Question: PacBioToCA problem in correction
0
gravatar for midox
3.2 years ago by
midox260
Tunisia
midox260 wrote:

Hello,

I try to run PacBioToCA to correct long reads.

But here is the error.

**###
###  Reading options from 'spec_file.spec'
###
Warning: no frag files specified, assuming self-correction of pacbio sequences.
Running with 8 threads and 200 partitions
which: no blasr in (/usr/local/public/perl-5-24.0/bin/:/usr/local/public/R/bin:/usr/local/public/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/genome/ProtTest/mpj/bin:/usr/lib64/openmpi/bin/:/usr/local/public/python-2.7.13/bin:/bin:/sbin:/tmp/8753.1.infinit.q:/usr/local/public/perl-5-24.0/bin/:/usr/local/public/R/bin:/usr/local/public/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/genome/ProtTest/mpj/bin:/usr/lib64/openmpi/bin/:/usr/local/public/python-2.7.13/bin:/bin:/sbin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/usr/local/genome/bin:/usr/local/public/java/bin:/usr/local/public/bin:/usr/local/adm/bin:/usr/local/adm/script:/usr/local/genome/emboss/bin:/usr/local/genome/meme/bin:/usr/local/genome/src/microbiomeutil-r20110519/ChimeraSlayer:/usr/local/genome/infernal-1.1.1/bin:/usr/local/genome/src/MaxBin-2.2.1:/usr/local/genome/cd-hit:/usr/local/genome/kaiju/bin:/usr/local/genome/fastx_toolkit/bin:/usr/local/genome/hmmer/bin:/usr/local/genome/ssu-align-0.1.1/bin:/usr/local/genome/sratoolkit/bin:/usr/local/genome/kSNP:/usr/local/genome//gt-1.5.9/bin:/usr/local/genome/IM-TORNADO-2.0.3.3/bin:/usr/local/genome/qpdf/bin:/usr/local/genome/novoalign-2.08.01:/usr/local/genome/ncbi-blast-2.2.31+/bin:/usr/local/genome/CLARKSCV1.2.3/exe/:/usr/local/genome/CLARKSCV1.2.3/:/usr/local/genome/MUMmer:/usr/local/genome/amos/bin:/usr/local/genome/art_bin_MountRainier:/usr/local/genome/xplor-nih-2.44:/usr/local/genome/abyss/bin:/usr/local/genome/vcflib/bin:/usr/local/genome/kraken/bin:/usr/local/genome/phylip/bin:/usr/local/genome/phylobayes3.3f/exe_lin64/:/usr/local/genome/mafft/bin:/usr/local/genome/hhsuite/bin:/usr/local/genome/mgltools/bin:/usr/local/genome/prokka/bin:/usr/local/genome/ProtTest:/usr/local/genome/debarder:/usr/local/genome/reago-1.1-master:/usr/local/genome/colony2-20170125:/usr/local/genome/src/phast-1.4/bin:/usr/local/genome/script:/projet/maiage/save/mkchouk/bin:/usr/local/genome/bin:/usr/local/public/java/bin:/usr/local/public/bin:/usr/local/adm/bin:/usr/local/adm/script:/usr/local/genome/emboss/bin:/usr/local/genome/meme/bin:/usr/local/genome/src/microbiomeutil-r20110519/ChimeraSlayer:/usr/local/genome/infernal-1.1.1/bin:/usr/local/genome/src/MaxBin-2.2.1:/usr/local/genome/cd-hit:/usr/local/genome/kaiju/bin:/usr/local/genome/fastx_toolkit/bin:/usr/local/genome/hmmer/bin:/usr/local/genome/ssu-align-0.1.1/bin:/usr/local/genome/sratoolkit/bin:/usr/local/genome/kSNP:/usr/local/genome//gt-1.5.9/bin:/usr/local/genome/IM-TORNADO-2.0.3.3/bin:/usr/local/genome/qpdf/bin:/usr/local/genome/novoalign-2.08.01:/usr/local/genome/ncbi-blast-2.2.31+/bin:/usr/local/genome/CLARKSCV1.2.3/exe/:/usr/local/genome/CLARKSCV1.2.3/:/usr/local/genome/MUMmer:/usr/local/genome/amos/bin:/usr/local/genome/art_bin_MountRainier:/usr/local/genome/xplor-nih-2.44:/usr/local/genome/abyss/bin:/usr/local/genome/vcflib/bin:/usr/local/genome/kraken/bin:/usr/local/genome/phylip/bin:/usr/local/genome/phylobayes3.3f/exe_lin64/:/usr/local/genome/mafft/bin:/usr/local/genome/hhsuite/bin:/usr/local/genome/mgltools/bin:/usr/local/genome/prokka/bin:/usr/local/genome/ProtTest:/usr/local/genome/debarder:/usr/local/genome/reago-1.1-master:/usr/local/genome/colony2-20170125:/usr/local/genome/script:/projet/maiage/save/mkchouk/bin)
********* Starting correction...
 CA: /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin
AMOS:/usr/local/genome/amos/bin
SMRTportal:/projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin (blasr 1.3.1.142244)
Bowtie:/usr/local/genome/bin
******** Configuration Summary ********
...
...
----------------------------------------END Fri Apr 14 11:57:08 2017 (0 seconds)
Created 0 overlap jobs.  Last batch '', last job ''.
----------------------------------------START CONCURRENT Fri Apr 14 11:57:08 2017
----------------------------------------END CONCURRENT Fri Apr 14 11:57:08 2017 (0 seconds)
----------------------------------------START Fri Apr 14 11:57:08 2017
find -L /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim-overlap \( -name \*ovb.gz -or -name \*ovb \) -print > /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.list
----------------------------------------END Fri Apr 14 11:57:08 2017 (0 seconds)
----------------------------------------START Fri Apr 14 11:57:08 2017
/projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild  -obt  -o /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.BUILDING  -g /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore  -M 8192 -L /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.list > /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.err 2>&1
----------------------------------------END Fri Apr 14 11:57:08 2017 (0 seconds)
ERROR: Failed with signal HUP (1)
================================================================================
runCA failed.
----------------------------------------
Stack trace:
 at /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 1628.
    main::caFailure("failed to build the obt store", "/projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/L"...) called at /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 3819
    main::overlapTrim() called at /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 6252
----------------------------------------
Last few lines of the relevant log file (/projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.err):
----------------------------------------
Failure message:
failed to build the obt store
----------------------------------------END Fri Apr 14 11:57:08 2017 (2 seconds)
Failed to execute /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d LIB 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=100 "batOptions=-RS -NS -CS" consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 gridEnginePropagateHold="pBcR_asm"  LIB.longest25.frg**

