yyoshiaki / ikra

RNAseq pipeline centered on Salmon
https://doi.org/10.5281/zenodo.4718200
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docker: Error response from daemon: OCI runtime create failed: container_linux.go:345: starting container process caused "exec: \"fasterq-dump\": executable file not found in $PATH": unknown. #47

Closed ykohki closed 5 years ago

ykohki commented 5 years ago

ikra.shについて、 実行コマンド bash ../ikra/ikra.sh ../ikra/test/Illumina_PE/Illumina_PE_SRR.csv mouse -t 12

*******
+ SRR=SRR7501484
++ echo PID_1,SRR7501484,PE
++ cut -d, -f3
+ LAYOUT=PE
+ '[' PE = SE ']'
+ [[ ! -f SRR7501484_1.fastq.gz ]]
+ [[ '' == '' ]]
+ docker run -u 10011:10018 --rm -v /home/kyamada/ikra_master/run/test/Illumina_PE_SRR:/home -e HOME=/home --workdir /home inutano/sra-toolkit:2.9.0 fasterq-dump SRR7501484 --split-files --threads 12
docker: Error response from daemon: OCI runtime create failed: container_linux.go:345: starting container process caused "exec: \"fasterq-dump\": executable file not found in $PATH": unknown.

のエラーが出て、止まってしまいます。

csvに関しては、テスト用のものも、自作したもの実行した際も同じエラーです。

yyoshiaki commented 5 years ago

fixed #48 #49