newbie about sns HOT 12 CLOSED

It looks like you already started running the pipeline. Is it still running? If it stopped, did you check for errors?

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thanks for your reply!...i am assuming its still running but i checked and ls into the logs-sbatch and this is what it shows..
[torunp01@bigpurple-ln1 logs-sbatch]$ ls
slurm-17662022.out slurm-17662064.out

Does that mean its still running, or its done?

Thank you again!

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Please check the usage page on how to check if it's running and how to check for errors.

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Hi Igor,

There are no issues with the WES bring run right now...how do i retrieve the files from the remote servers on to my local desktop?

Thanks
Pedro

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These are some graphical FTP/SSH clients you can try:

• CyberDuck (multi-platform)
• Fetch (macOS)
• FileZilla (multi-platform)
• WinSCP (Windows)

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Hello this is the error message i get:

Slurm Job_id=17754920 Name=sns.wes.ptm1__214518 Failed, Run time 00:31:08, FAILED, ExitCode 1

there is nothing more in the email notification...and below is the error message i got after checking for errors after the notification i got via email

[torunp01@bigpurple-ln1 new_234518]$ grep "ERROR:" logs-sbatch/*
fastq-clean.sh ERROR: FASTQ R1 AND R2 HAVE DIFFERENT NUMBER OF READS
wes.sh ERROR: SEGMENT fastq-clean DID NOT FINISH

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Right. That tells you that there was an error. In the logs-sbatch directory, there is a log file corresponding to job 17754920. That will have more info.

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from sns.

That is not from a log file. I am referring to the logs in the logs-sbatch directory. There should be one named slurm-17754920.out.

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You can read it like any other file: cat filename

from sns.

I think some of the later comments here are actually referring to a more recent issue: #8

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