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Old 03-01-2011, 09:12 AM   #1
jkersh
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Location: boulder, co

Join Date: Apr 2010
Posts: 11
Default Bfast match abort error

I have just started playing around with Bfast for single-end alignment of E. coli mutants to a reference genome. I got through all of the steps in making the reference and making the index files successfully, but now when I try to run the match command it aborts. I have found that I can run it successfully using a single index as the main index with no secondary indexes, but as soon as I try to use a secondary index it aborts (see below). Any ideas? I was trying to run the moderate accuracy mode described in the paper to see how it does with finding small indels.


$ /usr/local/src/bfast-0.6.4e/bfast/bfast match -f Parent113010.fa -r /data/prior/Illumina/PEL2_nocode_qualfilt.fq -i 1 -I 3 -n 4 -t -w 0 -T Temp/ > bfast.matches.PEL2.bmf
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName Parent113010.fa.
Validating readsFileName /data/prior/Illumina/PEL2_nocode_qualfilt.fq.
Validating tmpDir path Temp/.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: Parent113010.fa
mainIndexes 1
secondaryIndexes 3
readsFileName: /data/prior/Illumina/PEL2_nocode_qualfilt.fq
offsets: [Using All]
loadAllIndexes: [Not Using]
compression: [Not Using]
space: [NT Space]
startReadNum: 1
endReadNum: 2147483647
keySize: [Not Using]
maxKeyMatches: 8
maxNumMatches: 384
whichStrand: [Both Strands]
numThreads: 4
queueLength: 250000
tmpDir: Temp/
timing: [Using]
************************************************************
Searching for main indexes...
Found 1 index (1 file).
Searching for secondary indexes...
Found 1 index (1 file).
************************************************************
Reading in reference genome from Parent113010.fa.nt.brg.
In total read 1 contigs for a total of 4633479 bases
************************************************************
Reading /data/prior/Illumina/PEL2_nocode_qualfilt.fq into a temp file.
Will process 4625285 reads.
************************************************************
Searching index file 1/1 (index #1, bin #1)...
Reading index from Parent113010.fa.nt.1.1.bif.
Read index from Parent113010.fa.nt.1.1.bif.
Reads processed: 4625285
Cleaning up index.
Searching index file 1/1 (index #1, bin #1) complete...
Found 4596991 matches.
Found matches for 4596991 reads.
Copying unmatched reads for secondary index search.
Splitting unmatched reads into temp files.
*** glibc detected *** /usr/local/src/bfast-0.6.4e/bfast/bfast: double free or corruption (!prev): 0x0000000013ab3670 ***
======= Backtrace: =========
/lib64/libc.so.6[0x2aeabe14830f]
/lib64/libc.so.6(cfree+0x4b)[0x2aeabe14876b]
/lib64/libc.so.6(fclose+0x14b)[0x2aeabe136d5b]
/usr/lib64/libz.so.1[0x33d6a030b4]
/usr/local/src/bfast-0.6.4e/bfast/bfast[0x408c38]
/usr/local/src/bfast-0.6.4e/bfast/bfast[0x4238a4]
/usr/local/src/bfast-0.6.4e/bfast/bfast[0x424389]
/usr/local/src/bfast-0.6.4e/bfast/bfast[0x42ad42]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x2aeabe0f3994]
/usr/local/src/bfast-0.6.4e/bfast/bfast[0x401b59]
======= Memory map: ========
