Question: bowtie2 index file not found by tophat - galaxy cloudman instance error
gravatar for julien.textoris
2.3 years ago by
julien.textoris0 wrote:


I'm quite new to galaxy, and started after a few tutorials on usegalaxy to launch a cloud instance on amazon. Everything seems ok, but i'm getting a strange error while starting tophat :

 Fatal error: Tool execution failed

   [2016-08-21 08:23:26] Beginning TopHat run (v2.0.14)
   [2016-08-21 08:23:26] Checking for Bowtie
          Bowtie version:
   [2016-08-21 08:23:26] Checking for Bowtie index files (genome)..
   Error: Could not find Bowtie 2 index files (/mnt/galaxyIndices/hg38/bowtie2_index/hg38/hg38.*.bt2)

What is strange is that the files are present at the expected location :

ubuntu@ip-172-31-4-210:/mnt/galaxyIndices/hg38/bowtie2_index/hg38$ ll
total 4226896
drwxr-xr-x 2 galaxy galaxy        130 May 15  2015 ./
drwxr-xr-x 3 galaxy galaxy         17 May 15  2015 ../
-rw-r--r-- 1 galaxy galaxy 1020663364 May 15  2015 hg38.1.bt2
-rw-r--r-- 1 galaxy galaxy  762328952 May 15  2015 hg38.2.bt2
-rw-r--r-- 1 galaxy galaxy      15065 May 15  2015 hg38.3.bt2
-rw-r--r-- 1 galaxy galaxy  762328946 May 15  2015 hg38.4.bt2
lrwxrwxrwx 1 galaxy galaxy         17 May 15  2015 hg38.fa -> ../../seq/hg38.fa
-rw-r--r-- 1 galaxy galaxy 1020663364 May 15  2015 hg38.rev.1.bt2
-rw-r--r-- 1 galaxy galaxy  762328952 May 15  2015 hg38.rev.2.bt2

As I used the default image, it seems unlikely that it is a configuration error. Could this come from the fastq files ? Or could you tell me where to look to explain this error ?

Thanks in advance,


I'm trying to analyze public data retrieved by FTP from ENA EBI (PRJNA258216). Files are grouped into a collection of paired end fastq files for samples SRR1550994, SRR1550999, SRR1551077, SRR1551110. I checked QC, then ran FASTQGroomer on the collection. Galaxy 16.04 installed from image AMI 16.03 20160311b01

rna-seq tophat cloudman • 682 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by julien.textoris0

Hmm - I'm not able to reproduce this; jobs run fine on a freshly launched stock instance. It appears FASTQGroomer sets the datatype to "fastqsanger" but perhaps make sure that is the case (you can change the datatype by clicking on the dataset's pencil icon). If that doesn't fix it, you could email me your instance IP address with a shared history and I could take a look there.

ADD REPLYlink written 2.3 years ago by Enis Afgan690

Quick help for checking fastq format and actions to take to ensure or reformat to fastqsanger format are here:

ADD REPLYlink written 2.3 years ago by Jennifer Hillman Jackson25k
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