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Old 09-03-2011, 05:53 PM   #15
kwicher
Junior Member
 
Location: Cambridge

Join Date: Jan 2011
Posts: 7
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Thank you.

I run the bfast match with -s 1 and -e 1 (the same is for -e 100) and the full error message is:
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName /mnt/fastfs/KW_Temp/bfast/refseq.fas.
Validating readsFileName /mnt/fastfs/KW_Temp/SSP2_16.single.fastq.
Validating tmpDir path ./.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: /mnt/fastfs/KW_Temp/bfast/refseq.fas
mainIndexes [Auto-recognizing]
secondaryIndexes [Not Using]
readsFileName: /mnt/fastfs/KW_Temp/SSP2_16.single.fastq
offsets: [Using All]
loadAllIndexes: [Not Using]
compression: [Not Using]
space: [Color Space]
startReadNum: 1
endReadNum: 1
keySize: [Not Using]
maxKeyMatches: 8
maxNumMatches: 384
whichStrand: [Both Strands]
numThreads: 1
queueLength: 250000
tmpDir: ./
timing: [Not Using]
************************************************************
Searching for main indexes...
Found 10 index (10 total files).
Not using secondary indexes.
************************************************************
Reading in reference genome from /mnt/fastfs/KW_Temp/bfast/refseq.fas.cs.brg.
In total read 35860 contigs for a total of 91307366 bases
************************************************************
Reading /mnt/fastfs/KW_Temp/SSP2_16.single.fastq into a temp file.
*** glibc detected *** /mnt/fastfs/bin/bfast: free(): invalid next size (fast): 0x000000000065cf10 ***
======= Backtrace: =========
/lib/libc.so.6[0x2b30d30649a8]
/lib/libc.so.6(cfree+0x76)[0x2b30d3066ab6]
/mnt/fastfs/bin/bfast[0x415f9a]
/mnt/fastfs/bin/bfast[0x418af4]
/mnt/fastfs/bin/bfast[0x424124]
/mnt/fastfs/bin/bfast[0x425ffa]
/mnt/fastfs/bin/bfast[0x42d260]
/lib/libc.so.6(__libc_start_main+0xe6)[0x2b30d300f1a6]
/mnt/fastfs/bin/bfast[0x401e49]
======= Memory map: ========
00400000-0044d000 r-xp 00000000 00:15 1003536386 /mnt/fastfs/bin/bfast
0064d000-0064f000 rw-p 0004d000 00:15 1003536386 /mnt/fastfs/bin/bfast
0064f000-0347c000 rw-p 0064f000 00:00 0 [heap]
2b30d250d000-2b30d2529000 r-xp 00000000 68:01 14196756 /lib/ld-2.7.so
2b30d2529000-2b30d252a000 r-xp 2b30d2529000 00:00 0 [vdso]
2b30d252a000-2b30d252d000 rw-p 2b30d252a000 00:00 0
2b30d254d000-2b30d2666000 rw-p 2b30d254d000 00:00 0
2b30d2728000-2b30d272a000 rw-p 0001b000 68:01 14196756 /lib/ld-2.7.so
2b30d272a000-2b30d27ac000 r-xp 00000000 68:01 14196741 /lib/libm-2.7.so
2b30d27ac000-2b30d29ab000 ---p 00082000 68:01 14196741 /lib/libm-2.7.so
2b30d29ab000-2b30d29ad000 rw-p 00081000 68:01 14196741 /lib/libm-2.7.so
2b30d29ad000-2b30d29bc000 r-xp 00000000 68:01 14197946 /lib/libbz2.so.1.0.4
2b30d29bc000-2b30d2bbb000 ---p 0000f000 68:01 14197946 /lib/libbz2.so.1.0.4
2b30d2bbb000-2b30d2bbd000 rw-p 0000e000 68:01 14197946 /lib/libbz2.so.1.0.4
2b30d2bbd000-2b30d2bd3000 r-xp 00000000 68:01 2328701 /usr/lib/libz.so.1.2.3.3
2b30d2bd3000-2b30d2dd3000 ---p 00016000 68:01 2328701 /usr/lib/libz.so.1.2.3.3
2b30d2dd3000-2b30d2dd4000 rw-p 00016000 68:01 2328701 /usr/lib/libz.so.1.2.3.3
2b30d2dd4000-2b30d2dd5000 rw-p 2b30d2dd4000 00:00 0
2b30d2dd5000-2b30d2deb000 r-xp 00000000 68:01 14196761 /lib/libpthread-2.7.so
2b30d2deb000-2b30d2feb000 ---p 00016000 68:01 14196761 /lib/libpthread-2.7.so
2b30d2feb000-2b30d2fed000 rw-p 00016000 68:01 14196761 /lib/libpthread-2.7.so
2b30d2fed000-2b30d2ff1000 rw-p 2b30d2fed000 00:00 0
2b30d2ff1000-2b30d313b000 r-xp 00000000 68:01 14196749 /lib/libc-2.7.so
2b30d313b000-2b30d333a000 ---p 0014a000 68:01 14196749 /lib/libc-2.7.so
2b30d333a000-2b30d333d000 r--p 00149000 68:01 14196749 /lib/libc-2.7.so
2b30d333d000-2b30d333f000 rw-p 0014c000 68:01 14196749 /lib/libc-2.7.so
2b30d333f000-2b30d3466000 rw-p 2b30d333f000 00:00 0
2b30d3472000-2b30d3488000 r-xp 00000000 68:01 14196739 /lib/libgcc_s.so.1
2b30d3488000-2b30d3688000 ---p 00016000 68:01 14196739 /lib/libgcc_s.so.1
2b30d3688000-2b30d3689000 rw-p 00016000 68:01 14196739 /lib/libgcc_s.so.1
2b30d4000000-2b30d4021000 rw-p 2b30d4000000 00:00 0
2b30d4021000-2b30d8000000 ---p 2b30d4021000 00:00 0
7ffffffea000-7ffffffff000 rw-p 7ffffffea000 00:00 0 [stack]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

The first read in fastq file is:
@SSP2_16:559_41_123/1
TGNCCTNNGGGNNTGAGGTNTANNNGNCNNNNCNNCNGNNTNNNNACAN
+
!@,!-(<!!*<9!!698.3&!6,!!!3!8!!!!:!!%!)!!(!!!!&(%!

K

Last edited by kwicher; 09-03-2011 at 05:56 PM. Reason: added info
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