SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
pacBioToCa .spec file options jpearl01 Pacific Biosciences 31 11-20-2014 06:48 AM
PacBioToCA no output nanto Bioinformatics 6 06-15-2014 06:35 PM
PACBIOtoCA for MAC joxcargator73 Bioinformatics 1 03-26-2013 12:20 AM
pacbioToCA failed shiningway Bioinformatics 3 02-28-2013 03:47 PM
errors with PacBioToCA in Celera shuang Bioinformatics 2 03-08-2012 08:42 AM

Reply
 
Thread Tools
Old 03-31-2013, 06:54 PM   #1
zszong@hotmail.com
Member
 
Location: Burnaby

Join Date: Sep 2012
Posts: 17
Default pacbioToCA: merTrim failed

Hi everyone,

I have been trying to get pacbioToCA to work for the past 3 weeks without luck. Every time it failed at the MerTrim stage.

To troubleshoot this, I download the example data set from the pacBioToCA wiki: http://sourceforge.net/apps/mediawik...o_RS_Sequences.

I followed very carefully to generate frg file, convert fasta to fastq. These were all fine. But when I did the error correct from command line: /home/zzong/bin/wgs-7.0/Linux-amd64/bin/pacBioToCA -length 500 -partitions 200 -l pacbio -t 16 -s pacbio.spec -fastq pacbio.filtered_subreads.fastq illumina.frg > run.out 2>&1

I got the merTrim error again. I suspect it has something to do with the spec file. However, it was downloaded from the sampleData set. Are there some parameters need to be adjusted? Could someone help to have a look what went wrong and help me out? The error messages in the run.out file are as follow:

Many thanks in advance!

Stuart
#######################
pacbio.spc
# original asm settings
utgErrorRate = 0.25
utgErrorLimit = 4.5

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


Error messages:
###############################################
Running with 16 threads and 200 partitions
Starting correction...
CA: /home/zzong/bin/wgs-7.0/Linux-amd64/bin
AMOS:/home/zzong/bin/amos-3.1.0/src/Bank
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname PacBio -type sanger -innie -technology pacbio -reads /home/zzong/project/chlamy/sampleData/pacbio.filtered_subreads.fastq > /home/zzong/project/chlamy/sampleData//pacbio.frg
----------------------------------------END Sun Mar 31 19:40:43 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio sge=" -sync y" sgePropagateHold=corAsm stopAfter=initialStoreBuilding illumina.frg /home/zzong/project/chlamy/sampleData//pacbio.frg
----------------------------------------START Sun Mar 31 19:40:43 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/gatekeeper -o /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore.BUILDING -T -F /home/zzong/project/chlamy/sampleData/illumina.frg /home/zzong/project/chlamy/sampleData//pacbio.frg > /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore.err 2>&1
----------------------------------------END Sun Mar 31 19:40:45 2013 (2 seconds)
numFrags = 28747
Stop requested after 'initialstorebuilding'.
----------------------------------------END Sun Mar 31 19:40:45 2013 (2 seconds)
----------------------------------------START Sun Mar 31 19:40:45 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio ovlHashLibrary=2 ovlRefLibrary=1-1 obtHashLibrary=1-1 obtRefLibrary=1-1 sge=" -sync y" sgePropagateHold=corAsm stopAfter=overlapper
----------------------------------------START Sun Mar 31 19:40:45 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -B -C -v -m 14 -memory 128000 -threads 16 -c 0 -L 2 -s /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore:chain -o /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/meryl.err 2>&1
----------------------------------------END Sun Mar 31 19:40:47 2013 (2 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/estimate-mer-threshold -g /home/zzong/project/chlamy/sampleData/temppacbio/asm.gkpStore:chain -m /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0.estMerThresh.out 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0.estMerThresh.err
----------------------------------------END Sun Mar 31 19:40:47 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -Dt -n 62 -s /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.ovl.fasta 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.ovl.fasta.err
----------------------------------------END Sun Mar 31 19:40:47 2013 (0 seconds)
----------------------------------------START Sun Mar 31 19:40:47 2013
/home/zzong/bin/wgs-7.0/Linux-amd64/bin/meryl -Dt -n 62 -s /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm-C-ms14-cm0 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.obt.fasta 2> /home/zzong/project/chlamy/sampleData/temppacbio/0-mercounts/asm.nmers.obt.fasta.err
----------------------------------------END Sun Mar 31 19:40:48 2013 (1 seconds)
Reset OBT mer threshold from auto to 62.
Reset OVL mer threshold from auto to 62.
----------------------------------------START CONCURRENT Sun Mar 31 19:40:48 2013
/home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim/mertrim.sh 1 > /home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim/asm.0001.err 2>&1
----------------------------------------END CONCURRENT Sun Mar 31 19:40:48 2013 (0 seconds)
================================================================================

runCA failed.

----------------------------------------
Stack trace:

at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 1237.
main::caFailure('merTrim failed. See *.err in /home/zzong/project/chlamy/samp...', undef) called at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 2794
main::merTrim() called at /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA line 5875

----------------------------------------
Failure message:

merTrim failed. See *.err in /home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim

----------------------------------------END Sun Mar 31 19:40:48 2013 (3 seconds)
Failed to execute /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio ovlHashLibrary=2 ovlRefLibrary=1-1 obtHashLibrary=1-1 obtRefLibrary=1-1 sge=" -sync y" sgePropagateHold=corAsm stopAfter=overlapper
zszong@hotmail.com is offline   Reply With Quote
Old 04-02-2013, 02:08 PM   #2
zszong@hotmail.com
Member
 
Location: Burnaby

Join Date: Sep 2012
Posts: 17
Default

Hi All,

From the error message "Failed to execute /home/zzong/bin/wgs-7.0/Linux-amd64/bin/runCA -s pacbio.spec -p asm -d temppacbio ovlHashLibrary=2 ovlRefLibrary=1-1 obtHashLibrary=1-1 obtRefLibrary=1-1 sge=" -sync y" sgePropagateHold=corAsm stopAfter=overlapper "

Does this mean there is a library missing?

Again, Thanks for your input!

Stuart
zszong@hotmail.com is offline   Reply With Quote
Old 04-05-2013, 04:37 PM   #3
mjhsieh
Member
 
Location: USA

Join Date: Jan 2013
Posts: 10
Default

Quote:
Originally Posted by zszong@hotmail.com View Post
Hi All,
Does this mean there is a library missing?
Probably not, from the original error,
Quote:
merTrim failed. See *.err in /home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim
you might have better luck checking the err files in /home/zzong/project/chlamy/sampleData/temppacbio/0-mertrim directory.
mjhsieh is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 03:26 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO