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Old 02-18-2016, 11:40 AM   #51
DNA Sorcerer
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Location: Canada

Join Date: Mar 2010
Posts: 24
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Ops, I had forgotten to load java module before. I did now, bbmap run for a couple of minutes and stopped. This is the output:

Quote:
Hello from inside a Grid Engine job running on cl157
Job beginning at Thu Feb 18 17:03:05 NST 2016
Job ending at Thu Feb 18 17:03:05 NST 2016
java -Djava.library.path=/home/cslamovi/CLARKSCV1.2.2-b/bbmap/jni/ -ea -Xmx1310m -cp /home/cslamovi/CLARKSCV1.2.2-b/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=contigs.fasta nodisk in1=scratch/s_3_1_sequence.fastq in2=scratch/s_3_2_sequence.fastq covstats=omgen.coverage
Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, ref=contigs.fasta, nodisk, in1=scratch/s_3_1_sequence.fastq, in2=scratch/s_3_2_sequence.fastq, covstats=omgen.coverage]

BBMap version 35.82
Retaining first best site only for ambiguous mappings.
No output file.
Executing dna.FastaToChromArrays2 [contigs.fasta, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gz=true, maxlen=536670912, writechroms=false, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=true]

Set genScaffoldInfo=true
Set genome to 1

Loaded Reference: 0.335 seconds.
Loading index for chunk 1-1, build 1
Indexing threads started for block 0-1
Indexing threads finished for block 0-1
Generated Index: 8.592 seconds.
Executing jgi.CoveragePileup [covhist=null, covstats=omgen.coverage, basecov=null, bincov=null, physcov=false, 32bit=false, nzo=false, twocolumn=false, secondary=false, covminscaf=0, ksb=true, binsize=1000, startcov=false, strandedcov=false, rpkm=null, normcov=null, normcovo=null, in1=scratch/s_3_1_sequence.fastq, in2=scratch/s_3_2_sequence.fastq]

Set NONZERO_ONLY to false
Set TWOCOLUMN to false
Set USE_SECONDARY_ALIGNMENTS to false
Set KEEP_SHORT_BINS to true
Set USE_COVERAGE_ARRAYS to false
Set USE_BITSETS to true
Analyzed Index: 6.904 seconds.
Changed from ASCII-33 to ASCII-64 on input quality 97 while prescanning.
Cleared Memory: 1.798 seconds.
Processing reads in paired-ended mode.
Started read stream.
Started 1 mapping thread.
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