sv failed

[kspham]

Hi Brad/Rory:
Sorry for reporting too many issues, but seems that the sv pipeline failed :(. It goes through
cn.mops well, but raised errors in delly/lumpy
5872 [2014-12-09 11:36] samblaster: split and discordant reads : 3s_merged
5873 [2014-12-09 11:36] samblaster: Version 0.1.20
5874 [2014-12-09 11:36] samblaster: Inputting from stdin
5875 [2014-12-09 11:36] samblaster: Outputting to stdout
5876 [2014-12-09 11:36] samblaster: Opening /dev/fd/62 for write.
5877 [2014-12-09 11:36] samblaster: Opening /dev/fd/63 for write.
5878 [2014-12-09 12:47] [bam_sort_core] merging from 624 files...
5879 [2014-12-09 12:47] [W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
5880 [2014-12-09 12:47] samblaster: Loaded 84 header sequence entries.
5881 [2014-12-09 12:47] samblaster: Can't find first and/or second of pair in sam block of length 1 for id: D2FC08P1:238:C27VVACXX:5:1101:1195:59613
5882 [2014-12-09 12:47] samblaster: Are you sure the input is sorted by read ids?
5883 [2014-12-09 12:47]
5884 [2014-12-09 12:47] samtools: writing to standard output failed: Broken pipe
5885 [2014-12-09 12:47] samtools: error closing standard output: -1
5886 [2014-12-09 12:47] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0122.bam' is truncated. Continue anyway.
5887 [2014-12-09 12:48] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0123.bam' is truncated. Continue anyway.
5888 [2014-12-09 12:48] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0124.bam' is truncated. Continue anyway.
5889 [2014-12-09 12:49] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0126.bam' is truncated. Continue anyway.
5890 [2014-12-09 12:50] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0127.bam' is truncated. Continue anyway.
5891 [2014-12-09 12:50] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0128.bam' is truncated. Continue anyway.
5892 [2014-12-09 12:51] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0129.bam' is truncated. Continue anyway.
5893 [2014-12-09 12:52] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0133.bam' is truncated. Continue anyway.
5894 [2014-12-09 12:54] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0136.bam' is truncated. Continue anyway.
5895 [2014-12-09 12:55] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0139.bam' is truncated. Continue anyway.
5896 [2014-12-09 12:57] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0142.bam' is truncated. Continue anyway.
5897 [2014-12-09 12:57] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0143.bam' is truncated. Continue anyway.
5898 [2014-12-09 12:58] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0144.bam' is truncated. Continue anyway.
5899 [2014-12-09 13:02] [bam_merge_core] '/raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign/3s_merged/3s_merged-ready-namesort.0152.bam' is truncated. Continue anyway.
5900 [2014-12-09 14:56] Uncaught exception occurred
5901 Traceback (most recent call last):
5902 File "/raid/sonpham/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run

[chapmanb]

Son;
Sorry about the problem. This error occurs when trying to re-run samblaster on the prealigned input to identify discordant. It tries to namesort the input BAM file and then feed to samblaster but it looks like something problematic happens during the name sorting. The two things I'd check for are:

• Is the 3s_merged BAM file in /raid/sonpham/schipairs/sv/pair3/workwithoutduplicate/prealign truncated or otherwise problematic?
• Do you have enough disk space?

The best bet to debug would be to look at the samtools sort -n command in log/bcbio-nextgen-commands.log and run this outside of bcbio. Does it work correctly or is it running into errors? Thanks for the help debugging.

[lpantano]

Closing this since It seems it ended working someway.

let us know if we can help further.

thanks!