BS-SNPer error

[sr320]

I am trying to run BS-SNPer.

code

find *.bam \
| xargs basename -s _s456_trimmed_bismark_bt2.deduplicated.sorted.bam | xargs -I{} perl /gscratch/srlab/programs/BS-Snper-1.0/BS-Snper.pl \
-fa /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa \
--input {}_s456_trimmed_bismark_bt2.deduplicated.sorted.bam \
--output snp.candidate.out --methcg meth.cg --methchg meth.chg --methchh meth.chh --minhetfreq 0.1 --minhomfreq 0.85 --minquali 15 --mincover 10 --maxcover 1000 --minread2 2 --errorate 0.02 --mapvalue 20 >SNP.out 2>SNP.log

error

cat *log
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
vQualMin = 15.
nLayerMax = 1000.
vSnpRate = 0.100000.
vSnpPerBase = 0.020000.
mapqThr = 20.
Init chrome name-len array completed, total 3816038 bp of 32 chromosomes.
32 chromes loaded.
Init chrome name-idx hash table completed.
Init chrome seq array completed.
Meth process begins...
Chrome updated to Contig0!
Chrome updated to Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-1.0/BS-Snper.pl line 66.
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa

[sr320]

update -- I installed new version of software as I notice line number was irrelevant thus

find *.bam \
| xargs basename -s _s456_trimmed_bismark_bt2.deduplicated.sorted.bam | xargs -I{} perl /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl \
-fa /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa \
--input {}_s456_trimmed_bismark_bt2.deduplicated.sorted.bam \
--output snp.candidate.out --methcg meth.cg --methchg meth.chg --methchh meth.chh --minhetfreq 0.1 --minhomfreq 0.85 --minquali 15 --mincover 10 --maxcover 1000 --minread2 2 --errorate 0.02 --mapvalue 20 >SNP.out 2>SNP.log

now produces

refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_7_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
vQualMin = 15.
nLayerMax = 1000.
vSnpRate = 0.100000.
vSnpPerBase = 0.020000.
mapqThr = 20.
Init chrome name-len array completed, total 3816038 bp of 32 chromosomes.
32 chromes loaded.
Init chrome name-idx hash table completed.
Init chrome seq array completed.
Meth process begins...
Chrome updated to Contig0!
Chrome updated to Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
Unknown option: input
FLAG: 1

and code pl script is at https://github.com/hellbelly/BS-Snper/blob/master/BS-Snper.pl

[kubu4]

The error is this: --input. That's not an option/flag for the program.

Initiate the command like so: perl BS-Snper.pl <sorted_bam_file>

[kubu4]

A more precise example using your code above would be:

perl BS-Snper.pl {}_s456_trimmed_bismark_bt2.deduplicated.sorted.bam \
--fa /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa

Also, notice I added an additional - to your FastA input flag (your code above only had a single - instead of the necessary two hyphens.

[sr320]

When I run

find *.bam \
| xargs basename -s _s456_trimmed_bismark_bt2.deduplicated.sorted.bam | xargs -I{} perl /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl \
{}_s456_trimmed_bismark_bt2.deduplicated.sorted.bam \
--fa /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa \
--output snp.candidate.out --methcg meth.cg --methchg meth.chg --methchh meth.chh --minhetfreq 0.1 --minhomfreq 0.85 --minquali 15 --mincover 10 --maxcover 1000 --minread2 2 --errorate 0.02 --mapvalue 20 >SNP.out 2>SNP.log

I get

head -30 *log
FLAG: 1
refSeqFile = /gscratch/srlab/sr320/data/olurida-bs/genome/Olurida_v081_100000.fa.
bamFileName = zr1394_10_s456_trimmed_bismark_bt2.deduplicated.sorted.bam.
snpFileName = snp.candidate.out.
methCgFileName = meth.cg.
methChgFileName = meth.chg.
methChhFileName = meth.chh.
vQualMin = 15.
nLayerMax = 1000.
vSnpRate = 0.100000.
vSnpPerBase = 0.020000.
mapqThr = 20.
Init chrome name-len array completed, total 3816038 bp of 32 chromosomes.
32 chromes loaded.
Init chrome name-idx hash table completed.
Init chrome seq array completed.
Meth process begins...
Chrome updated to Contig0!
Chrome updated to Contig1!
Contig1 not found in chrome name array.
Error! at /gscratch/srlab/programs/BS-Snper-master/BS-Snper.pl line 110.
FLAG: 1

[kubu4]

What does SNP.out have to say?

[sr320]

empty file

[sr320]

Very likely issue. Using different version of genome (only large contigs)
Will redo Bismark with modified genome and go from there.