cufflinks works, cuffcompare works. problem is with cuffdiff. entire pipeline is tophat/cufflinks. i've tried my reference gtf, the combined gtf, regenerating the sam files, my own local executable, our system level executable (both v0.8.1).
version: cufflinks-0.8.1
gdb says the segfault occurs on line 174 of gff.cpp:
cmd:
sample from combined.gtf:
sample from vee.sam:
sample from cee.sam:
version: cufflinks-0.8.1
gdb says the segfault occurs on line 174 of gff.cpp:
Code:
173. GffLine::GffLine(GffReader* reader, const char* l) { 174. line=Gstrdup(l);
Code:
~/cufflinks-0.8.1/src/cuffdiff combined.gtf inputs/vee.sam inputs/cee.sam
Code:
chromosome_10 Cufflinks exon 21426 21528 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "CUFF.30735.0"; class_code "u"; chromosome_10 Cufflinks exon 21441 21826 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00007198"; exon_number "1"; oId "CUFF.28869.0"; class_code "u"; chromosome_10 Cufflinks exon 21581 21866 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.30738.0"; class_code "u"; tss_id "TSS1"; chromosome_10 Cufflinks exon 22318 22417 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "2"; oId "CUFF.30738.0"; class_code "u"; tss_id "TSS1"; chromosome_10 Cufflinks exon 22572 22791 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "3"; oId "CUFF.30738.0"; class_code "u"; tss_id "TSS1"; chromosome_10 Cufflinks exon 22349 22395 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00007199"; exon_number "1"; oId "CUFF.28872.0"; class_code "u"; chromosome_10 Cufflinks exon 22755 22853 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00007200"; exon_number "1"; oId "CUFF.28875.0"; class_code "u"; chromosome_10 Cufflinks exon 30444 30520 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.30777.0"; nearest_ref "c10_t4.0"; class_code "c"; chromosome_10 Cufflinks exon 30576 30642 . + . gene_id "XLOC_000002"; transcript_id "TCONS_00000004"; exon_number "1"; oId "CUFF.30780.0"; class_code ".";
Code:
HWI-EAS440_0001_1_101_1060_262 16 chromosome_1 202 1 36M * 0 0 AGAGTCGAACTGGCCACTAAGCCACACGCATACACA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_1_9_922_1813 0 chromosome_1 249 1 36M * 0 0 CGGCCGCCTAAGTAAGGGCACATGCATGCTGTTGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 HWI-EAS440_0001_1_104_318_312 0 chromosome_1 485 1 36M * 0 0 TGGGCAGTGACAAATCTTAGCAACACGGGATGAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 HWI-EAS440_0001_1_102_1682_1855 0 chromosome_1 493 1 36M * 0 0 GACAAATCTTAGCAACACGGGATGAATCTCAGTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_1_116_1293_882 0 chromosome_1 493 1 36M * 0 0 TACAAATCTTAGCAACACGGGATGAATCTCAGTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 HWI-EAS440_0001_1_39_238_1487 0 chromosome_1 493 1 36M * 0 0 CACAAATCTTAGCAACACGGGATGAATCTCAGTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 HWI-EAS440_0001_1_93_1308_1823 0 chromosome_1 496 1 36M * 0 0 AAATCTTAGCAACACGGGATGAATCTCAGTGGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_1_6_1247_1568 0 chromosome_1 501 1 36M * 0 0 TTAGCAACACGGGATGAATCTCAGTGGATCGTAGCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_1_5_1558_914 0 chromosome_1 502 1 36M * 0 0 TAGCAACACGGGATGAATCTCAGTGGATCGTAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_1_7_1756_389 0 chromosome_1 505 1 36M * 0 0 CAACACGGGATGAATCTCAGTGGATCGTAGCAGCAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0
Code:
HWI-EAS440_0001_2_27_801_1517 16 chromosome_1 17 1 36M * 0 0 CCCAATCCTGAAAAGCGATTTCCACATACATAAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_2_98_465_797 16 chromosome_1 203 1 36M * 0 0 GAGTCGAACTGGCCACTAAGCCACACGCATACACAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_2_98_338_972 0 chromosome_1 493 1 36M * 0 0 GACAAATCTTAGCAACACGGGATGAATCTCAGTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_2_2_857_1311 0 chromosome_1 495 1 36M * 0 0 CAAATCTTAGCAACACGGGATGAATCTCAGTGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_2_119_633_903 0 chromosome_1 496 1 36M * 0 0 AAATCTTAGCAACACGGGATGAATCTCAGTGGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_2_30_1193_818 0 chromosome_1 496 1 36M * 0 0 AAATCTTAGCAACACGGGATGAATCTCAGTGGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_2_91_1490_372 0 chromosome_1 497 1 36M * 0 0 AATCTTAGCAACACGGGATGAATCTCAGTGGATCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_2_10_1482_383 16 chromosome_1 499 1 36M * 0 0 TCGTAGCAACACGGGATGAATCTCAGTGGATCGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 HWI-EAS440_0001_2_111_1039_52 0 chromosome_1 499 1 36M * 0 0 TCTTAGCAACACGGGATGAATCTCAGTGGATCGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 HWI-EAS440_0001_2_17_484_1454 0 chromosome_1 499 1 36M * 0 0 TCTTAGCAACACGGGATGAATCTCAGTGGATCGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0