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Old 02-10-2010, 05:33 AM   #1
javijevi
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Default Strange memory corruption error in BFAST match step

Hi, I have a set of 300 million 50-bp long SOLiD reads, and I would like to use BFAST to map them to a reference genome. I've successfully created the color-space reference genome .brfg file, and the 10 color-space reference genome indexes recommended in the BFAST book.

When trying 'bfast match -f reference_genome -A 1 -r reads.fastq > matches.bmf' in a 32 GB RAM machine, I got the memory corruption error copied below. Following BFAST book recommendations, I splitted the global fastq file in 10 filse with 30 million reads each. Since they also produced the same memory corruption error, I further splitted the reads in files with 3 million reads each. First three files were run successfully, but fourth file gave the same memory corruption error again. Then I splitted this file in 3 files with 1 million reads each. Again, first run was fine, but second run gave the same memory corruption error.

The strange thing is that running the fifth 3 million reads file (which is a little bigger than fourth one) did not give the memory corruption error. So, I do not think that I need more RAM because some 3 million reads could be processed, whereas some 1 million could not.

Any idea?

Files size are 33 GB for the 300 million reads fastq file, and 3.6 GB for each of 10 indexes

(...normal output here...)
Reading reads.fastq into temp files.
*** glibc detected *** bfast: malloc(): memory corruption: 0x000000000065cf30 ***
======= Backtrace: =========
/lib/libc.so.6[0x7f8ad88d3a14]
/lib/libc.so.6(__libc_malloc+0x90)[0x7f8ad88d5360]
/lib/libc.so.6(vasprintf+0x3e)[0x7f8ad88ca66e]
/lib/libc.so.6(asprintf+0x88)[0x7f8ad88ad098]
/lib/libc.so.6(__assert_fail+0xb8)[0x7f8ad888a2a8]
bfast[0x41770d]
bfast[0x418927]
bfast[0x423b3b]
bfast[0x4259c5]
bfast[0x42b2d2]
/lib/libc.so.6(__libc_start_main+0xf4)[0x7f8ad887d1c4]
bfast[0x401ce9]
======= Memory map: ========
00400000-0044d000 r-xp 00000000 08:03 2711591 /usr/local/bin/bfast
0064d000-0064f000 rw-p 0004d000 08:03 2711591 /usr/local/bin/bfast
0064f000-010d8000 rw-p 0064f000 00:00 0 [heap]
7f8abc000000-7f8abc021000 rw-p 7f8abc000000 00:00 0
7f8abc021000-7f8ac0000000 ---p 7f8abc021000 00:00 0
7f8ac1c0c000-7f8ac1c19000 r-xp 00000000 08:03 647184 /lib/libgcc_s.so.1
7f8ac1c19000-7f8ac1e19000 ---p 0000d000 08:03 647184 /lib/libgcc_s.so.1
7f8ac1e19000-7f8ac1e1a000 rw-p 0000d000 08:03 647184 /lib/libgcc_s.so.1
7f8ac1e1a000-7f8ad885f000 rw-p 7f8ac1e1a000 00:00 0
7f8ad885f000-7f8ad89b7000 r-xp 00000000 08:03 647441 /lib/libc-2.7.so
7f8ad89b7000-7f8ad8bb7000 ---p 00158000 08:03 647441 /lib/libc-2.7.so
7f8ad8bb7000-7f8ad8bba000 r--p 00158000 08:03 647441 /lib/libc-2.7.so
7f8ad8bba000-7f8ad8bbc000 rw-p 0015b000 08:03 647441 /lib/libc-2.7.so
7f8ad8bbc000-7f8ad8bc1000 rw-p 7f8ad8bbc000 00:00 0
7f8ad8bc1000-7f8ad8bd7000 r-xp 00000000 08:03 647459 /lib/libpthread-2.7.so
7f8ad8bd7000-7f8ad8dd7000 ---p 00016000 08:03 647459 /lib/libpthread-2.7.so
7f8ad8dd7000-7f8ad8dd9000 rw-p 00016000 08:03 647459 /lib/libpthread-2.7.so
7f8ad8dd9000-7f8ad8ddd000 rw-p 7f8ad8dd9000 00:00 0
7f8ad8ddd000-7f8ad8dec000 r-xp 00000000 08:03 647294 /lib/libbz2.so.1.0.4
7f8ad8dec000-7f8ad8feb000 ---p 0000f000 08:03 647294 /lib/libbz2.so.1.0.4
7f8ad8feb000-7f8ad8fed000 rw-p 0000e000 08:03 647294 /lib/libbz2.so.1.0.4
7f8ad8fed000-7f8ad9003000 r-xp 00000000 08:03 4089806 /usr/lib/libz.so.1.2.3.3
7f8ad9003000-7f8ad9203000 ---p 00016000 08:03 4089806 /usr/lib/libz.so.1.2.3.3
7f8ad9203000-7f8ad9204000 rw-p 00016000 08:03 4089806 /usr/lib/libz.so.1.2.3.3
7f8ad9204000-7f8ad9284000 r-xp 00000000 08:03 647446 /lib/libm-2.7.so
7f8ad9284000-7f8ad9483000 ---p 00080000 08:03 647446 /lib/libm-2.7.so
7f8ad9483000-7f8ad9485000 rw-p 0007f000 08:03 647446 /lib/libm-2.7.so
7f8ad9485000-7f8ad94a2000 r-xp 00000000 08:03 647435 /lib/ld-2.7.so
7f8ad9543000-7f8ad9694000 rw-p 7f8ad9543000 00:00 0
7f8ad969d000-7f8ad96a2000 rw-p 7f8ad969d000 00:00 0
7f8ad96a2000-7f8ad96a4000 rw-p 0001d000 08:03 647435 /lib/ld-2.7.so
7fff956b3000-7fff956c8000 rw-p 7ffffffea000 00:00 0 [stack]
7fff957fe000-7fff95800000 r-xp 7fff957fe000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
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Old 02-10-2010, 06:30 AM   #2
nickloman
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Sounds like a bug in BFAST. Memory corruption errors are caused by incorrect use of malloc()/free() not running out of memory. Suggest you contact the BFAST authors. They might ask you to send an example file which has the problem.
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Old 02-10-2010, 06:39 AM   #3
javijevi
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Quote:
Originally Posted by nickloman View Post
Sounds like a bug in BFAST. Memory corruption errors are caused by incorrect use of malloc()/free() not running out of memory. Suggest you contact the BFAST authors. They might ask you to send an example file which has the problem.
I think BFAST author follows closely this forum...

