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missing bissnp beds #440

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
From Ben on 3/5/13:

I am trying to find Bis-SNP results for single-lane TCGA samples.  For
the following lanes, I can find TDF files but not 6plus2.bed files.
Can either of you see why?   Zack could you kick off the post-vcf
pipeline for these?  Or are these ones that are already on the queue
to be rerun?

D1W2BACXX_7_NIC1254A89
D1W2BACXX_8_NIC1254A91
D1W2BACXX_6_NIC1254A94
D1P4HACXX_8_NIC1254A96

Original issue reported on code.google.com by zack...@gmail.com on 6 Mar 2013 at 9:47

GoogleCodeExporter commented 8 years ago 
I look at them, it looks like these directories are generated before we 
correctly move 6plus2.bed file to the result directory.
So we need to run part of bissnp pipeline to generate the bed file for those 
lanes.

Zack,
I already changed the pipeline that you can add --skip flag to avoid some part 
of pipeline:

--skip_indel_align
--skip_mdups
--skip_base_recal
--skip_genotyping
--skip_vcf_filter
--skip_vcf_sort
--skip_filter_bed_file
--skip_bed_file
--skip_wig_file

for those lanes to generate bed file, you can just generate by the following 
commands:

perl bissnp_pipeline.pl input.bam hg19.fa --skip_indel_align --skip_mdups 
--skip_base_recal --skip_genotyping --skip_vcf_filter --skip_vcf_sort 
--skip_wig_file

thanks,

yaping

Original comment by zack...@gmail.com on 6 Mar 2013 at 9:48

GoogleCodeExporter commented 8 years ago 
i queued up jobs to create the beds but the fail right away:

[ramjan@hpc2721 D1W2BACXX_7_NIC1254A89]$ pwd
/export/uec-gs1/laird/shared/production/ga/flowcells/D1W2BACXX/results/D1W2BACXX
/D1W2BACXX_7_NIC1254A89

/home/rcf-17/ramjan/software/bissnp/bissnp_pipeline.pl 
ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.bam 
/home/rcf-17/ramjan/genomes/hg19_rCRSchrm/hg19_rCRSchrm.fa --skip_indel_align 
--skip_mdups --skip_base_recal --skip_genotyping --skip_vcf_filter 
--skip_vcf_sort --skip_wig_file

rm: cannot remove 
`ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.realign
.bam': No such file or directory
rm: cannot remove 
`ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.realign
.bai': No such file or directory
rm: cannot remove 
`ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.realign
.mdups.bam': No such file or directory
rm: cannot remove 
`ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.realign
.mdups.bai': No such file or directory
rm: cannot remove 
`ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.realign
.mdups.recal.cpg.raw.vcf': No such file or directory
rm: cannot remove 
`ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.realign
.mdups.recal.snp.raw.vcf': No such file or directory
Died at /home/uec-00/shared/production/software/bissnp/vcf2bed6plus2.pl line 73.
perl /home/uec-00/shared/production/software/bissnp/vcf2bed6plus2.pl 
ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.realign.
mdups.recal.cpg.raw.sort.vcf CG 

Died at /home/uec-00/shared/production/software/bissnp/vcf2bed6plus2.pl line 73.
perl /home/uec-00/shared/production/software/bissnp/vcf2bed6plus2.pl 
--only_good_call 
ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.realign.mdups.recal.realign.
mdups.recal.cpg.filtered.sort.vcf CG

Original comment by zack...@gmail.com on 6 Mar 2013 at 9:52

GoogleCodeExporter commented 8 years ago 
Hi Zack,
I am afraid you input the wrong parameter to script:
it should accept the raw bam file name, instead of realign.mdups.recal.bam

the command line should be:

/home/rcf-17/ramjan/software/bissnp/bissnp_pipeline.pl 
ResultCount_D1W2BACXX_7_NIC1254A89.hg19_rCRSchrm.fa.bam 
/home/rcf-17/ramjan/genomes/hg19_rCRSchrm/hg19_rCRSchrm.fa --skip_indel_align 
--skip_mdups --skip_base_recal --skip_genotyping --skip_vcf_filter 
--skip_vcf_sort --skip_wig_file

yaping

Original comment by lyping1...@gmail.com on 6 Mar 2013 at 10:04

GoogleCodeExporter commented 8 years ago 
ohh ok. will try with the other bam

Original comment by zack...@gmail.com on 6 Mar 2013 at 10:10

GoogleCodeExporter commented 8 years ago 
rerun complete

Original comment by zack...@gmail.com on 14 Mar 2013 at 11:28