Hi,
I am using cnvCapSeq-0.1.2 software which has bowtie 2 integrated into a pipline. When I am trying to launch it I am getting an error:
First I palced the reference in fasta format for chr1 into folder within bowtie2 directory. It did not work. Then I tried to create bowtie index for the reference it did not help either. I have also tried to download refernce using pipeline provided in scripts folder which did not help as well (i modified it to only download chr1). I have 257 gb free for my tmp folder. At the moment index files are in the same folder as reference fasta file. Where should I place them?
What can case the issue?
I am using cnvCapSeq-0.1.2 software which has bowtie 2 integrated into a pipline. When I am trying to launch it I am getting an error:
Code:
Realigning using Bowtie2... Could not locate a Bowtie index corresponding to basename "/home/laba/Desktop/bowtie2-2.2.4/chr1_index/chr1.fa" Overall time: 00:00:00 Error: Encountered internal Bowtie 2 exception (#1) Command: /home/laba/Desktop/bowtie2-2.2.4/bowtie2-align-s --wrapper basic-0 -t -x /home/laba/Desktop/bowtie2-2.2.4/chr1_index/chr1.fa --rg-id NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123_sorted.bam --rg LB:LB_NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123_sorted.bam --rg SM:SM_NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123 --rg PL:illumina --rg PU:PU_NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123 --rg DS:DS_NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123 --rg CN:CN_NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123 -a --very-sensitive --maxins 300000 -p 4 -1 ./pre_processing_results/RP_results/realign/reads/NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.abnormal._1.fq -2 ./pre_processing_results/RP_results/realign/reads/NA06984.mapped.ILLUMINA.bwa.CEU.low_coverage.20101123.abnormal._2.fq
What can case the issue?
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