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Old 12-17-2015, 02:12 AM   #1
francism
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Location: Nigeria

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Default SOAPdenovo analysis

Having problem with saopdenovo analysis using two LIb i.e LIB (300) and LIB (500).[LIB] 0, avg_ins 300, reverse 0.
[LIB] 1, avg_ins 500, reverse 0.
398381277 node(s) allocated, 974962448 kmer(s) in reads, 974962448 kmer(s) processed.
*** glibc detected *** /opt/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer: double free or corruption (out): 0x0000000000e87710 ***
======= Backtrace: =========
[0x51aea6]
[0x4545b5]
[0x451195]
[0x43af32]
[0x4ebb00]
[0x4001b9]
======= Memory map: ========
00400000-005e2000 r-xp 00000000 08:01 27788141 /opt/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer
007e2000-007e5000 rw-p 001e2000 08:01 27788141 /opt/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer
007e5000-0097e000 rw-p 00000000 00:00 0
00e86000-0a944000 rw-p 00000000 00:00 0 [heap]
406b9000-406ba000 ---p 00000000 00:00 0
406ba000-40eba000 rw-p 00000000 00:00 0 [stack:31271]
40eba000-40ebb000 ---p 00000000 00:00 0
40ebb000-416bb000 rw-p 00000000 00:00 0 [stack:31272]
416bb000-416bc000 ---p 00000000 00:00 0
416bc000-41ebc000 rw-p 00000000 00:00 0 [stack:31273]
41ebc000-41ebd000 ---p 00000000 00:00 0
41ebd000-426bd000 rw-p 00000000 00:00 0 [stack:31274]
426bd000-426be000 ---p 00000000 00:00 0
426be000-42ebe000 rw-p 00000000 00:00 0 [stack:31275]
42ebe000-42ebf000 ---p 00000000 00:00 0
42ebf000-436bf000 rw-p 00000000 00:00 0 [stack:31276]
436bf000-436c0000 ---p 00000000 00:00 0
436c0000-43ec0000 rw-p 00000000 00:00 0 [stack:31277]
43ec0000-43ec1000 ---p 00000000 00:00 0
43ec1000-446c1000 rw-p 00000000 00:00 0 [stack:31278]
446c1000-446c2000 ---p 00000000 00:00 0
446c2000-44ec2000 rw-p 00000000 00:00 0 [stack:31279]
44ec2000-44ec3000 ---p 00000000 00:00 0
44ec3000-456c3000 rw-p 00000000 00:00 0 [stack:31280]
456c3000-456c4000 ---p 00000000 00:00 0
456c4000-456c7000 rw-p 00000000 00:00 0 [stack:8192]
456c7000-456c8000 ---p 00000000 00:00 0
456c8000-456cb000 rw-p 00000000 00:00 0 [stack:8193]
456cb000-456cc000 ---p 00000000 00:00 0
456cc000-456cf000 rw-p 00000000 00:00 0
456cf000-456d0000 ---p 00000000 00:00 0
456d0000-45ed0000 rw-p 00000000 00:00 0
45ed0000-45ed1000 ---p 00000000 00:00 0
45ed1000-466d1000 rw-p 00000000 00:00 0
466d1000-466d2000 ---p 00000000 00:00 0
466d2000-46ed2000 rw-p 00000000 00:00 0
7f855c5b1000-7f85fde54000 rw-p 00000000 00:00 0
7f85fde54000-7f869f6f7000 rw-p 00000000 00:00 0
7f869f6f7000-7f8740f9a000 rw-p 00000000 00:00 0
7f8740f9a000-7f87e283d000 rw-p 00000000 00:00 0
7f87e283d000-7f88840e0000 rw-p 00000000 00:00 0
7f88840e0000-7f8925983000 rw-p 00000000 00:00 0
7f8925984000-7f89c7227000 rw-p 00000000 00:00 0
7f89c7227000-7f8a68aca000 rw-p 00000000 00:00 0
7f8ab971d000-7f8b5afc0000 rw-p 00000000 00:00 0
7f8c1e8e4000-7f8c239ac000 rw-p 00000000 00:00 0
7f8c239ac000-7f8cc524f000 rw-p 00000000 00:00 0
7f8cc524f000-7f8cc82c7000 rw-p 00000000 00:00 0
7f8cccb7e000-7f8ccebce000 rw-p 00000000 00:00 0
7f8cd0000000-7f8cd0062000 rw-p 00000000 00:00 0
7f8cd0062000-7f8cd4000000 ---p 00000000 00:00 0
7f8cd4635000-7f8dcf6a3000 rw-p 00000000 00:00 0
7fff0d7b3000-7fff0d7d4000 rw-p 00000000 00:00 0 [stack]
7fff0d7e8000-7fff0d7ea000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted

Please, can someone help me to check what is causing this problem.
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Old 12-17-2015, 03:13 AM   #2
GenoMax
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Perhaps SoapDeNovo is running out of memory? Does the error occur right away or some time into analysis?
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Old 12-17-2015, 03:41 AM   #3
francism
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it occurs into the analysis after 25mins.
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Old 12-17-2015, 03:47 AM   #4
GenoMax
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Then I am inclined towards the running out of memory possibility. What are you assembling and how much memory do you have available? Have you looked at top/iostat to see if memory is getting exhausted?
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