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Old 03-07-2014, 08:48 AM   #6
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
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Brian: Trying out BBMap and I am having problems indexing the reference. My species is Pig which has the following Fasta entry lines in the genome.fa file:

Quote:
grep '>' ../References/GENOME_DIR/genome.fa
>10
>11
>12
>13
>14
>15
>16
>17
>18
>1
>2
>3
>4
>5
>6
>7
>8
>9
>MT
>X
>Y
However it appears that BBMap is only creating 6 chromosomes as follows:

Quote:
Executing align2.BBMap [build=1, overwrite=true, match=long, fastareadlen=500, ref=../References/GENOME_DIR/genome.fa]

BBMap version 31.32
Set OVERWRITE to true
Cigar strings enabled.
Retaining first best site only for ambiguous mappings.
No output file.
Writing reference.
Executing dna.FastaToChromArrays [../References/GENOME_DIR/genome.fa, 1, writeinthread=false, genscaffoldinfo=true, retain, waitforwriting=false, gzip=true, chromc=false, maxlen=536670912, writechroms=true, minscaf=1, midpad=300, startpad=8000, stoppad=8000, nodisk=false]

Set genScaffoldInfo=true
Writing ref/genome/1/chr1.chrom.gz
Writing ref/genome/1/chr2.chrom.gz
Writing ref/genome/1/chr3.chrom.gz
Writing ref/genome/1/chr4.chrom.gz
Writing ref/genome/1/chr5.chrom.gz
Writing ref/genome/1/chr6.chrom.gz
Set genome to 1

Loaded Reference: 0.008 seconds.
Loading index for chrom 1-6, genome 1
No index available; generating from reference genome: /group/gcore/machine/sbs/run00289/131127_M00657_0033_000000000-A6EDC/hr00671_and-yanhua/006356_-945-Flag-1-946-/ref/index/1/chr1-3_index_k13_c2_b1.block
No index available; generating from reference genome: /group/gcore/machine/sbs/run00289/131127_M00657_0033_000000000-A6EDC/hr00671_and-yanhua/006356_-945-Flag-1-946-/ref/index/1/chr4-6_index_k13_c2_b1.block
Indexing threads started for block 0-3
Indexing threads started for block 4-6
Indexing threads finished for block 4-6
Indexing threads finished for block 0-3
Generated Index: 274.860 seconds.
Finished Writing: 29.271 seconds.
No reads to process; quitting.

Total time: 362.577 seconds.
Any ideas? Feel free to send me email westerman at purdue dot edu
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