Hi,
I tried to use bsmooth for bs-seq alignment for a while. However, still can't figure out the exact command used for alignment. Below is error mesg
time perl ~tli/bin/bsmooth-align-0.8.1/bin/bswc_bowtie2_align.pl --bowtie2=/usr/bin/bowtie2 --bscpg --fastq --sam=bsm --fr --ff --rf --rr --no-unpaired --out=. -- ~tli/gc3018/genome/hg19bsmooth/hg19.idx -- ~tli/gc3018/genome/hg19/chr*fa -- simulated_1.fastq -- simulated_2.fastq -- --
Original index name: /gscuser/tli/gc3018/genome/hg19bsmooth/hg19.idx
Stripped index name: /gscuser/tli/gc3018/genome/hg19bsmooth/hg19.idx
Reference files:
/gscuser/tli/gc3018/genome/hg19/chr1.fa
/gscuser/tli/gc3018/genome/hg19/chr10.fa
/gscuser/tli/gc3018/genome/hg19/chr11.fa
/gscuser/tli/gc3018/genome/hg19/chr12.fa
/gscuser/tli/gc3018/genome/hg19/chr13.fa
/gscuser/tli/gc3018/genome/hg19/chr14.fa
/gscuser/tli/gc3018/genome/hg19/chr15.fa
/gscuser/tli/gc3018/genome/hg19/chr16.fa
/gscuser/tli/gc3018/genome/hg19/chr17.fa
/gscuser/tli/gc3018/genome/hg19/chr18.fa
/gscuser/tli/gc3018/genome/hg19/chr19.fa
/gscuser/tli/gc3018/genome/hg19/chr2.fa
/gscuser/tli/gc3018/genome/hg19/chr20.fa
/gscuser/tli/gc3018/genome/hg19/chr21.fa
/gscuser/tli/gc3018/genome/hg19/chr22.fa
/gscuser/tli/gc3018/genome/hg19/chr3.fa
/gscuser/tli/gc3018/genome/hg19/chr4.fa
/gscuser/tli/gc3018/genome/hg19/chr5.fa
/gscuser/tli/gc3018/genome/hg19/chr6.fa
/gscuser/tli/gc3018/genome/hg19/chr7.fa
/gscuser/tli/gc3018/genome/hg19/chr8.fa
/gscuser/tli/gc3018/genome/hg19/chr9.fa
/gscuser/tli/gc3018/genome/hg19/chrM.fa
/gscuser/tli/gc3018/genome/hg19/chrX.fa
/gscuser/tli/gc3018/genome/hg19/chrY.fa
Name-map files:
bowtie2 executable: /usr/bin/bowtie2
bowtie2 arguments: simulated_1.fastq
Methylation output directory: .
Keep Watson/Crick .sam: bsm
Keep Watson/Crick .bam: no
Read-level measurements: just CpGs
Four-strand?: no
Paired-end?: no
Unpaired inputs:
simulated_2.fastq
Ignore evidence from unparied alignment of paired mate: 1
Input format: fastq
Skip first # reads: (no skipping)
Stop after # reads: (no limit)
Temporary directory: /tmp/5PALCMIVoU.tmp
Intermediate Watson file name: /tmp/5PALCMIVoU.tmp/bsreads_watson.tab6
Intermediate Crick file name: /tmp/5PALCMIVoU.tmp/bsreads_crick.tab6
Locating tools...
Found bowtie2: /usr/bin/bowtie2
Checking index...
Checking reads...
Parsing name-map files...
Creating named pipes...
Forked off paired feeder process (pid=6456)...
Opening simultaneous alignment pipes:
/usr/bin/bowtie2 -x /gscuser/tli/gc3018/genome/hg19bsmooth/hg19.idx.watson simulated_1.fastq --quiet --ff --norc --sam-no-qname-trunc --reorder --tab6 /tmp/5PALCMIVoU.tmp/bsreads_watson.tab6 |
/usr/bin/bowtie2 -x /gscuser/tli/gc3018/genome/hg19bsmooth/hg19.idx.crick simulated_1.fastq --quiet --ff --norc --sam-no-qname-trunc --reorder --tab6 /tmp/5PALCMIVoU.tmp/bsreads_crick.tab6 |
Parsing reference...
Warning: Output file 'simulated_1.fastq' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Warning: Output file 'simulated_1.fastq' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Writing reads from file 'simulated_2.fastq' ...
Looks like it used simulated_1.fastq as bowtie2 arguments.
