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Sruthi S

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Jan 14, 2022, 11:50:50 AMJan 14
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Hi sir,
I was working with the .fq.gz file and aligner module HISAT2. But I got an error after that with an empty SAM file. Can you please look into it?

Thank you,
Sruthi S



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Barbara Hill

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Jan 14, 2022, 12:56:36 PMJan 14
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Hello Sruthi, 

Please send your job id, so that we may look into the details of this issue.

Best
-Barbara

Sruthi S

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Jan 14, 2022, 1:21:10 PMJan 14
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Hi Mam,
this is the link. 

And also, I recently uploaded .fq file into the files tab, but I am not sure how to select that and work from there.

Thank You,
SruthiS




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Sruthi S

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Jan 14, 2022, 1:32:07 PMJan 14
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Hi mam,
I had uploaded a fq file in the genepattern and run using HISAT2 aligner. But they are saying that it is the expected file format.
I have attached the screenshot for your reference.

Kindly check
Sruthi S



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Barbara Hill

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Jan 14, 2022, 3:00:25 PMJan 14
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Hi Sruthi,

The file format is fine. The issue is that your job ran out of memory. If you click on the stderr.txt file you will see this error.

Reload the job, then scroll to the bottom of the job submit form, expand the Job Options, and increase the memory requested. I would suggest starting with 4 or 8GB - if you request more you will wait longer for your job to run, as there are more small memory hosts than large.

Please let us know if that resolves the issue.

Best
-Barbara

Sruthi S

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Jan 14, 2022, 3:06:58 PMJan 14
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Ok mam, thank you. Can you please tell me how to make a cls file, like they are asking samples, define sample and assign class?

Thank you,
Sruthi S



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Barbara Hill

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Jan 14, 2022, 3:08:16 PMJan 14
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Hi Sruthi,

Please see the file formats guide for more information:
https://genepattern.org/file-formats-guide#CLS

Best
-Barbara

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