Error: Could not find Bowtie 2 index files (–p.*.bt2)

[taehee]

I did run tophat-2.1.0.OSX_x86_64 with a command line.

tophat2 –p 4 –G /Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2014-05-23-16-05-10/Genes/genes.gtf –o /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs --library-type=fr-unstranded --no-novel-juncs /Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs/2-WT-Day0_1.fastq /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs/2-WT-Day0_2.fastq

But, I had an error at below.

[2015-09-25 17:15:17] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-25 17:15:17] Checking for Bowtie
Bowtie version: 2.2.5.0
[2015-09-25 17:15:17] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (–p.*.bt2)

So, firstly I checked the 'PATH' of the index files. But there was no problem.

/Users/Taehyuk/Desktop/genomes/mm10_iGenomes/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/

And then, I confirmed the .*.bt2 files downloaded from iGenomes in the 'PATH'. But those were also fine.

-rwxr-xr-x@ 1 Taehyuk staff 886713321 May 23 2012 genome.1.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884440 May 23 2012 genome.2.bt2
-rwxr-xr-x@ 1 Taehyuk staff 4715 May 23 2012 genome.3.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884433 May 23 2012 genome.4.bt2
lrwxr-xr-x@ 1 Taehyuk staff 29 Jun 14 2012 genome.fa -> ../WholeGenomeFasta/genome.fa
-rwxr-xr-x@ 1 Taehyuk staff 886713321 May 23 2012 genome.rev.1.bt2
-rwxr-xr-x@ 1 Taehyuk staff 661884440 May 23 2012 genome.rev.2.bt2

I did try to use the most recent bowtie2 (2.2.6). But the result was the same.

[2015-09-25 17:23:42] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-25 17:23:42] Checking for Bowtie
Bowtie version: 2.2.6.0
[2015-09-25 17:23:42] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (–p.*.bt2)

I also tried to replace the index files with those from Bowtie2 site (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), but I couldn't fix it.

I have read several threads in this forum to solve this issue, but I couldn't find a suitable solution. Could you give me any suggestions to figure out this issue please? Many thanks!

taehee

[dpryan]

It looks like you're using "–" when you need a "-". The first one is a special character, the second a dash.

[taehee]

Thank you dpryan! I replaced the special character with a dash. However the result was not changed..

[dpryan]

It's related to however you're typing "-p 4", since it's interpreting that as the index base name.

[GenoMax]

Another hunch.

Can you try providing a different name for the output directory? Instead of –o /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs say –o /Users/Taehyuk/Desktop/jae_wt and mll4_0day/2-WT-Day0_th_out.

[taehee]

Thank you for the comments. I did try to omit "-p 4" in command and to change the output directory name to "2-WT-Day0_th_out". But unfortunately, it is still the same result.

Taehyuks-MacBook-Pro:~ Taehyuk$ tophat2 -G /Users/Taehyuk/Desktop/genome/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2014-05-23-16-05-10/Genes/genes.gtf -o /Users/Taehyuk/Desktop/jae_wt and mll4_0day/2-WT-Day0_th_out --library-type=fr-unstranded --no-novel-juncs /Users/Taehyuk/Desktop/genome/Mus_musculus_UCSC_mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs/2-WT-Day0_1.fastq /Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs/2-WT-Day0_2.fastq

[2015-09-26 10:12:45] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2015-09-26 10:12:45] Checking for Bowtie
Bowtie version: 2.2.6.0
[2015-09-26 10:12:45] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (and.*.bt2)

For the reference, bash_profiles of tophat2, bowtie2 and samtools are fine.

Taehyuks-MacBook-Pro:~ Taehyuk$ type tophat2
tophat2 is hashed (/usr/bin/tophat2/tophat-2.1.0.OSX_x86_64/tophat2)
Taehyuks-MacBook-Pro:~ Taehyuk$ type bowtie2
bowtie2 is hashed (/usr/bin/bowtie2/bowtie2-2.2.6/bowtie2)
Taehyuks-MacBook-Pro:~ Taehyuk$ type samtools
samtools is hashed (/usr/bin/samtools/samtools-1.2/samtools)

[GenoMax]

Is there a space in the folder name (between jae_wt and mll4_0day)? "/Users/Taehyuk/Desktop/jae_wt and mll4_0day/fastqs". If so replace those with an "_".

[taehee]

Many thanks GenoMax! I've simplified both file and directory names without any space, and it is working. Thank you!