newbie

[ptoru001]

HI All,

I have just run a sns/wes and a little confused of what to do next....
i am in the folder where i see : samples.fastq-raw.csv sns
logs-sbatch samples.fastq-clean.csv settings.txt summary
FASTQ-CLEAN QC-FastQC,

I believe I added the BED file as a reference, but I am not sure..

How would I be able to retrieve these files for generating reports on these different files?

Thank you and sorry for the trouble.

[igordot]

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

[ptoru001]

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!

[igordot]

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

[ptoru001]

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

[igordot]

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

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

[ptoru001]

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

[igordot]

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.

[ptoru001]

Good Morning Igor, Here are the messages from the log: CMD: sbatch --time=99:00:00 --nodes=1 --ntasks=1 --cpus-per-task=9 --mem=72G --job-name=sns.wes.ptm1__214518 ***@***.*** --mail-type=FAIL,REQUEUE --export=NONE --wrap='bash /gpfs/home/torunp01/new_234518/sns/routes/wes.sh /gpfs/home/torunp01/new_234518 ptm1__214518' Submitted batch job 17754920 CMD: sbatch --time=99:00:00 --nodes=1 --ntasks=1 --cpus-per-task=9 --mem=72G --job-name=sns.wes.ptm1__214518 ***@***.*** --mail-type=FAIL,REQUEUE --export=NONE --wrap='bash /gpfs/home/torunp01/new_234518/sns/routes/wes.sh /gpfs/home/torunp01/new_234518 ptm1__214518' How would I resolve this? Thank you Pedro From: igor ***@***.***> Date: Tuesday, July 5, 2022 at 5:07 PM To: igordot/sns ***@***.***> Cc: Pedro Toruno ***@***.***>, Author ***@***.***> Subject: Re: [igordot/sns] newbie (Issue #7) Note: This message originated from outside the FIU Faculty/Staff email system. 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. — Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APEULTSL2SLI4VZDPT4FGR3VSSP2HANCNFSM52NITOUA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[igordot]

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.

[ptoru001]

I understand How do I “read” that specific log file Get Outlook for iOS<https://aka.ms/o0ukef>

…

________________________________ From: igor ***@***.***> Sent: Wednesday, July 6, 2022 1:22:43 PM To: igordot/sns ***@***.***> Cc: Pedro Toruno ***@***.***>; Author ***@***.***> Subject: Re: [igordot/sns] newbie (Issue #7) Note: This message originated from outside the FIU Faculty/Staff email system. 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. — Reply to this email directly, view it on GitHub<#7 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APEULTV7TRKLWDGP5E77S7DVSW6GHANCNFSM52NITOUA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[igordot]

You can read it like any other file: cat filename

[igordot]

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