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stormseq's Issues

Stormseq GUI stops responding

Hello,

I tested StormSeq whole genome alignment using the NA12878 exome from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20120117_ceu_trio_b37_decoy/CEUTrio.HiSeq.WEx.b37_decoy.NA12878.clean.dedup.recal.20120117.bam

on spot instances based on the m1.large. The next day after I started, the GUI appeared blank as if I had never started the test, but the machines were still running. I left it going over the weekend for a total of at least 4 days but never saw any results or any indication in the browser that it was doing anything although there were always around 12 machines running. I finally terminated. Do you have any idea what happened?

Thanks,
Steve

Stormseq test got stuck on setup phase.

To whom it may concerned.

Hi, I am currently testing stormseq with my samples.
However, I got stuck on the page of stormseq with serveral errors.
The error comment is like below.
Case 1. There was an error : file-fail not found.
Case 2. There was an error : qc-fail Malformed paired end file. (read name should have /1 or /2 tag)

Let me tell you about my env. First.
I am trying to test my 2 files(3.7GB each) which are one sample’s paired end seq. result.
The data type I tried is illumina truseq and File extension is XXX_R1.fastq.gz / XXX_R2.fastq.gz. (except that, every options are as default (BWA, GATK Lite, etc)
So technically, the number of genome is one (2 files though). So I checked [One] in test page and got the error case 1 above. (Of course the sample is in root position in my bucket)
Then tried [Multiple] with files in same folder as the page guided but got the error case 2. (as far as I know, My sample have tags in the head)
In this stage, I cannot proceed the test any more so I need your help.
Here is my question below.

  1. I need to know the exact meaning of the option [One / Multiple] and What I should checked in my case (again, one samples paired end seq. 2 files as result)
  2. Is there any additional format or requirements for the .fastq file? If so, Please let me know about it.

Looking forward to having your answer and thank you in advance.

Thanks & Regards,
Jaehoon, Jang

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