can you help me.

Thanks.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by midox260
0
gravatar for Pierre Lindenbaum
3.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

which: no blasr in ...

It's a $PATH problem or a blasr is not installed:

ADD COMMENTlink written 3.2 years ago by Pierre Lindenbaum129k

i istalled blasr. how integrate this in PATH please?

ADD REPLYlink written 3.2 years ago by midox260

https://unix.stackexchange.com/questions/26047

ADD REPLYlink written 3.2 years ago by Pierre Lindenbaum129k

it's the same problem:

###

Reading options from 'spec_file.spec'

#

Warning: no frag files specified, assuming self-correction of pacbio sequences. Running with 8 threads and 200 partitions *** Starting correction... CA: /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin AMOS:/usr/local/genome/amos/bin SMRTportal:/projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin (blasr 1.3.1.142244) Bowtie:/usr/local/genome/bin ..... .... /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/overlapStoreBuild -obt -o /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.BUILDING -g /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/asm.gkpStore -M 8192 -L /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.list > /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.err 2>&1 ----------------------------------------END Fri Apr 14 16:19:05 2017 (0 seconds)

ERROR: Failed with signal HUP (1)

runCA failed.


Stack trace:

at /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 1628. main::caFailure("failed to build the obt store", "/projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/L"...) called at /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 3819 main::overlapTrim() called at /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA line 6252


Last few lines of the relevant log file (/projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA/LIB/0-overlaptrim/asm.obtStore.err):


Failure message:

failed to build the obt store

----------------------------------------END Fri Apr 14 16:19:05 2017 (1 seconds) Failed to execute /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/Linux-amd64/bin/runCA -s /projet/maiage/save/mkchouk/Bureau/wgs-8.3rc2/test_fataToCA//tempLIB/LIB.spec -p asm -d LIB 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=100 "batOptions=-RS -NS -CS" consensus=pbutgcns merSize=22 cnsMaxCoverage=1 cnsReuseUnitigs=1 gridEnginePropagateHold="pBcR_asm" LIB.longest25.frg

ADD REPLYlink written 3.2 years ago by midox260

have you any response to this? please

ADD REPLYlink written 3.2 years ago by midox260
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