重测序

重测序分析的是并行任务运行怎么出错?命令是nohup ParaFly -c  work285.sh -CPU 8 > work285.sh-4.o& , 而不用并行命令 直接运行nohup sh work285.sh >work285-3.sh.o& 这个命令就不报错,这是怎么回事?


sh: -I: command not found

warning, cmd:     -I $workdir/3.map/result/${i}.sorted.dedup.bam \ failed with ret: 32512, going to retry.

sh: -c: line 0: unexpected EOF while looking for matching `"'

sh: -c: line 1: syntax error: unexpected end of file

sh: -O: command not found

warning, cmd: sh: -c: line 1: syntax error: unexpected end of file

warning, cmd:   echo "RUN CMD: gatk --java-options '-Xmx100g' HaplotypeCaller -R $REF   \ failed with ret: 256, going to retry.

    -O ${i}.g.vcf.gz --max-alternate-alleles 4  --sample-ploidy 2 \ failed with ret: 32512, going to retry.

warning, cmd: for i in $(cat $workdir/data/data.txt); do failed with ret: 256, going to retry.

sh: -I: command not found

sh: -c: line 0: unexpected EOF while looking for matching `"'

sh: -c: line 1: syntax error: unexpected end of file

warning, cmd:     -I $workdir/3.map/result/${i}.sorted.dedup.bam \ failed with ret: 32512, going to retry.

warning, cmd:     -ERC GVCF --tmp-dir $tmpdir" failed with ret: 256, going to retry.

sh: -O: command not found

warning, cmd:     -O ${i}.g.vcf.gz --max-alternate-alleles 4  --sample-ploidy 2 \ failed with ret: 32512, going to retry.

Using GATK jar /share/work/biosoft/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar

Running:

    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx100g -jar /share/work/biosoft/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar HaplotypeCaller -R

USAGE: HaplotypeCaller [arguments]

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1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

ParaFly 这个命令要求sh文件里面一行是一个任务,不必要的注释换行符变量等需要删掉;

建议吧命令用for循环结合echo打印出来,手动编辑命令的sh文件再批量运行:

可以学习学习Linux基础:https://www.omicsclass.com/article/1006


实在不会就所有的输入输出文件用绝对路径,手动编辑命令文件;

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