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#22 Assembling a MinION dataset - spec falcon_sense options problems
I have been trying to use PBcR to assemble the example MinION dataset given in http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR#Assembling_a_MinION_dataset with the spec file as given. However when I do, I get the following stack:
###
### Reading options from '../sampleDataOxford/oxford.spec'
###
###
### Reading options from the command line.
###
Warning: no frag files specified, assuming self-correction of pacbio sequences.
Running with 64 threads and 200 partitions
which: no bank-transact in <path>
********* Starting correction...
CA: /gpfs0/apps/well/wgs/8.3rc1/Linux-amd64/bin
AMOS:
SMRTportal:/apps/well/wgs/8.3rc1/Linux-amd64/bin (blasr 1.3.1.142244)
Bowtie:/apps/well/bowtie2/2.2.5
******** Configuration Summary ********
bankPath =
gridEngineNameOption = -cwd -N
gridEngineHoldOption = -hold_jid "WAIT_TAG"
maxCoverage = 40
utgErrorLimit = 6.5
fastqFile = ../../data/sampleDataOxford/
gridEnginePropagateCommand = qalter -hold_jid "WAIT_TAG"
partitions = 200
asmOvlErrorRate = 0.3
QV = 54.5
assemble = 1
gridEngineArrayOption = -t ARRAY_JOBS
asmObtErrorRate = 0.03
gridEngineJobID = JOB_ID
specFile = ../sampleDataOxford/oxford.spec
longReads = 1
cnsMinFrags = 1000
falconOptions = --max_n_read 200 --min_idt 0.50 --output_multi --local_match_count_threshold 0
unitigger = bogart
mhap =
ovlRefBlockLength = 100000000000
gridOptionsOverlap = -pe threads 16 -l mem=2GB
cnsErrorRate = 0.25
assembleCoverage = 25
mhapVersion = 1.5b1
cnsConcurrency = 64
asmUtgErrorRate = 0.3
blasr =
merylThreads = 64
ovlRefBlockSize = 0
batOptions = -RS -CS
falconcns = 1
utgErrorRate = 0.25
gridOptions =
mhapPrecompute = 1
cgwErrorRate = 0.25
pbcns = 0
ovlStoreMemory = 1033892
asmOBT = 0
scriptOnGrid = 0
asmMerSize = 22
length = 500
merSize = 14
utgGraphErrorLimit = 0
utgGraphErrorRate = 0.3
gridEngineSyncOption = -sync y
gridEngineTaskID = SGE_TASK_ID
useGrid = 0
utgMergeErrorRate = 0.3
genomeSize = 4650000
gridOptionsCorrection = -pe threads 16 -l mem=2GB
cleanup = 1
gridOptionsConsensus = -pe threads 16
coverageCutoff = 0
doOverlapBasedTrimming = 0
gridOptionsScript = -pe threads 1
gridEngineArrayName = ARRAY_NAME
samFOFN =
ovlErrorRate = 0.25
ovlHashBlockLength = 1000000000
ovlConcurrency = 1
merylMemory = 1033892
asmObtErrorLimit = 4.5
gridEngineOutputOption = -j y -o
repeats =
falconForce = 1
onlyContained = 0
consensusConcurrency = 64
shortReads =
utgMergeErrorLimit = 0
gridEngineNameToJobIDCommand =
doFragmentCorrection = 1
asmCgwErrorRate = 0.3
ovlMemory = 1009
shell = /bin/bash
ovlThreads = 64
gridEngineArraySubmitID = $TASK_ID
frgMinLen = 64
gridEngineSubmitCommand = qsub
submitToGrid = 0
threads = 64
doUnitigSplitting = 0
asmCns = pbutgcns
libraryname = sampleDataOxford
maxUncorrectedGap = 1500
bowtie =
sensitive = 0
asmCnsErrorRate = 0.3
****************
----------------------------------------START Mon Aug 17 15:55:18 2015
/gpfs0/apps/well/wgs/8.3rc1/Linux-amd64/bin/runCA -s /data2/users/rachel/projects/initial/phillippy_method/sampleDataOxford//tempsampleDataOxford/sampleDataOxford.spec -p asm -d tempsampleDataOxford stopAfter=initialStoreBuilding /data2/users/rachel/projects/initial/phillippy_method/sampleDataOxford//tempsampleDataOxford/sampleDataOxford.frg
usage: runCA -d <dir> -p <prefix> [options] <frg> ...
