Re: [galaxy-dev] Join version 1.0.0 error

2012-10-31 Thread Scooter Willis 
Did a subtract first to get a known list of rs SNPs that will be found in the 
tumor SNPs. That ran without error. Doing a join of the subtracted list of rs 
SNPs and the tumor SNPs.

So something different in the join code then in the subtract code.

From: Scooter Willis mailto:hwil...@scripps.edu>>
Date: Wednesday, October 31, 2012 5:42 PM
To: "galaxy-dev@lists.bx.psu.edu" 
mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Join version 1.0.0 error

Using large amazon instance

Trying to do an interval join of SNPs as output from pileup 120,000 
regions(5.5Mb) with with snp135Common 12,000,000(425Mb) and get the following 
errors. The goal is to pickup rs id's for known SNPs in the list of SNPs.

Is this a memory issue?

I was able to do the operation against chr1 as a test. Thought about chaining 
the outputs and doing against a file for each chromosome to make smaller files 
but then I have a mess where rs id's are in different columns.

71: Join on data 38 and data 36
0 bytes
An error occurred running this job: 
/opt/sge/default/spool/execd/ip-10-191-53-90/job_scripts/14: line 13: 5517 
Killed python /mnt/galaxyTools/galaxy-central/tools/new_operations/gops_join.py 
/mnt/galaxyData/files/000/dataset_75.dat 
/mnt/galaxyData/files/000/dataset_77.dat
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[galaxy-dev] Join version 1.0.0 error

2012-10-31 Thread Scooter Willis 
Using large amazon instance

Trying to do an interval join of SNPs as output from pileup 120,000 
regions(5.5Mb) with with snp135Common 12,000,000(425Mb) and get the following 
errors. The goal is to pickup rs id's for known SNPs in the list of SNPs.

Is this a memory issue?

I was able to do the operation against chr1 as a test. Thought about chaining 
the outputs and doing against a file for each chromosome to make smaller files 
but then I have a mess where rs id's are in different columns.

71: Join on data 38 and data 36
0 bytes
An error occurred running this job: 
/opt/sge/default/spool/execd/ip-10-191-53-90/job_scripts/14: line 13: 5517 
Killed python /mnt/galaxyTools/galaxy-central/tools/new_operations/gops_join.py 
/mnt/galaxyData/files/000/dataset_75.dat 
/mnt/galaxyData/files/000/dataset_77.dat
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