Bumblebee
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Data
- Location:
/fs/szattic-asmg4/Bees/Bombus_impatiens
- There are 7 pairs of data files (paired ends) : lanes 1..3,5..8 (lane 4 wasn't used)
- Tasks to figure out:
1. Erroneous reads/bases, which we need to correct or discard 2. GC bias, so we can compute a-stats properly 3. Redundancy in the long paired ends, which are lane 1 and lane 2.
- Lane 1: 3Kbp insert; 34,944,099 reads
- Lane 3: 8Kbp insert; 32,540,640 reads
- Formatting:
/fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/fastqToCA \
-insertsize 3000 300 \
-libraryname 1 \
-type illumina \
-fastq /fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_1_sequence.txt,/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_2_sequence.txt > 1.frg
=>
{LIB
act:A
acc:1
ori:I
mea:3000.000
std:300.000
src:
.
nft:10
fea:
forceBOGunitigger=1
isNotRandom=0
doNotTrustHomopolymerRuns=0
doRemoveDuplicateReads=0
doNotQVTrim=0
goodBadQVThreshold=0
doNotOverlapTrim=0
usePackedFragments=1
illuminaFastQType=illumina
illuminaSequence=/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_1_sequence.txt,/fs/szattic-asmg4/Bees/Bombus_impatiens/s_1_2_sequence.txt
.
}
rm -fr asm.* /fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/gatekeeper \ -o /scratch1/Bombus_impatiens/Assembly/1.redo/./asm.gkpStore.BUILDING \ -T -F \ -E /scratch1/Bombus_impatiens/Assembly/1.redo/./asm.gkpStore.errorLog \ /scratch1/Bombus_impatiens/Assembly/1.redo/1.frg => Segmentation fault
Assembly
/fs/szdevel/dpuiu/SourceForge/wgs-assembler.030210/Linux-amd64/bin/runCA