BTW, it seems that BFAST does not like some read/s, so that memory corruption error only appears in subsets of reads having it/them. This would explain why it appears in some subsets and does not appear in others, irrespective of the file size or the reads number.
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Old 02-10-2010, 08:16 AM   #4
javijevi
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Quote:
Originally Posted by javijevi View Post
BTW, it seems that BFAST does not like some read/s, so that memory corruption error only appears in subsets of reads having it/them. This would explain why it appears in some subsets and does not appear in others, irrespective of the file size or the reads number.
Maybe this is not true, since I have a 250,000 reads fastq file producing the memory corruption error, whereas the two 125,000 reads fastq files obtained by splitting it did not cause the error. Strange, very strange...
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Old 02-10-2010, 10:49 AM   #5
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Quote:
Originally Posted by javijevi View Post
Maybe this is not true, since I have a 250,000 reads fastq file producing the memory corruption error, whereas the two 125,000 reads fastq files obtained by splitting it did not cause the error. Strange, very strange...
Very strange indeed. Could you post the amount of RAM available, the full command used, the Operating System you are using? Also, if you post the reference and reads as well as the indexes you used, I can try to reproduce/debug.

Hopefully we can figure this out!

Nils
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Old 08-06-2010, 05:40 AM   #6
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Hi, has there been progress on debugging this issue? I am getting a similar error when trying to align a million Illumina reads on a Linux machine with 64G RAM. Any help you can give would be greatly appreciated!

