#34 SamAlignmentExtractor

v1.0_(example)
closed
nobody
None
1
2014-06-04
2014-06-03
No

Receiving an "unexpected end of file" error during downstream processing of .sam files created with SamAlignmentExtractor. Files GNomEx>A1662>Files>MergedBams

m005847:~ pete$ nohup java -Xmx6G -jar /usr/local/Apps/SamAlignmentExtractor -a ~/Desktop/TopHat/A1662/GV_A.bam -b ~/Desktop/rmsk.bed &

m005847:~ pete$ gzcat ~/Desktop/rmsk.sam.gz | tail -2

gzip: /Volumes/MacHome/pete/Desktop/rmsk.sam.gz: unexpected end of file
HWI-ST179R:412:D1YHYACXX:1:2104:18830:68810 89 chrUn_gl000220 95724 50 4M1I11M22245N85M * 0 0 ACAGCATTTGGTGTATGTGCTTGGCTGAGGAGCCAATGGGGCGAAGCTACCATCTGTGGGATTATGACTGAACGCCTCTAAGTCAGAATCCCGCCCAGGCG @CCCCDB?DCACA>A<C??A<2C:>>?CDDCDCCCCBB;;DBCACCC@@DDCCDDDCECCCCCFEDBFDFEBE?GHCGDIIHFGGHIIHFFHHDDDFF@@@ MD:Z:3C96 XG:i:1 NH:i:1 NM:i:2 XM:i:1 XO:i:1 AS:i:-1XS:A:-
HWI-ST179R:412:D1YHYACXX:1:2107:10518:7712m005847:~ pete$

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Discussion

  • David Nix
    David Nix
    2014-06-04

    Looks like you've run out of memory. See the error message at the end of the nohup.out file. Try, -Xmx20G

     
  • David Nix
    David Nix
    2014-06-04

    • status: open --> closed