Closed najoshi closed 1 year ago
So I am trying to run hts_Stats (in a pipeline) on an old fastq file.... it has quality values that use an offset of 64. This seems to be causing problems when running hts_Stats. I get this error:
Error in `hts_Stats': free(): invalid pointer: 0x0000000002487a71 ======= Backtrace: ========= [0x568e81] [0x5713c6] [0x575447] [0x4386f0] [0x43872c] [0x438691] [0x4384cd] [0x40e99c] [0x40a3a1] [0x42ec98] [0x42ecd0] [0x434215] [0x43331d] [0x43211d] [0x430e63] [0x42f663] [0x42ebe8] [0x43b966] [0x43b996] [0x41741a] [0x414199] [0x410e1b] [0x40d125] [0x4013b5] [0x546556] [0x546b45] [0x401159] ======= Memory map: ======== 00400000-0069c000 r-xp 00000000 00:2f 502202560 /afs/genomecenter.ucdavis.edu/software/htstream/1.3.3/lssc0-linux/bin/hts_Stats 0089c000-008a6000 rw-p 0029c000 00:2f 502202560 /afs/genomecenter.ucdavis.edu/software/htstream/1.3.3/lssc0-linux/bin/hts_Stats 008a6000-008b0000 rw-p 00000000 00:00 0 0245e000-024a2000 rw-p 00000000 00:00 0 [heap] 7f9378000000-7f9378033000 rw-p 00000000 00:00 0 7f9378033000-7f937c000000 ---p 00000000 00:00 0 7f937edfa000-7f937edfb000 rw-p 00000000 00:00 0 7ffc2274f000-7ffc22770000 rw-p 00000000 00:00 0 [stack] 7ffc227b8000-7ffc227bb000 r--p 00000000 00:00 0 [vvar] 7ffc227bb000-7ffc227bd000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped)
Here is the command I ran:
hts_Stats -F -L test.log -1 test1.fq.gz -2 test2.fq.gz -f test
And I have attached the two fq files that reproduce the error. I'm running on Ubuntu 16.04 using htstream 1.3.3.
test2.fq.gz test1.fq.gz
I've investigated this issue, looks like you are using quality scores outside the range we currently support, working on a fix now. @msettles
So I am trying to run hts_Stats (in a pipeline) on an old fastq file.... it has quality values that use an offset of 64. This seems to be causing problems when running hts_Stats. I get this error:
Error in `hts_Stats': free(): invalid pointer: 0x0000000002487a71 ======= Backtrace: ========= [0x568e81] [0x5713c6] [0x575447] [0x4386f0] [0x43872c] [0x438691] [0x4384cd] [0x40e99c] [0x40a3a1] [0x42ec98] [0x42ecd0] [0x434215] [0x43331d] [0x43211d] [0x430e63] [0x42f663] [0x42ebe8] [0x43b966] [0x43b996] [0x41741a] [0x414199] [0x410e1b] [0x40d125] [0x4013b5] [0x546556] [0x546b45] [0x401159] ======= Memory map: ======== 00400000-0069c000 r-xp 00000000 00:2f 502202560 /afs/genomecenter.ucdavis.edu/software/htstream/1.3.3/lssc0-linux/bin/hts_Stats 0089c000-008a6000 rw-p 0029c000 00:2f 502202560 /afs/genomecenter.ucdavis.edu/software/htstream/1.3.3/lssc0-linux/bin/hts_Stats 008a6000-008b0000 rw-p 00000000 00:00 0 0245e000-024a2000 rw-p 00000000 00:00 0 [heap] 7f9378000000-7f9378033000 rw-p 00000000 00:00 0 7f9378033000-7f937c000000 ---p 00000000 00:00 0 7f937edfa000-7f937edfb000 rw-p 00000000 00:00 0 7ffc2274f000-7ffc22770000 rw-p 00000000 00:00 0 [stack] 7ffc227b8000-7ffc227bb000 r--p 00000000 00:00 0 [vvar] 7ffc227bb000-7ffc227bd000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped)
Here is the command I ran:
hts_Stats -F -L test.log -1 test1.fq.gz -2 test2.fq.gz -f test
And I have attached the two fq files that reproduce the error. I'm running on Ubuntu 16.04 using htstream 1.3.3.
test2.fq.gz test1.fq.gz