*** glibc detected *** bfast: malloc(): memory corruption: 0x000000000fd57f40 ***
======= Backtrace: =========
/lib64/libc.so.6[0x384406faf1]
/lib64/libc.so.6(__libc_malloc+0x7d)[0x3844070c9d]
/lib64/libc.so.6(vasprintf+0x3e)[0x3844066e6e]
/lib64/libc.so.6(asprintf+0x88)[0x384404bfa8]
/lib64/libc.so.6(__assert_fail+0xbf)[0x384402971f]
bfast[0x4167ad]
bfast[0x417957]
bfast[0x422646]
bfast[0x4242df]
bfast[0x42a172]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x384401d8a4]
bfast[0x401b09]
======= Memory map: ========
00400000-0044a000 r-xp 00000000 00:1a 443580418 /home/gfs08/nc276/programs/bfast-0.6.4d/bin/bfast
0064a000-0064c000 rw-p 0004a000 00:1a 443580418 /home/gfs08/nc276/programs/bfast-0.6.4d/bin/bfast
0fd4a000-15fea000 rw-p 0fd4a000 00:00 0 [heap]
3843c00000-3843c1a000 r-xp 00000000 08:01 720069 /lib64/ld-2.5.so
3843e19000-3843e1a000 r--p 00019000 08:01 720069 /lib64/ld-2.5.so
3843e1a000-3843e1b000 rw-p 0001a000 08:01 720069 /lib64/ld-2.5.so
3844000000-3844146000 r-xp 00000000 08:01 720070 /lib64/libc-2.5.so
3844146000-3844346000 ---p 00146000 08:01 720070 /lib64/libc-2.5.so
3844346000-384434a000 r--p 00146000 08:01 720070 /lib64/libc-2.5.so
384434a000-384434b000 rw-p 0014a000 08:01 720070 /lib64/libc-2.5.so
384434b000-3844350000 rw-p 384434b000 00:00 0
3844400000-3844482000 r-xp 00000000 08:01 720071 /lib64/libm-2.5.so
3844482000-3844681000 ---p 00082000 08:01 720071 /lib64/libm-2.5.so
3844681000-3844682000 r--p 00081000 08:01 720071 /lib64/libm-2.5.so
3844682000-3844683000 rw-p 00082000 08:01 720071 /lib64/libm-2.5.so
3844c00000-3844c15000 r-xp 00000000 08:01 3580079 /lib64/libpthread-2.5.so
3844c15000-3844e14000 ---p 00015000 08:01 3580079 /lib64/libpthread-2.5.so
3844e14000-3844e15000 r--p 00014000 08:01 3580079 /lib64/libpthread-2.5.so
3844e15000-3844e16000 rw-p 00015000 08:01 3580079 /lib64/libpthread-2.5.so
3844e16000-3844e1a000 rw-p 3844e16000 00:00 0
3845800000-3845814000 r-xp 00000000 08:01 1464653 /usr/lib64/libz.so.1.2.3
3845814000-3845a13000 ---p 00014000 08:01 1464653 /usr/lib64/libz.so.1.2.3
3845a13000-3845a14000 rw-p 00013000 08:01 1464653 /usr/lib64/libz.so.1.2.3
3848c00000-3848c0f000 r-xp 00000000 08:01 1464655 /usr/lib64/libbz2.so.1.0.3
3848c0f000-3848e0e000 ---p 0000f000 08:01 1464655 /usr/lib64/libbz2.so.1.0.3
3848e0e000-3848e10000 rw-p 0000e000 08:01 1464655 /usr/lib64/libbz2.so.1.0.3
2ac513b5f000-2ac513b62000 rw-p 2ac513b5f000 00:00 0
2ac513b72000-2ac5328f8000 rw-p 2ac513b72000 00:00 0
2ac53290a000-2ac532920000 r-xp 00000000 08:01 2703644 /opt/gcc-4.3.1/lib64/libgcc_s.so.1
2ac532920000-2ac532b1f000 ---p 00016000 08:01 2703644 /opt/gcc-4.3.1/lib64/libgcc_s.so.1
2ac532b1f000-2ac532b20000 rw-p 00015000 08:01 2703644 /opt/gcc-4.3.1/lib64/libgcc_s.so.1
2ac534000000-2ac534021000 rw-p 2ac534000000 00:00 0
2ac534021000-2ac538000000 ---p 2ac534021000 00:00 0
7fff06fd5000-7fff06fea000 rw-p 7ffffffea000 00:00 0 [stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
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Old 08-07-2010, 04:34 PM   #7
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Could you try the latest source via GIT to see if that resolves it? If not, could you try to find the offending read(s) so it is easier to debug?
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Old 03-17-2011, 06:54 AM   #8
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Hi,

It's been a while since the last post in this thread, but i was wondering if someone found a solution to the problem yet? I have the exact same problem as described.
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Old 03-17-2011, 09:40 AM   #9
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Quote:
Originally Posted by MaartenR View Post
Hi,

