Cannot get to my files

[KowalskiBio]

Hello, I am starting to use your program and I cannot get it to work. The directory is correct, when I go there via cd command and check content via ls, it writes my fastq files (SRRnumber_1/2.fastq.gz. So I know they are there. What am I missing? Thanks for reply

cp: cannot stat '/auto/kowalski/fastq/SRR8750770_R1.f*q.gz': No such file or directory [Fri Jul 26 19:04:19 2024] Error in rule getReads: jobid: 0 output: data/output/test2/reads/SRR8750770_forward.fastq.gz, data/output/test2/reads/SRR8750770_reverse.fastq.gz

RuleException: CalledProcessError in line 24 of /auto/brno2/home/kowalski/RASflow/workflow/qualitycontrol.rules: Command ' set -euo pipefail; scp -i None auto/kowalski/fastq/SRR8750770R1.f*q.gz data/output/test2/reads/SRR8750770_forward.fastq.gz ' returned non-zero exit status 1. File "/auto/kowalski/RASflow/workflow/quality_control.rules", line 24, in __rule_getReads File "/storage/kowalski/miniconda3/envs/rasflow/lib/python3.6/concurrent/futures/thread.py", line 56, in run Exiting because a job execution failed. Look above for error message

My metadata file: sample group subject SRR27494859 accumbens Hancock SRR27494858 accumbens Hancock SRR27494754 dlpc Hancock SRR27494755 dlpc Hancock SRR8750749 caudate Khrameeva SRR8750750 caudate Khrameeva SRR8750751 caudate Khrameeva SRR8750752 caudate Khrameeva SRR8750753 accumbens Khrameeva SRR8750754 accumbens Khrameeva SRR8750755 accumbens Khrameeva SRR8750756 accumbens Khrameeva SRR8750769 putamen Khrameeva SRR8750770 putamen Khrameeva SRR8750771 putamen Khrameeva SRR8750772 putamen Khrameeva SRR8750785 globusp Khrameeva SRR8750786 globusp Khrameeva SRR8750787 globusp Khrameeva SRR8750788 globusp Khrameeva SRR8750797 ec Khrameeva SRR8750798 ec Khrameeva SRR8750799 ec Khrameeva SRR8750800 ec Khrameeva SRR25755687 striatum Swchwamborn SRR25755688 midbrain Swchwamborn

[KowalskiBio]

I should add that I tried to run the example and It worked just fine.

[zhxiaokang]

Could you ls your directory so that I can see the exact file names. As you wrote 'SRRnumber_1/2.fastq.gz' and there isn't "R" before '1/2', but the rule actually looks for 'R' as states "/auto/kowalski/fastq/SRR8750770_R1.f*q.gz"

[KowalskiBio]

I am very sorry, the cause of error was rather hidden and on my side. My security keys were not working properly, therefore I couldn't use scp -i. When I changed it to cp and deleted the key portion, it started working. I have another question, but my former question was resolved. I should add that I had to edit the script and remove the R in "_R1" and "_R2", because all of my files are without the R, but that was fast and simple. Thanks for your help!

[zhxiaokang]

Yes, the script needs to be edited accordingly to match the real file names' format. Glad to hear that it now works for you!