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  • #84

Closed
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Opened Dec 26, 2016 by castualwang@skywang
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The job will stop after processing

I imput the command:

impy run -m <input/MG.R1.fq> -m <input/MG.R2.fq> -t <input/MT.R1.fq> -t <input/MT.R2.fq> -o <output directory>
After the processing, the job stop!
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       ALL
        1       ANALYSIS
        1       ASSEMBLY
        1       BINNING
        1       PREPROCESSING
        1       REPORT
        1       annotate
        1       assembly_contig_length
        3       bwa_index
        2       call_contig_depth
        2       call_gene_depth
        2       cat_se_trimmed
        1       collapse_hybrid_assemblies
        1       diagramm
        1       download_librairies_files
        2       extract_unmapped_from_hybrid_assembly
        1       extract_unmapped_from_megahit
        2       fastqc_preprocessed
        2       fastqc_raw
        1       filter_rna
        1       idba_hybrid_assembly_1
        1       idba_hybrid_assembly_2
        2       krona
        1       local_librarie_files
        1       make_report
        2       mapping_on_assembly
        1       maxbin
        1       maxbin_contig2bin
        1       megahit_assembly_from_preprocessing
        1       megahit_assembly_from_unmapped
        1       metaquast
        1       mg_filtering
        1       mt_filtering
        1       prepare_input_data
        3       reads_count
        2       rename_stat_output
        1       symlink_mg_preprocessed_files
        1       symlink_mt_preprocessed_files
        2       trimming
        1       update_tbl2asn
        2       variant_calling
        1       visualize
        1       visualize_maxbin
        1       vizbin
        59
rule prepare_input_data:
        input: /home/imp/data/mg.r1.fq, /home/imp/data/mg.r2.fq, /home/imp/data/mt.r1.fq, /home/imp/data/mt.r2.fq
        output: Preprocessing/mg.r1.fq, Preprocessing/mg.r2.fq, Preprocessing/mt.r1.fq, Preprocessing/mt.r2.fq
1 of 59 steps (2%) done
ProtectedOutputException in line 1 of /home/imp/code/rules/Assembly/common/bwa.index.rule:
Write-protected output files for rule bwa_index:
/home/imp/databases/filtering/hg38.fa.amb
/home/imp/databases/filtering/hg38.fa.bwt
/home/imp/databases/filtering/hg38.fa.pac
/home/imp/databases/filtering/hg38.fa.sa
/home/imp/databases/filtering/hg38.fa.ann
/home/imp/data/mg.r1.fq => Preprocessing/mg.r1.fq
/home/imp/data/mg.r2.fq => Preprocessing/mg.r2.fq
/home/imp/data/mt.r1.fq => Preprocessing/mt.r1.fq
/home/imp/data/mt.r2.fq => Preprocessing/mt.r2.fq

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Reference: IMP/IMP#84