-d <dir> Use <dir> as the working directory. Required
-p <prefix> Use <prefix> as the output prefix. Required
-s <specFile> Read options from the specifications file <specfile>.
<specfile> can also be one of the following key words:
[no]OBT - run with[out] OBT
noVec - run with OBT but without Vector
-version Version information
-help This information
-options Describe specFile options, and show default values
<frg> CA formatted fragment file
Complete documentation at http://wgs-assembler.sourceforge.net/
'falconOptions' is not a valid option; see 'runCA -options' for a list of valid options.
'falconForce' is not a valid option; see 'runCA -options' for a list of valid options.
----------------------------------------END Mon Aug 17 15:55:18 2015 (0 seconds)
gkStore::gkStore()-- GateKeeper Store '/data2/users/rachel/projects/initial/phillippy_method/sampleDataOxford//tempsampleDataOxford/asm.gkpStore' doesn't exist.
Error: The PacBio library 0 must be the last library loaded but it preceedes 0. Please double-check your input files and try again. at /apps/well/wgs/8.3rc1/Linux-amd64/bin/PBcR line 1462.
When I try instead with the two falcon options commented out in the spec file, it runs for longer, eventually failing with:
----------------------------------------START Tue Aug 18 12:28:55 2015
/usr/bin/env perl /gpfs0/apps/well/wgs/8.3rc1/Linux-amd64/bin/caqc.pl -euid /data2/users/rachel/projects/initial/phillippy_method/sampleDataOxford/JR_FAA56953_22072015_Kox_CAV1374/9-terminator/asm.asm
Can't locate Statistics/Descriptive.pm in @INC (@INC contains: /apps/well/bioperl/1.6.923 /apps/well/bioperl/1.6.923 /apps/well/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /gpfs0/apps/well/wgs/8.3rc1/Linux-amd64/bin/caqc.pl line 18.
BEGIN failed--compilation aborted at /gpfs0/apps/well/wgs/8.3rc1/Linux-amd64/bin/caqc.pl line 18.
----------------------------------------END Tue Aug 18 12:28:55 2015 (0 seconds)
ERROR: Failed with signal INT (2)
The Cleaner has arrived. Doing 'none'.
----------------------------------------END Tue Aug 18 12:28:55 2015 (1816 seconds)
I've tried with a few different PBcR builds (8.2, 8.3rc1, 8.3rc2) and for each with the falcon_sense options in the spec file, or commented out. With them in, I universally get the 'not a valid option' error, and when they are left out, it breaks with different errors for each sample (6 bacterial genomes). I've also tried downloading FALCON and adding to my path with no success.
Am I missing some prerequisite software, or misunderstanding the how-to guide for assembline the MinION dataset?
Only version 8.3rc2 has the added support for the falcon options required for nanopore assembly. If you previously had a failed run with CA 8.3rc1, make sure the temporary folder (tempsampleDataOxford) is removed and try re-running the command using CA 8.3rc2. Since 8.3rc1 was not designed to handle these options it most likely left behind an incomplete temporary directory which 8.3rc2 is trying to resume from and failing.
Serge
Related
Support Requests:
#22Thanks! This has fixed the falcon_sense problem. I've run into a new one with
fastqToCA: /lib64/libc.so.6: version `GLIBC_2.14' not found
but since this is an issue with updating a library, I've taken it to rescomp.
This is most likely because the assembler was built with a newer GCC (4.8.3) than you have available on your system. If you can build the code from source on your system or install the newer GCC release, the issue should be resolved.
Related
Support Requests:
#22