pkerpedjiev / bwa-pssm Goto Github PK

Hi, I've been trying to run bwa-pssm on a set of artificially generated reads but the following pair causes a seg fault:

==> debug2_s1.fq <==
@r26223_from_NC_000913_h10_ids100-h0 ln302#0/1
ACCGGCGGCTTCGCGGTGGAACGTCTGTGTGCGCCCGAAGCGGTCCACCAGCCCGGTCAGTACCCGGTACGGCGGCAGCGGCGCAGGCAGCACCTCATCC
+
=GI:IHII@IIGI@IIBFIIIIIIIIIBHIIIGHBIIIIIIIIIIG:AGIAHHIHDB<DI#IEFG>CBGG<HE#DC??D#

==> debug2_s2.fq <==
@r26223_from_NC_000913_h10_ids100-h0 ln302#0/2
CCGGTGAGGACGGTTACAGCCGCAGCGAGTCACTGTGGCTGGTGCGCGGCGGCGTGGCGAAACTGGATGAAGGTCACCGGCTGGCCGCACTCTGGCAGGC
+
FHFHFIIIHIDIIIIIIGF@IIH<IBIGHHIIIGHII4IE8G9IGIIFBDCIIDDADHEIDIGFHHI;GGGBACEBGG@;EHDA@E#DBCH###@#=#BI

bwa pssm seems to run just fine, but then the output of the sampe step is as follows:

@sq SN:NC_000913 LN:4639675
@pg ID:bwa PN:bwa VN:0.6.0-r70-dev
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_read_seq] 0.0% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: too few good pairs
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_sai2sam_pe_core] time elapses: 0.00 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec
[bwa_sai2sam_pe_core] print alignments... r26223_from_NC_000913_h10_ids100-h0 83 NC_00091 3760790 0 100M = 3760588 -302 GGATGAGGTGCTGCCTGCGCCGCTGCCGCCGTACCGGGTACTGACCGGGCTGGTGGACCGCTTCGGGCGCACACAGACGTTCCACCGCGAAGCCGCCGGT #D??CD#EHGFEI#IDFIGHHIFGCEIIIHDBII<:GIIIIIIIIIIBHGIIIHBIIIIIIIIIFBII@IGII@IIHI:IG= XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:100 PS:f:195.145996 NB:i:3 PP:f:0.333333 XA:Z:NC_000913,-729390,100M,0;NC_000913,-3760790,100M,0;NC_000913,-3617799,100M,0; XS:A:0.000000;0.000000;0.000000;
r26223_from_NC_000913_h10_ids100-h0 163 NC_000913 3760588 0 100M = 3760790 302 CCGGTGAGGACGGTTACAGCCGCAGCGAGTCACTGTGGCTGGTGCGCGGCGGCGTGGCGAAACTGGATGAAGGTCACCGGCTGGCCGCACTCTGGCAGGC FHFHFIIIHIDIIIIIIGF@IIH<IBIGHHIIIGHII4IE8G9IGIIFBDCIIDDADHEIDIGFHHI;GGGBACEBGG@;EHDA@E#DBCH###@#=#BI XT:A:R NM:i:0 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:100 PS:f:192.384003 NB:i:3 PP:f:0.333333 XA:Z:NC_000913,+729188,100M,0;NC_000913,+3617597,100M,0;NC_000913,+3760588,100M,0; XS:A:0.000000;0.000000;0.000000;
0.00 sec
Segmentation fault (core dumped)

--while running it with valgrind gives the following output:
==5709== Invalid free() / delete / delete[]
==5709== at 0x4A0595D: free (vg_replace_malloc.c:366)
==5709== by 0x418DCA: bwa_free_read_seq (in /home/wilma/local/src/bwa-pssm/bwa-pssm-v0.4)
==5709== by 0x424B16: bwa_sai2sam_pe_core (in /home/wilma/local/src/bwa-pssm/bwa-pssm-v0.4)
==5709== by 0x424FE6: bwa_sai2sam_pe (in /home/wilma/local/src/bwa-pssm/bwa-pssm-v0.4)
==5709== by 0x3BCB21ECDC: (below main) (in /lib64/libc-2.12.so)
==5709== Address 0x396295 is not stack'd, malloc'd or (recently) free'd
==5709==
==5709== Invalid free() / delete / delete[]
==5709== at 0x4A0595D: free (vg_replace_malloc.c:366)
==5709== by 0x418DCA: bwa_free_read_seq (in /home/wilma/local/src/bwa-pssm/bwa-pssm-v0.4)
==5709== by 0x424B2A: bwa_sai2sam_pe_core (in /home/wilma/local/src/bwa-pssm/bwa-pssm-v0.4)
==5709== by 0x424FE6: bwa_sai2sam_pe (in /home/wilma/local/src/bwa-pssm/bwa-pssm-v0.4)
==5709== by 0x3BCB21ECDC: (below main) (in /lib64/libc-2.12.so)
==5709== Address 0x37333c is not stack'd, malloc'd or (recently) free'd

I'd appreciate any help on this. Thanks!

• Grace

http://home.gna.org/gdsl/ seems to be down forever now. Do you know a new way to get the dependencies?