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denglab / SeqSero2

SeqSero2
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No such file or directory #34

Closed Chris091089 closed 3 years ago

Chris091089 commented 3 years ago

Good afternoon and I tried to run seqsero2 from a docker container, however it appears that my fastq file does not exist and I have them in that folder.

the command used is docker run seqsero2 SeqSero2_package.py -p 10 -t 1 -i BB30 *

I hope you can help me.

docker run seqsero2 SeqSero2_package.py -p 10 -t 1 -i BB30* gzip: BB30_S1_R1.fastq.gz: No such file or directory

LSTUGA commented 3 years ago

May I ask whcih docker image for seqsero2 you are using?

Here is something you can try. Use -v flag to mount your local folder to the docker container. Just replace "YOUR_LOCAL_FOLDER" in the command below with the path to your data. docker run -v /YOUR_LOCAL_FOLDER:/data seqsero2 SeqSero2_package.py -p 10 -t 2 -i BB30_S1_R1.fastq.gz BB30_S1_R2.fastq.gz

BTW, if you have paired-end reads, I would suggest using the "-t 2" option.

Chris091089 commented 3 years ago

Thank you very much for the help I have solved my problem.