Error! cannot open file for writing

[lindsaynhayes]

I am getting the above error message when I run genrich in ATAC mode and try to write log or bed files using -f, -k, and -b. I am running for 6 replicates. I initially tried:

${gen_path}/./Genrich -t ${in_path}/S22.query.bam,${in_path}/S33.query.bam,${in_path}/S36.query.bam,${in_path}/S39.query.bam,${in_path}/S45.query.bam,${in_path}/S54.query.bam -o {out_path}/CON.P4.narrowPeak -v -j -e chrM -f {out_path}/CON.bed -k {out_path}/CON.pileup.bed

but got that Error! {out_path}/CON.pileup.bed: cannot open file for writing so I thought since I had replicates maybe the -f was causing problems so I removed it, but got the same error message.

Then I changed the filename to -k {out_path}/CON.log but got same error message.

Finally, I tried -b {out_path}/CON.bed but still got the same error message.

Do I need to specify a temporary file location to write these output files on slurm? Is there a -tmp command available?

Thanks for your advice! Lindsay

[jsh58]

Lindsay,

Thanks for the question. I think there are two possibilities:

• {out_path} does not exist
• you do not have write permission to {out_path}

Also, Genrich does not write any temporary files.

[lindsaynhayes]

I specified the output path. It works when I run one sample, but when I run all 6 then I get the error. Maybe I need to request more memory when I run the job I will try that. Thanks for your help.

[jsh58]

Sorry, that's ${out_path}. You were missing $.

[lindsaynhayes]

ahhh.. that's a stupid mistake. thanks!

Lindsay