I’m trying to use pacbioToCa to correct the pacbio reads with some 90bp pair end Illumina reads. This a 11Mb bacterial genome. It failed at the overlap.sh step. There were 49 overlap.sh processes and only 4 of them generated output files. I'm using a stand alone Linux machine with 8 core and 16GB memory.
Some out files in the 0-overlaptrim-overlap directory show this kind of err:
~/0-overlaptrim-overlap/overlap.sh: line 61: 9271 Killed
$bin/overlapInCore -G --hashbits 24 --hashload 0.75 -t 2 $opt
-k 10 -k /data1/PacBioClip30x/0-mercounts/asm.nmers.obt.fasta -o /data1/PacBioClip30x/0-overlaptrim-overlap/$bat/$job.ovb.WORKING.gz -H 1-1 -R 1-1 /data1/PacBioClip30x/asm.gkpStore
Some other out files in the same directory show memory issue:
Could not malloc memory (3623878656 bytes)
overlapInCore: AS_UTL_alloc.C:73: void* safe_malloc(size_t): Assertion `p != __null' failed.
The spec file I used is the following. Could you tell me what I can add/modify to run pacbioToCA? Thanks a lot for any help.
# original asm settings
utgErrorRate = 0.25
utgErrorLimit = 6.5
cnsErrorRate = 0.25
cgwErrorRate = 0.25
ovlErrorRate = 0.25
#merSize=14
merylMemory = 128000
merylThreads = 16
ovlStoreMemory = 8192
# grid info
useGrid = 0
scriptOnGrid = 0
frgCorrOnGrid = 0
ovlCorrOnGrid = 0
ovlHashBits = 24
ovlThreads = 2
ovlHashBlockLength = 20000000
ovlRefBlockSize = 50000000
frgCorrThreads = 2
frgCorrBatchSize = 100000
ovlCorrBatchSize = 100000
ovlConcurrency = 6
cnsConcurrency = 16
frgCorrConcurrency = 8
ovlCorrConcurrency = 16
cnsConcurrency = 16
#shortReads
frgMinLen = 65 # smaller than your read length
ovlMinLen = 48 # about 75% of your frgMinLen
merSize = 10
Some out files in the 0-overlaptrim-overlap directory show this kind of err:
~/0-overlaptrim-overlap/overlap.sh: line 61: 9271 Killed
$bin/overlapInCore -G --hashbits 24 --hashload 0.75 -t 2 $opt
-k 10 -k /data1/PacBioClip30x/0-mercounts/asm.nmers.obt.fasta -o /data1/PacBioClip30x/0-overlaptrim-overlap/$bat/$job.ovb.WORKING.gz -H 1-1 -R 1-1 /data1/PacBioClip30x/asm.gkpStore
Some other out files in the same directory show memory issue:
Could not malloc memory (3623878656 bytes)
overlapInCore: AS_UTL_alloc.C:73: void* safe_malloc(size_t): Assertion `p != __null' failed.
The spec file I used is the following. Could you tell me what I can add/modify to run pacbioToCA? Thanks a lot for any help.
# original asm settings
utgErrorRate = 0.25
utgErrorLimit = 6.5
cnsErrorRate = 0.25
cgwErrorRate = 0.25
ovlErrorRate = 0.25
#merSize=14
merylMemory = 128000
merylThreads = 16
ovlStoreMemory = 8192
# grid info
useGrid = 0
scriptOnGrid = 0
frgCorrOnGrid = 0
ovlCorrOnGrid = 0
ovlHashBits = 24
ovlThreads = 2
ovlHashBlockLength = 20000000
ovlRefBlockSize = 50000000
frgCorrThreads = 2
frgCorrBatchSize = 100000
ovlCorrBatchSize = 100000
ovlConcurrency = 6
cnsConcurrency = 16
frgCorrConcurrency = 8
ovlCorrConcurrency = 16
cnsConcurrency = 16
#shortReads
frgMinLen = 65 # smaller than your read length
ovlMinLen = 48 # about 75% of your frgMinLen
merSize = 10
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