Could not locate a Bowtie index corresponding to basename

[YKY]

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:

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

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?

[GenoMax]

Can you post a listing of the files in "/home/laba/Desktop/bowtie2-2.2.4/chr1_index/"?

[YKY]

I have tried two provide two different directories.

/home/laba/Desktop/bowtie2-2.2.4/aux contains:
chr1.1.bt2 chr1.2.bt2 chr1.3.bt2 chr1.4.bt2 chr1.fa chr1.fai chr1.rev.1.bt2 chr1.rev.2.bt2
For this directory I downloaded the refernce for build 37 substted chr1 and indexed it with bowtie 2

another directory I tried to provide to bowtie2
/home/laba/Desktop/bowtie2-2.2.4/chr1_index/ contains:
chr1.1.bt2 chr1.2.bt2 chr1.3.bt2 chr1.4.bt2 chr1.fa chr1_random.fa chr1.rev.1.bt2 chr1.rev.2.bt2
I downloaded the reference using pipeline for human genome in bowtie2/scripts folder. Apart from fasta files other files were name hg18* after it did not work I renamed them to chr1*, which did not work either.

[GenoMax]

If the index files were originally named hg18* then you can't rename them to chr1*. The thing to do is either restore the names back to the original or download a new copy and use hg18 as "basename" for the index.

As for the chr1 subset you should use "chr1" as the basename.

[YKY]

I've tried what you suggesting and replaced bowtie parameter form /home/laba/Desktop/bowtie2-2.2.4 to /chr1_index/chr1.fa to .../hg18 but it did not help.

As I mentioned I've indexed chr1 reference separately before. And all filenames matched and were in the same directory, but it did not help.

[GenoMax]

Assuming I am looking at the same cnvCapSeq program here is what the Readme file says about the index files. Are you closely following these directions?

The read pair pipeline requires the FASTA sequence file against
which the the multi-mapped reads will be re-aligned. This file should
be placed in the /aux folder and renamed to chr*.fasta, where * is
the chromosome name. The fasta files also need to be indexed using
Bowtie2.

[YKY]

Yes. Thats what I did intitially. You can see contents of the aux folder in my second post. When it did not work I've started trying to provide another directory to bowtie.

EDIT
Also I dont have readme file for RP_pipeline. Only pipline itself. Maybe you are on different version? Mine is 0.1.2
EDIT2
And for aux folder I indexed chr1.fa reference file separately. Using bowtie2

[GenoMax]

Here is the link for the software (assuming it is the same one as what you are using): http://ftp.jaist.ac.jp/pub/sourcefor...vCapSeq/0.1.2/ You can find the readme file there.

Just trying to see if I can help. I don't use this software.

[YKY]

Thanks. Yea I found it now. I've tried to put aux folder into cnvCapSeq directory, changing aux variable in pipeline back to what it was "./aux", still no luck.
EDIT
Before that I was placing it into bowtie2 directory