Cannot add a path to the input fastq

[qifasong]

I am sorry to disturb you. I have successfully install mitofinder-1.4.2. When I add an exact path before the input fastq file in the command, I get an erro saying the file not existing.

mitofinder_v1.4.2.sif -j mywork -1 ${datapath}/mt1.fq -2 ${datapath}/mt2.fq -r ${refpath}/NC_012920.1.gb -a ${respath}/out.fasta -o 2

However, the file exists. I can testify it by add [ -f $filename ] or cat its content directly by command line.

Many thanks
Qifa Song

[RemiAllio]

Hi,

Can you try running :
singularity run -B ${path_to_your_files_directory}:${path_to_your_files_directory} mitofinder_v1.4.2.sif -j mywork -1 ${datapath}/mt1.fq -2 ${datapath}/mt2.fq -r ${refpath}/NC_012920.1.gb -a ${respath}/out.fasta -o 2

Let me know if it helps!

Best,
Rémi

[qifasong]

Sincerely thank you. I try the following commands:
singularity run -B ~/Downloads/singularity-ce-3.10.1/builddir/mitofinder_v1.4.2.sif -j mywork -1 ${datapath}/mt1.fq -2 ${datapath}/mt2.fq -r ${refpath}/NC_012920.1.gb -a ${respath}/out.fasta -o 2

I get this error:

Error for command "run": unknown shorthand flag: 'j' in -j

[RemiAllio]

Hi,

this part of the command I sent you is missing ${path_to_your_files_directory}:${path_to_your_files_directory}

Can you try :
singularity run -B ${datapath}:${datapath},${respath}:${respath},${refpath}:${refpath} ~/Downloads/singularity-ce-3.10.1/builddir/mitofinder_v1.4.2.sif -j mywork -1 ${datapath}/mt1.fq -2 ${datapath}/mt2.fq -r ${refpath}/NC_012920.1.gb -a ${respath}/out.fasta -o 2

You can also check this singularity tutorial to see how to bind you path when you are using a singularity image.

Sorry for the inconvenience,
Best,
Rémi

[qifasong]

Dear Rémi,
Your instructions work well. My script can find the paths now. Can I specify a different path for
each sample ahead?

Thanks
Qifa song

[RemiAllio]

Hi,

As long as your ${datapath} ${respath} ${refpath} variables are updated for each sample, everything should be okay.

Best,
Rémi