00400000-0044b000 r-xp 00000000 fd:04 1344273 /usr/local/src/bfast-0.6.4e/bfast/bfast
0064b000-0064d000 rw-p 0004b000 fd:04 1344273 /usr/local/src/bfast-0.6.4e/bfast/bfast
13aaa000-196f4000 rw-p 13aaa000 00:00 0 [heap]
41f22000-41f23000 ---p 41f22000 00:00 0
41f23000-42923000 rw-p 41f23000 00:00 0
42923000-42924000 ---p 42923000 00:00 0
42924000-43324000 rw-p 42924000 00:00 0
48d2d000-48d2e000 ---p 48d2d000 00:00 0
48d2e000-4972e000 rw-p 48d2e000 00:00 0
33d6a00000-33d6a14000 r-xp 00000000 fd:04 1111537 /usr/lib64/libz.so.1.2.3
33d6a14000-33d6c13000 ---p 00014000 fd:04 1111537 /usr/lib64/libz.so.1.2.3
33d6c13000-33d6c14000 rw-p 00013000 fd:04 1111537 /usr/lib64/libz.so.1.2.3
2aaaaaaac000-2aaaaaaad000 rw-p 2aaaaaaac000 00:00 0
2aaaaaaae000-2aaaaaaaf000 rw-p 2aaaaaaae000 00:00 0
2aaaaaacc000-2aaaaaad9000 r-xp 00000000 fd:04 10911746 /lib64/libgcc_s-4.1.2-20080825.so.1
2aaaaaad9000-2aaaaacd9000 ---p 0000d000 fd:04 10911746 /lib64/libgcc_s-4.1.2-20080825.so.1
2aaaaacd9000-2aaaaacda000 rw-p 0000d000 fd:04 10911746 /lib64/libgcc_s-4.1.2-20080825.so.1
2aaaac000000-2aaaac021000 rw-p 2aaaac000000 00:00 0
2aaaac021000-2aaab0000000 ---p 2aaaac021000 00:00 0
2aaab0000000-2aaab0021000 rw-p 2aaab0000000 00:00 0
2aaab0021000-2aaab4000000 ---p 2aaab0021000 00:00 0
2aaab4000000-2aaab4121000 rw-p 2aaab4000000 00:00 0
2aaab4121000-2aaab8000000 ---p 2aaab4121000 00:00 0
2aaab8000000-2aaac0000000 rw-p 2aaab8000000 00:00 0
2aeabd80a000-2aeabd826000 r-xp 00000000 fd:04 10916099 /lib64/ld-2.5.so
2aeabd826000-2aeabd827000 rw-p 2aeabd826000 00:00 0
2aeabd828000-2aeabd829000 rw-p 2aeabd828000 00:00 0
2aeabd844000-2aeabd845000 rw-p 2aeabd844000 00:00 0
2aeabda25000-2aeabda26000 r--p 0001b000 fd:04 10916099 /lib64/ld-2.5.so
2aeabda26000-2aeabda27000 rw-p 0001c000 fd:04 10916099 /lib64/ld-2.5.so
2aeabda27000-2aeabdaa9000 r-xp 00000000 fd:04 10915348 /lib64/libm-2.5.so
2aeabdaa9000-2aeabdca8000 ---p 00082000 fd:04 10915348 /lib64/libm-2.5.so
2aeabdca8000-2aeabdca9000 r--p 00081000 fd:04 10915348 /lib64/libm-2.5.so
2aeabdca9000-2aeabdcaa000 rw-p 00082000 fd:04 10915348 /lib64/libm-2.5.so
2aeabdcaa000-2aeabdcb9000 r-xp 00000000 fd:04 9240588 /usr/lib64/libbz2.so.1.0.3
2aeabdcb9000-2aeabdeb8000 ---p 0000f000 fd:04 9240588 /usr/lib64/libbz2.so.1.0.3
2aeabdeb8000-2aeabdeba000 rw-p 0000e000 fd:04 9240588 /usr/lib64/libbz2.so.1.0.3
2aeabdeba000-2aeabdebb000 rw-p 2aeabdeba000 00:00 0
2aeabdebb000-2aeabded1000 r-xp 00000000 fd:04 10911775 /lib64/libpthread-2.5.so
2aeabded1000-2aeabe0d0000 ---p 00016000 fd:04 10911775 /lib64/libpthread-2.5.so
2aeabe0d0000-2aeabe0d1000 r--p 00015000 fd:04 10911775 /lib64/libpthread-2.5.so
2aeabe0d1000-2aeabe0d2000 rw-p 00016000 fd:04 10911775 /lib64/libpthread-2.5.so
2aeabe0d2000-2aeabe0d6000 rw-p 2aeabe0d2000 00:00 0
2aeabe0d6000-2aeabe224000 r-xp 00000000 fd:04 10911751 /lib64/libc-2.5.so
2aeabe224000-2aeabe423000 ---p 0014e000 fd:04 10911751 /lib64/libc-2.5.so
2aeabe423000-2aeabe427000 r--p 0014d000 fd:04 10911751 /lib64/libc-2.5.so
2aeabe427000-2aeabe428000 rw-p 00151000 fd:04 10911751 /lib64/libc-2.5.so
2aeabe428000-2aeabe665000 rw-p 2aeabe428000 00:00 0
7fffc6c46000-7fffc6c5b000 rw-p 7ffffffe9000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
Aborted
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