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thegenemyers / DALIGNER

Find all significant local alignments between reads
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daligner crash #22

Closed dgordon562 closed 8 years ago

dgordon562 commented 9 years ago

This is the daligner that is part of v0.3.3 Falcon.

With a particular pair of files it gives (see below).

Let me know what other information I can provide you...

. . . Building index for raw_reads.193

Kmer count = 399,655,782 Using 11.91Gb of space Revised kmer count = 334,780,204 Index occupies 4.99Gb

Comparing c(raw_reads.545) to raw_reads.193

Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 997,361,227 Highwater of 39.67Gb space * glibc detected * daligner: free(): invalid pointer: 0x00002bb67c0008c0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x37b6c75e66] daligner[0x4097a2] daligner[0x406f1d] daligner[0x402817] /lib64/libc.so.6(__libc_start_main+0xfd)[0x37b6c1ed5d] daligner[0x401339] ======= Memory map: ======== 00400000-00421000 r-xp 00000000 00:36 3895273357 /net/gs/vol1/home/dg ordon/falcon150714/FALCON-integrate/DALIGNER/daligner 00620000-00621000 rw-p 00020000 00:36 3895273357 /net/gs/vol1/home/dg ordon/falcon150714/FALCON-integrate/DALIGNER/daligner 00621000-00624000 rw-p 00000000 00:00 0 01d80000-01dd9000 rw-p 00000000 00:00 0 [heap] 37b6800000-37b6820000 r-xp 00000000 fd:00 41418757 /lib64/ld-2.12.so 37b6a1f000-37b6a20000 r--p 0001f000 fd:00 41418757 /lib64/ld-2.12.so 37b6a20000-37b6a21000 rw-p 00020000 fd:00 41418757 /lib64/ld-2.12.so 37b6a21000-37b6a22000 rw-p 00000000 00:00 0 . . .

pb-jchin commented 9 years ago

@dgordon562 you will need to give @thegenemyers some example data, otherwise it is probably very hard to see what is going on. I suggest trying to use "-M" option to see if you can push the job through.

thegenemyers commented 9 years ago

Sorry for the very late reply.

Are you running on a 40Gb+ memory machine? Looks like it ran out of memory and then did not exit gracefully. If that is not the problem then I would like to know the exact code line on which it died -- you can get this by compiling the the -g flag instead of the -O3, run with gdb or lldb and ask for a backtrace. That or I need the input which seems like a non-starter given its size.

Cheers,
     Gene

On 7/27/15, 6:01 PM, dgordon562 wrote:

This is the daligner that is part of v0.3.3 Falcon.

With a particular pair of files it gives (see below).

Let me know what other information I can provide you...

. . . Building index for raw_reads.193

Kmer count = 399,655,782 Using 11.91Gb of space Revised kmer count = 334,780,204 Index occupies 4.99Gb

Comparing c(raw_reads.545) to raw_reads.193

Capping mutual k-mer matches over 10000 (effectively -t100) Hit count = 997,361,227 Highwater of 39.67Gb space * glibc detected * daligner: free(): invalid pointer: 0x00002bb67c0008c0 *** ======= Backtrace: ========= /lib64/libc.so.6[0x37b6c75e66] daligner[0x4097a2] daligner[0x406f1d] daligner[0x402817] /lib64/libc.so.6(__libc_start_main+0xfd)[0x37b6c1ed5d] daligner[0x401339] ======= Memory map: ======== 00400000-00421000 r-xp 00000000 00:36 3895273357 /net/gs/vol1/home/dg ordon/falcon150714/FALCON-integrate/DALIGNER/daligner 00620000-00621000 rw-p 00020000 00:36 3895273357 /net/gs/vol1/home/dg ordon/falcon150714/FALCON-integrate/DALIGNER/daligner 00621000-00624000 rw-p 00000000 00:00 0 01d80000-01dd9000 rw-p 00000000 00:00 0 [heap] 37b6800000-37b6820000 r-xp 00000000 fd:00 41418757 /lib64/ld-2.12.so 37b6a1f000-37b6a20000 r--p 0001f000 fd:00 41418757 /lib64/ld-2.12.so 37b6a20000-37b6a21000 rw-p 00020000 fd:00 41418757 /lib64/ld-2.12.so 37b6a21000-37b6a22000 rw-p 00000000 00:00 0 . . .

— Reply to this email directly or view it on GitHub https://github.com/thegenemyers/DALIGNER/issues/22.

dgordon562 commented 9 years ago

Hi, Gene,

Yes, the computer has 180GB of RAM. I will get you a backtrace.

Best wishes, David