CHIMERASCAN 0.4.5 runs for hours then gets killed by my system

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What steps will reproduce the problem?
1. #CHIMERASCAN-0.4.5 setup
export 
PYTHONPATH=/shared/app/chimerascan-0.4.5/lib64/python2.6/site-packages:$PYTHONPA
TH
export PATH=/shared/app/chimerascan-0.4.5/chimerascan/:$PATH
python /shared/app/chimerascan-0.4.5/chimerascan/chimerascan_run.py -p 8 
/shared/app/BOWTIE/indexes/CHIMERASCAN_INDEXES $a1 $a2 
/home/hazards/Project_DW/Sample_99/Nov14_CHIMERASCAN_OUT
2. $a1 $a2  are variables referring to specific read pair fastq files
3. I am running the program on human lung derived RNASeq fastq generated by an 
Illumina sequencer

What is the expected output? What do you see instead?
chimeras.bedpe was expected

Here's what I see:
.
.
.
2013-11-15 09:18:55,808 - root - WARNING - Could not extract sequence of length 
>101 from 3' partner at gene_uc002ect.2:0-101, only retrieved sequence of 
length 94
2013-11-15 09:18:56,438 - root - WARNING - Could not extract sequence of length 
>101 from 3' partner at gene_uc010vft.1:0-101, only retrieved sequence of 
length 90
2013-11-15 09:18:56,771 - root - WARNING - Could not extract sequence of length 
>101 from 5' partner at gene_uc011mtj.1:0-96, only retrieved sequence of length 
96
2013-11-15 09:19:06,915 - root - WARNING - Could not extract sequence of length 
>101 from 3' partner at gene_uc010zpm.1:1741-1842, only retrieved sequence of 
length 99
2013-11-15 09:19:09,269 - root - INFO - Filtering encompassing chimeras with 
few supporting reads
2013-11-15 09:57:34,874 - root - INFO - Extracting breakpoint sequences from 
chimeras
2013-11-15 10:16:30,598 - root - INFO - Building bowtie index of breakpoint 
spanning sequences
2013-11-15 10:35:32,445 - root - INFO - Extracting encompassing reads that may 
extend past breakpoints
2013-11-15 10:51:26,686 - root - INFO - Separating unmapped and single-mapping 
reads that may span breakpoints
2013-11-15 11:05:38,719 - root - INFO - Extracting single-mapped reads that may 
span breakpoints
/home/hazards/.lsbatch/1384447987.22825.shell: line 42: 10199 Killed            
      python /shared/app/chimerascan-0.4.5/chimerascan/chimerascan_run.py -p 8 
/shared/app/BOWTIE/indexes/CHIMERASCAN_INDEXES 

What version of the product are you using? On what operating system?
Chimerscan 0.4.5
Bowtie 1.0.0
Python 2.6.6
RHEL 6.2 Linux 
LSF 7.2


Please provide any additional information below.
The log files suggest that the initial runs complete through

isize_dist.txt, breakpoint_bowtie_index.log, and tmp_singlemap_seqs.txt

-rw-r--r-- 1 hazards hazards       1446 Nov 15 07:23 runconfig.xml
-rw-r--r-- 1 hazards hazards 5449339058 Nov 15 09:33 aligned_reads.bam
-rw-r--r-- 1 hazards hazards 7386269125 Nov 15 10:45 sorted_aligned_reads.bam
-rw-r--r-- 1 hazards hazards    9578704 Nov 15 10:48 
sorted_aligned_reads.bam.bai
-rw-r--r-- 1 hazards hazards       6613 Nov 15 10:48 isize_dist.txt
drwxr-xr-x 2 hazards hazards        104 Nov 16 20:22 log
drwxr-xr-x 2 hazards hazards       8192 Nov 16 21:38 tmp


Sample_86/Nov14_CHIMERASCAN_OUT/log:
total 24
-rw-r--r-- 1 hazards hazards   465 Nov 15 09:33 bowtie_alignment.log
-rw-r--r-- 1 hazards hazards   457 Nov 15 15:07 bowtie_trimmed_realignment.log
-rw-r--r-- 1 hazards hazards 12663 Nov 16 20:53 breakpoint_bowtie_index.log