Thanks!
litd
I tried to use bsmooth for bs-seq alignment for a while. However, still can't figure out the exact command used for alignment. Below is error mesg
time perl ~tli/bin/bsmooth-align-0.8.1/bin/bswc_bowtie2_align.pl --bowtie2=/usr/bin/bowtie2 --bscpg --fastq --sam=bsm --fr --ff --rf --rr --no-unpaired --out=. -- ~tli/gc3018/genome/hg19bsmooth/hg19.idx -- ~tli/gc3018/genome/hg19/chr*fa -- simulated_1.fastq -- simulated_2.fastq -- --
Original index name: /gscuser/tli/gc3018/genome/hg19bsmooth/hg19.idx
Stripped index name: /gscuser/tli/gc3018/genome/hg19bsmooth/hg19.idx
Reference files:
/gscuser/tli/gc3018/genome/hg19/chr1.fa
/gscuser/tli/gc3018/genome/hg19/chr10.fa
/gscuser/tli/gc3018/genome/hg19/chr11.fa
/gscuser/tli/gc3018/genome/hg19/chr12.fa
/gscuser/tli/gc3018/genome/hg19/chr13.fa
/gscuser/tli/gc3018/genome/hg19/chr14.fa
/gscuser/tli/gc3018/genome/hg19/chr15.fa
/gscuser/tli/gc3018/genome/hg19/chr16.fa
/gscuser/tli/gc3018/genome/hg19/chr17.fa
/gscuser/tli/gc3018/genome/hg19/chr18.fa
/gscuser/tli/gc3018/genome/hg19/chr19.fa
/gscuser/tli/gc3018/genome/hg19/chr2.fa
/gscuser/tli/gc3018/genome/hg19/chr20.fa
/gscuser/tli/gc3018/genome/hg19/chr21.fa
/gscuser/tli/gc3018/genome/hg19/chr22.fa
/gscuser/tli/gc3018/genome/hg19/chr3.fa
/gscuser/tli/gc3018/genome/hg19/chr4.fa
/gscuser/tli/gc3018/genome/hg19/chr5.fa
/gscuser/tli/gc3018/genome/hg19/chr6.fa
/gscuser/tli/gc3018/genome/hg19/chr7.fa
/gscuser/tli/gc3018/genome/hg19/chr8.fa
/gscuser/tli/gc3018/genome/hg19/chr9.fa
/gscuser/tli/gc3018/genome/hg19/chrM.fa
/gscuser/tli/gc3018/genome/hg19/chrX.fa
/gscuser/tli/gc3018/genome/hg19/chrY.fa
Name-map files:
bowtie2 executable: /usr/bin/bowtie2
bowtie2 arguments: simulated_1.fastq
Methylation output directory: .
Keep Watson/Crick .sam: bsm
Keep Watson/Crick .bam: no
Read-level measurements: just CpGs
Four-strand?: no
Paired-end?: no
Unpaired inputs:
simulated_2.fastq
Ignore evidence from unparied alignment of paired mate: 1
Input format: fastq
Skip first # reads: (no skipping)
Stop after # reads: (no limit)
Temporary directory: /tmp/5PALCMIVoU.tmp
Intermediate Watson file name: /tmp/5PALCMIVoU.tmp/bsreads_watson.tab6
Intermediate Crick file name: /tmp/5PALCMIVoU.tmp/bsreads_crick.tab6
Locating tools...
Found bowtie2: /usr/bin/bowtie2
Checking index...
Checking reads...
Parsing name-map files...
Creating named pipes...
Forked off paired feeder process (pid=6456)...
Opening simultaneous alignment pipes:
/usr/bin/bowtie2 -x /gscuser/tli/gc3018/genome/hg19bsmooth/hg19.idx.watson simulated_1.fastq --quiet --ff --norc --sam-no-qname-trunc --reorder --tab6 /tmp/5PALCMIVoU.tmp/bsreads_watson.tab6 |
/usr/bin/bowtie2 -x /gscuser/tli/gc3018/genome/hg19bsmooth/hg19.idx.crick simulated_1.fastq --quiet --ff --norc --sam-no-qname-trunc --reorder --tab6 /tmp/5PALCMIVoU.tmp/bsreads_crick.tab6 |
Parsing reference...
Warning: Output file 'simulated_1.fastq' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Warning: Output file 'simulated_1.fastq' was specified without -S. This will not work in future Bowtie 2 versions. Please use -S instead.
Writing reads from file 'simulated_2.fastq' ...
Looks like it used simulated_1.fastq as bowtie2 arguments.
Thanks!
litd
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