What steps will reproduce the problem?
1. Running on one of my pairs of fastq files always seems to crash in the same
place
2.
3.
What is the expected output? What do you see instead?
I assume it is crashing, but I dont know why. Other samples succeeded using
the same configuration. There is no more information other than the output ends
with:
2013-10-01 12:16:09,037 - root - INFO - Extracting single-mapped reads that may
span breakpoints
2013-10-01 12:16:09,039 - root - DEBUG - Matching single-mapped frags to 5'
chimeras
What version of the product are you using? On what operating system?
chimerascan-0.4.3-1
on Gnu Linux
Please provide any additional information below.
Contents of my tmp directory
3.7G Sep 27 19:28 reads_2.fq
3.7G Sep 27 19:29 reads_1.fq
602M Sep 27 21:07 unaligned_1.fq
602M Sep 27 21:07 unaligned_2.fq
143K Sep 27 21:07 maxmulti_1.fq
143K Sep 27 21:07 maxmulti_2.fq
1.3G Sep 28 00:09 realigned_reads.bam
749M Sep 28 03:52 gene_paired_reads.bam
522M Sep 28 03:52 genome_paired_reads.bam
262M Sep 28 03:52 unmapped_reads.bam
885K Sep 28 03:52 complex_reads.bam
92M Sep 28 03:55 discordant_reads.bedpe
92M Sep 28 03:56 discordant_reads.srt.bedpe
5.4G Sep 28 05:18 encompassing_chimeras.txt
1.9G Sep 28 05:34 encompassing_chimeras.filtered.txt
1.9G Sep 28 05:41 encompassing_chimeras.breakpoint_sorted.txt
58M Sep 28 05:47 breakpoints.fa
61M Sep 28 05:48 breakpoints.txt
14M Sep 28 05:48 breakpoints.4.ebwt
2.5M Sep 28 05:48 breakpoints.3.ebwt
27M Sep 28 05:49 breakpoints.1.ebwt
6.8M Sep 28 05:49 breakpoints.2.ebwt
27M Sep 28 05:52 breakpoints.rev.1.ebwt
6.8M Sep 28 05:52 breakpoints.rev.2.ebwt
718K Sep 28 05:56 encomp_spanning_reads.fq
58M Sep 28 06:01 unaligned_spanning_reads.fq
410M Sep 28 06:08 singlemap_reads.srt.bam
4.3M Sep 28 06:08 singlemap_reads.srt.bam.bai
0 Oct 1 14:42 tmp_singlemap_seqs.txt
Original issue reported on code.google.com by rachel.m...@gmail.com on 1 Oct 2013 at 7:00
Original issue reported on code.google.com by
rachel.m...@gmail.comon 1 Oct 2013 at 7:00