker_3.fa.out, mask/S
RR5579964_repeatmasker_3.fa.tbl
    jobid: 0
    wildcards: sample=SRR5579964, n=3
    threads: 2

Activating conda environment: /gpfs/hpchome/taavi74/fastq/prjna361402/.snakemake/conda/5302d956
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = (unset),
        LC_ALL = (unset),
        LC_CTYPE = "UTF-8",
        LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to a fallback locale ("en_US.UTF-8").
RepeatMasker version open-4.0.7
Search Engine: NCBI/RMBLAST [ 2.6.0+ ]
parseTagData: ID field not to EMBL spec "Sola3-3_NV repeatmasker; DNA; ???;  BP.
" from DE   RepbaseID: Sola3-3_NVXX

 at /gpfs/hpchome/taavi74/fastq/prjna361402/.snakemake/conda/5302d956/share/RepeatMasker/RepeatMasker line 7611.
Master RepeatMasker Database: /gpfs/hpchome/taavi74/fastq/prjna361402/.snakemake/conda/5302d956/share/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: dc20170127-rb20170127 )

[Sun Dec  2 09:29:45 2018]
Error in rule repeatmasker:
    jobid: 0
    output: mask/SRR5579964_repeatmasker_3.fa.masked, mask/SRR5579964_repeatmasker_3.fa.out, mask/SRR5579964_repeatmasker_3.fa.tbl
    conda-env: /gpfs/hpchome/taavi74/fastq/prjna361402/.snakemake/conda/5302d956

RuleException:
CalledProcessError in line 61 of /gpfs/hpchome/taavi74/Projects/vs/rules/mask.smk:
Command 'source activate /gpfs/hpchome/taavi74/fastq/prjna361402/.snakemake/conda/5302d956; set -euo pipefail;  
    RepeatMasker -qq -pa 2 mask/SRR5579964_repeatmasker_3.fa -dir mask
    if head -n 1 mask/SRR5579964_repeatmasker_3.fa.out | grep -q "There were no repetitive sequences detected"
      then ln -sr mask/SRR5579964_repeatmasker_3.fa mask/SRR5579964_repeatmasker_3.fa.masked
    fi ' returned non-zero exit status 25.
  File "/gpfs/hpchome/taavi74/Projects/vs/rules/mask.smk", line 61, in __rule_repeatmasker
  File "/gpfs/hpchome/taavi74/miniconda3/envs/snakemake/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
tpall commented 5 years ago

To fix this, just delete conda environment and let snakemake to install fresh one.