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#341 runCA error!
Dear all,
I run runCA. I met this error many times. Could you help me check what it is err and how to fix it?
Thanks,
Fuyou
Warning: after correction only 6.71623837989097X for genome 1638032715. Not performing automated assembly.
To manually launch an assembly run:
/depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/runCA -s /scratch/snyder/f/fu115/Genome_assembly/PBonly//tempstriga/striga.spec -p asm -d striga ovlRefBlockLength=100000000000 ovlRefBlockSize=0 useGrid=0 scriptOnGrid=0 unitigger=bogart ovlErrorRate=0.03 utgErrorRate=0.025 cgwErrorRate=0.1 cnsErrorRate=0.1 utgGraphErrorLimit=0 utgGraphErrorRate=0.025 utgMergeErrorLimit=0 utgMergeErrorRate=0.025 frgCorrBatchSize=100000 doOverlapBasedTrimming=1 obtErrorRate=0.03 obtErrorLimit=4.5 frgMinLen=3000 ovlMinLen=500 "batOptions=-RS -NS -CS" consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 gridEnginePropagateHold="pBcR_asm" striga.longest25.frg
Then I run this command by manually.
I get the error files
as
----------------------------------------START Thu Dec 15 20:20:49 2016
/depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/gatekeeper -o /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/asm.gkpStore.BUILDING -T -F /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga.longest25.frg > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/asm.gkpStore.err 2>&1
----------------------------------------END Thu Dec 15 20:22:38 2016 (109 seconds)
numFrags = 488568
----------------------------------------START Thu Dec 15 20:22:38 2016
/depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/initialTrim \
-log /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim/asm.initialTrim.log \
-frg /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/asm.gkpStore \
/scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim/asm.initialTrim.summary \ 2> /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim/asm.initialTrim.err
----------------------------------------END Thu Dec 15 20:22:43 2016 (5 seconds)
----------------------------------------START Thu Dec 15 20:22:43 2016
/depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/meryl -B -C -v -m 22 -memory 516749 -threads 20 -c 0 -L 2 -s /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/asm.gkpStore:chain -o /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm-C-ms22-cm0 > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/meryl.err 2>&1
----------------------------------------END Thu Dec 15 20:34:48 2016 (725 seconds)
----------------------------------------START Thu Dec 15 20:34:48 2016
/depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/estimate-mer-threshold -m /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm-C-ms22-cm0 > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm-C-ms22-cm0.estMerThresh.out 2> /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm-C-ms22-cm0.estMerThresh.err
----------------------------------------END Thu Dec 15 20:34:49 2016 (1 seconds)
----------------------------------------START Thu Dec 15 20:34:49 2016
/depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/meryl -Dt -n 2593 -s /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm-C-ms22-cm0 > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm.nmers.obt.fasta 2> /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm.nmers.obt.fasta.err
----------------------------------------END Thu Dec 15 20:35:01 2016 (12 seconds)
----------------------------------------START Thu Dec 15 20:35:01 2016
/depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/meryl -Dt -n 2593 -s /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm-C-ms22-cm0 > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm.nmers.ovl.fasta 2> /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-mercounts/asm.nmers.ovl.fasta.err
----------------------------------------END Thu Dec 15 20:35:14 2016 (13 seconds)
Reset OBT mer threshold from to 2593.
Reset OVL mer threshold from to 2593.
----------------------------------------START Thu Dec 15 20:35:14 2016
/depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/overlap_partition \ -g /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/asm.gkpStore \ -bl 1000000000 \ -bs 0 \ -rs 0 \ -rl 100000000000 \ -o /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap \ /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/overlap_partition.err 2>&1
----------------------------------------END Thu Dec 15 20:35:14 2016 (0 seconds)
Created 4 overlap jobs. Last batch '001', last job '000004'.
----------------------------------------START CONCURRENT Thu Dec 15 20:35:14 2016
/scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/overlap.sh 1 > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/000001.out 2>&1
/scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/overlap.sh 2 > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/000002.out 2>&1
/scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/overlap.sh 3 > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/000003.out 2>&1
/scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/overlap.sh 4 > /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/000004.out 2>&1
----------------------------------------END CONCURRENT Thu Dec 15 20:45:03 2016 (589 seconds)
================================================================================
runCA failed.
Stack trace:
at /depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/runCA line 1650
main::caFailure('ERROR: Overlap job /scratch/snyder/f/fu115/Genome_assembly/P...', undef) called at /depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/runCA line 3900
main::checkOverlapper('trim') called at /depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/runCA line 3938
main::checkOverlap('trim') called at /depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/runCA line 4100
main::overlapTrim() called at /depot/bioinfo/apps/apps/wgs-8.3rc1/Linux-amd64/bin/runCA line 6554
Failure message:
ERROR: Overlap job /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/001/000001 FAILED.
ERROR: Overlap job /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/001/000002 FAILED.
ERROR: Overlap job /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/001/000003 FAILED.
ERROR: Overlap job /scratch/snyder/f/fu115/Genome_assembly/PBonly/striga/0-overlaptrim-overlap/001/000004 FAILED.
4 overlapper jobs failed
The error message is that you do not have sufficient coverage in corrected
reads to get a good assembly. You won't be able to assemble 6X of data so
it's not worth trying to run the runCA command manually.
I suggest you look at Canu (canu.readthedocs.com), especially the suggested
parameters for low coverage if you have 30X raw read coverage or less.
runCA/Celera Assembler is no longer maintained.
On Thu, Dec 15, 2016 at 9:14 PM, Fuyou Fu sunnycqcn@users.sf.net wrote:
Related
Bugs: #341
OK. Thanks.
Fuyou
On Fri, Dec 16, 2016 at 7:51 AM, Sergey Koren skoren@users.sf.net wrote:
--
Fuyou Fu, Ph.D.
Department of Botany and Plant Pathology
Purdue University
USA
Related
Bugs: #341