It's been a while since the last post in this thread, but i was wondering if someone found a solution to the problem yet? I have the exact same problem as described.
What version of bfast are you using?
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Old 03-17-2011, 10:28 AM   #10
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0.6.4F, but theres a slim chance i am using 0.6.4E. I will have to check at work tomorrow
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Old 03-17-2011, 10:37 AM   #11
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Does it occur every time? If it does, could you send me the test case so I can fix it?
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Old 03-17-2011, 10:41 AM   #12
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No, it worked before. But when i tried doing it again it gave that error. Tried rebuilding the sample but it gives the same error.
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Old 09-03-2011, 04:41 PM   #13
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Default Bfast memory corruption error on all 8 read files

Hello

I have 8 files with 50bp SE SOLiD reads. For each and single file I am getting the same error during match step:
*** glibc detected *** /mnt/fastfs/bin/bfast: malloc(): memory corruption: 0x000000000065cf30 *** (memory adresses are different of course).

I am using the bfast-0.6.5a and all standard parameters and masks, and I am mapping against the mRNA refseqs. Files with reads are about 5Gb and I have 32G memory.

Any ideas how to solve the problem

Thanks

K
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Old 09-03-2011, 05:28 PM   #14
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If you could submit a test case, as detailed here, it would make it much easier for me to debug.
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Old 09-03-2011, 05:53 PM   #15
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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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Old 09-03-2011, 06:54 PM   #16
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Excellent, could you post your fastq, how you created your indexes, and the small test FASTQ, so I can try to reproduce the behavior on my own machine?
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Old 09-04-2011, 04:13 AM   #17
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Thanks.
Here is how I converted the reference genome, indexed it and tried to make the alignment.
- converting genome
/mnt/fastfs/bin/bfast fasta2brg -A 1 -f refseq.fas

- INDEXING
qsub -q cb_quad -b y -e /mnt/fastfs/KW_Temp/bfast -o /mnt/fastfs/KW_Temp/bfast "/mnt/fastfs/bin/bfast index -f /mnt/fastfs/KW_Temp/bfast/refseq.fas -m <for each mask> -w 14 -A 1 -i <mask number>"

MASKS
M1 = 1111111111111111111111
M2 = 111110100111110011111111111
M3 = 10111111011001100011111000111111
M4 = 1111111100101111000001100011111011
M5 = 111111110001111110011111111
M6 = 11111011010011000011000110011111111
M7 = 1111111111110011101111111
M8 = 111011000011111111001111011111
M9 = 1111111111110011101111111
M10 = 1110110001011010011100101111101111

-ALIGNING:
qsub -q cb_quad -b y -e /mnt/fastfs/KW_Temp/bfast -o /mnt/fastfs/KW_Temp/bfast "/mnt/fastfs/bin/bfast match -f /mnt/fastfs/KW_Temp/bfast/refseq.fas -A 1 -r /mnt/fastfs/KW_Temp/input.fastq > /mnt/fastfs/KW_Temp/bfast/output.bmf"

I have done one test:
I extracted 5 seqs from fastq file and run test against this tiny file. It run without the problem.
It is really strange as using "-s 1 -e 5" options on full data set, so in fact providing the same sequences, causes the error reported earlier.

K
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Old 09-04-2011, 06:08 AM   #18
nilshomer
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Could you post a link to the files?
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Old 09-14-2011, 06:49 PM   #19
ajs
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After we encountered the malloc error, we noticed our fastq was in color space but our bfast commands were for nucleotide space. We then created brg and index files in color space, then successfully ran match in color space.
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Old 11-13-2011, 07:18 PM   #20
alig
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Default Bfast Malloc memory error

Hi,
Has there been a solution to the Malloc memory error when running Bfast?

I am having the same problem when trying to run bfast bwaaln

bfast+bwa-0.7.0a/bfast/bfast bwaaln -n 0.04 -o 1 -e -1 -d 5 -i 5 -l 25 -k 2 -M 3 -t 8 -O 11 -E 4 -c -q 20 bfast_bwa_index/hg18_noran_mask.fa T3460_R3.fastq > bfast_matches_R3_bwa_T3460.bmf
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.80 sec
[bwa_aln_core] write to the disk... ************************************************************
In function "bwa_aln_core": Fatal Error[MallocMemory]. Message: Could not allocate (malloc) memory.
***** Exiting due to errors *****

I am running on Ubuntu with 32 Gb RAM.

Any help would be greatly appreciated

thanks alig
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