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View Code? Open in Web Editor NEWSTORMSeq: Scalable Tools for Open-source Read Mapping
Home Page: stormseq.org
License: Other
STORMSeq: Scalable Tools for Open-source Read Mapping
Home Page: stormseq.org
License: Other
Searching US East (N. Virginia) for stormseq on Request Instances Wizard returns "Response contains invalid JSON"
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
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.
Looking forward to having your answer and thank you in advance.
Thanks & Regards,
Jaehoon, Jang
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