Snakemake 启动 Docker 导致问题

如何解决Snakemake 启动 Docker 导致问题

我检索了一个 Docker 文件，当我在全局环境中启动它时，它运行良好。 当我在 Snakefile 中启动它时，它也可以正确运行，但最后，snakefile 失败了：

Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter --genome_lib_dir /genome/ctat_genome_lib_build_dir
-done,see /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl  --fusions /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter --genome_lib_dir /genome/ctat_genome_lib_build_dir
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass > /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -961.028532
EM: Round [1] log likelihood: -961.028532
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass > /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /data/1_1_trimmed.fq.gz /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Execution Time = 0.75 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /data/1_1_trimmed.fq.gz /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /home/StarFusionOut/FusionInspector-validate/finspector.fa --gtf /home/StarFusionOut/FusionInspector-validate/finspector.gtf  > /home/StarFusionOut/FusionInspector-validate/fi_workdir/microH.dat
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /home/StarFusionOut/FusionInspector-validate/finspector.fa --gtf /home/StarFusionOut/FusionInspector-validate/finspector.gtf  > /home/StarFusionOut/FusionInspector-validate/fi_workdir/microH.dat
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /home/StarFusionOut/FusionInspector-validate/fi_workdir/microH.dat /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /home/StarFusionOut/FusionInspector-validate/fi_workdir/microH.dat /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM  >  /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/append_microH_info.ok
Running: cp /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /home/StarFusionOut/FusionInspector-validate/finspector.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.tsv
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads  > /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.tsv JunctionReads,CounterFusionRightReads  > /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /home/StarFusionOut/FusionInspector-validate --json_outfile /home/StarFusionOut/FusionInspector-validate/finspector.fusion_inspector_web.json --file_prefix finspector
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /home/StarFusionOut/FusionInspector-validate --json_outfile /home/StarFusionOut/FusionInspector-validate/finspector.fusion_inspector_web.json --file_prefix finspector
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/create_fi_igvjs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /home/StarFusionOut/FusionInspector-validate/finspector.fusion_inspector_web.json --input_file_prefix finspector --html_output /home/StarFusionOut/FusionInspector-validate/finspector.fusion_inspector_web.html
Warning - not locating file: /home/StarFusionOut/FusionInspector-validate/finspector.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.03 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /home/StarFusionOut/FusionInspector-validate/finspector.fusion_inspector_web.json --input_file_prefix finspector --html_output /home/StarFusionOut/FusionInspector-validate/finspector.fusion_inspector_web.html
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /genome/ctat_genome_lib_build_dir > /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv.annotated 
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv  --genome_lib_dir /genome/ctat_genome_lib_build_dir > /home/StarFusionOut/FusionInspector-validate/finspector.FusionInspector.fusions.abridged.tsv.annotated 
Running: touch /home/StarFusionOut/FusionInspector-validate/chckpts_dir/fusion_annotator.ok
[Thu Jun 24 16:10:45 2021]
Error in rule star_fusion:
    jobid: 4
    output: /tmpdata/XXX/YYY/TX/V1_Intermediate/Gene_Fusion/star_fusion/1/star-fusion.fusion_predictions.tsv,/tmpdata/XXX/YYY/TX/V1_Intermediate/Gene_Fusion/star_fusion/1/star-fusion.fusion_predictions.abridged.tsv
    shell:
        
        docker run --rm -v /tmpdata/XXX/YYY/TX/V1_Intermediate/Gene_Fusion/star_fusion/1:/home/StarFusionOut -v /tmpdata/XXX/YYY/TX/V1_Intermediate/Gene_Fusion/fastp:/data -v /tmpdata/Gene_Fusion/GRCh37_v19/GRCh37_gencode_v19_CTAT_lib_Mar012021.plug-n-play:/genome trinityctat/starfusion /usr/local/src/STAR-Fusion/STAR-Fusion --CPU 24 --genome_lib_dir /genome/ctat_genome_lib_build_dir --left_fq /data/1_1_trimmed.fq.gz --right_fq /data/1_2_trimmed.fq.gz --FusionInspector validate --output_dir /home/StarFusionOut
        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job star_fusion since they might be corrupted:
/tmpdata/XXX/YYY/TX/V1_Intermediate/Gene_Fusion/star_fusion/1/star-fusion.fusion_predictions.tsv,/tmpdata/XXX/YYY/TX/V1_Intermediate/Gene_Fusion/star_fusion/1/star-fusion.fusion_predictions.abridged.tsv
Shutting down,this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/ldap/NJEANRAY/Gene_Fusion/.snakemake/log/2021-06-24T150742.518571.snakemake.log

我与 Docker 开发人员讨论过，据他说，执行没有问题（我可以在 de Snakefile 之外运行它这一事实证实了这一点）。相反，Docker 似乎在其执行结束时启动了一条消息，但 Snakemake 对其进行了错误的解释。

这是启动 docker 的 Snakemake 代码：

rule star_fusion:
    input:
        R1=expand(FASTP+'/{{smp}}_1_trimmed.fq.gz',smp=SAMPLES),R2=expand(FASTP+'/{{smp}}_2_trimmed.fq.gz',smp=SAMPLES)
    params:
        data_dir=FASTP,outdir=expand(STAR_FUSION+'/{{smp}}',genome_dir=GENOME_LIB,CPU = 12,R1=expand('{{smp}}_1_trimmed.fq.gz',R2=expand('{{smp}}_2_trimmed.fq.gz',smp=SAMPLES)
    output:
        expand(STAR_FUSION+'/{{smp}}/star-fusion.fusion_predictions.tsv',expand(STAR_FUSION+'/{{smp}}/star-fusion.fusion_predictions.abridged.tsv',smp=SAMPLES)
    message:
        """
        --- Running STAR-Fusion ....
        """
    shell:
        """
        docker run --rm -v {params.outdir}:/home/StarFusionOut -v {params.data_dir}:/data -v {params.genome_dir}:/genome trinityctat/starfusion /usr/local/src/STAR-Fusion/STAR-Fusion --CPU 24 --genome_lib_dir /genome/ctat_genome_lib_build_dir --left_fq /data/{params.R1} --right_fq /data/{params.R2} --FusionInspector validate --output_dir /home/StarFusionOut
        """

你能不能给点建议？