Sample_86/Nov14_CHIMERASCAN_OUT/tmp:
total 110869964
-rw-r--r-- 1 hazards hazards  5797564944 Nov 15 08:03 reads_2.fq
-rw-r--r-- 1 hazards hazards  5797564944 Nov 15 08:03 reads_1.fq
-rw-r--r-- 1 hazards hazards  1792743679 Nov 15 09:32 unaligned_1.fq
-rw-r--r-- 1 hazards hazards  1792743679 Nov 15 09:32 unaligned_2.fq
-rw-r--r-- 1 hazards hazards      193024 Nov 15 09:32 maxmulti_1.fq
-rw-r--r-- 1 hazards hazards      193024 Nov 15 09:32 maxmulti_2.fq
-rw-r--r-- 1 hazards hazards  4876081081 Nov 15 15:07 realigned_reads.bam
-rw-r--r-- 1 hazards hazards  3120178382 Nov 15 23:38 gene_paired_reads.bam
-rw-r--r-- 1 hazards hazards  2072258813 Nov 15 23:38 genome_paired_reads.bam
-rw-r--r-- 1 hazards hazards   635025773 Nov 15 23:38 unmapped_reads.bam
-rw-r--r-- 1 hazards hazards      934624 Nov 15 23:38 complex_reads.bam
-rw-r--r-- 1 hazards hazards   295327399 Nov 15 23:45 discordant_reads.bedpe
-rw-r--r-- 1 hazards hazards   295327399 Nov 15 23:45 discordant_reads.srt.bedpe
-rw-r--r-- 1 hazards hazards 49046649769 Nov 16 17:34 encompassing_chimeras.txt
-rw-r--r-- 1 hazards hazards 17552465613 Nov 16 19:26 
encompassing_chimeras.filtered.txt
-rw-r--r-- 1 hazards hazards 17552465613 Nov 16 19:47 
encompassing_chimeras.breakpoint_sorted.txt
-rw-r--r-- 1 hazards hazards   603862877 Nov 16 20:22 breakpoints.fa
-rw-r--r-- 1 hazards hazards   652818329 Nov 16 20:22 breakpoints.txt
-rw-r--r-- 1 hazards hazards   140401371 Nov 16 20:23 breakpoints.4.ebwt
-rw-r--r-- 1 hazards hazards    25023302 Nov 16 20:23 breakpoints.3.ebwt
-rw-r--r-- 1 hazards hazards   234699054 Nov 16 20:39 breakpoints.1.ebwt
-rw-r--r-- 1 hazards hazards    70200692 Nov 16 20:39 breakpoints.2.ebwt
-rw-r--r-- 1 hazards hazards   234699054 Nov 16 20:53 breakpoints.rev.1.ebwt
-rw-r--r-- 1 hazards hazards    70200692 Nov 16 20:53 breakpoints.rev.2.ebwt
-rw-r--r-- 1 hazards hazards     3878595 Nov 16 21:27 encomp_spanning_reads.fq
-rw-r--r-- 1 hazards hazards   212324326 Nov 16 21:32 
unaligned_spanning_reads.fq
-rw-r--r-- 1 hazards hazards   649644709 Nov 16 21:38 singlemap_reads.srt.bam
-rw-r--r-- 1 hazards hazards     5238976 Nov 16 21:38 
singlemap_reads.srt.bam.bai
-rw-r--r-- 1 hazards hazards           0 Nov 16 21:38 tmp_singlemap_seqs.txt

I run the program on a local research cluster whose nodes have either 16Mb ram 
or 24Gb ram. restricting to the 24Gb ram machines has no effect. ie the program 
still runs and gets killed. I would assume that there is a size limitation but 
the some files as large as 5-7 Gb have completed while others fail as 
described. Re-running the jobs that fail repeats the failure. 

Original issue reported on code.google.com by [email protected] on 18 Nov 2013 at 9:59

[GoogleCodeExporter]

Hello,

I have the same issue. 

Could you help us? 

Best,
Luciano

Original comment by [email protected] on 21 Nov 2013 at 7:03

[GoogleCodeExporter]

Hello guys,

It seems chimerascan runs out of memory and for this reason the OS kills it. 

Bye,
Luciano

Original comment by [email protected] on 5 Dec 2013 at 10:51

[GoogleCodeExporter]

Hello,
is it solved?

Original comment by [email protected] on 31 Jul 2014 at 5:45

[GoogleCodeExporter]

I haven't tried it since then. Is it reported to be fixed now? If so, I would 
give it a try again.

Shweta 

Original comment by [email protected] on 31 Jul 2014 at 8:11

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

Hi, developers,

I met same problem as described above. The process got killed. How to solve 
this issue?? Thanks!

Ping

Original comment by [email protected] on 14 Dec 2014 at 2:58