Docker 无法找到文件,即使给出了正确的路径
Docker unable to locate file, even with correct path given
我是运行长docker命令
docker exec -t -i 9f5865473027 cloudgene run imputationserver@1.4.1 --files /illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz --refpanel apps@1000g-phase-3-v5@2.0.0 --conf /etc/hadoop/conf --population AFR --mode qconly --output /illumina/runs/con/chrX_impute
但这会出错
Error: Input Files (<a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41" target="_blank">VCF</a>): file '/illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz' not found.
为什么 docker 找不到指定了绝对路径(即使是相对路径)的文件?我怎样才能docker找到这个文件?
即使我这样做
docker exec -it 9f5865473027 ls /illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz
我仍然得到 ls: cannot access /illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz: No such file or directory
当我执行 docker exec -it 9f5865473027 ls .
时,它似乎在 /
或绝对顶级目录中,但使用此信息并输入没有 /
的文件名,因此 docker exec -it 9f5865473027 ls illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz
Docker 仍然找不到文件:(
我可以通过 docker 的 ls
看到更高的目录,但是我所在的目录 docker exec -it 9f5865473027 ls illumina/runs/con/chrX_impute
神秘地显示为空(实际上不是)
这个问题的解决方法是复制文件到容器中。每个“容器”似乎就像一台独立的计算机。
我所要做的就是
docker cp ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz 9f5865473027:/illumina/runs/con/chrX_impute/
然后文件显示为
docker exec -it 9f5865473027 ls illumina/runs/con/chrX_impute
ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz
我是运行长docker命令
docker exec -t -i 9f5865473027 cloudgene run imputationserver@1.4.1 --files /illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz --refpanel apps@1000g-phase-3-v5@2.0.0 --conf /etc/hadoop/conf --population AFR --mode qconly --output /illumina/runs/con/chrX_impute
但这会出错
Error: Input Files (<a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41" target="_blank">VCF</a>): file '/illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz' not found.
为什么 docker 找不到指定了绝对路径(即使是相对路径)的文件?我怎样才能docker找到这个文件?
即使我这样做
docker exec -it 9f5865473027 ls /illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz
我仍然得到 ls: cannot access /illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz: No such file or directory
当我执行 docker exec -it 9f5865473027 ls .
时,它似乎在 /
或绝对顶级目录中,但使用此信息并输入没有 /
的文件名,因此 docker exec -it 9f5865473027 ls illumina/runs/con/chrX_impute/ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz
Docker 仍然找不到文件:(
我可以通过 docker 的 ls
看到更高的目录,但是我所在的目录 docker exec -it 9f5865473027 ls illumina/runs/con/chrX_impute
神秘地显示为空(实际上不是)
这个问题的解决方法是复制文件到容器中。每个“容器”似乎就像一台独立的计算机。
我所要做的就是
docker cp ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz 9f5865473027:/illumina/runs/con/chrX_impute/
然后文件显示为
docker exec -it 9f5865473027 ls illumina/runs/con/chrX_impute
ALL.chrX.PAR2.phase3_v5.shapeit2_mvncall_integrated.noSingleton.genotypes.vcf.gz