Question: NGS mapping via Bowtie on paired end trimmed files is failing
0
gravatar for prandad1
10 weeks ago by
prandad10
prandad10 wrote:

Hi Galaxy support,

I have ran paired end files for a staphylococcus aureus genome (Illumina Miseq, paired end) through the upload, then trimmed using trimmomatic, and now am trying to align these to a reference staph aureus genome (which I got from the UCSC Archaea genome - Staphylococcus aureus Mu50) using Bowtie.

I am uploading each of the paired end file (paired versions), and then am uploading the Mu50 genome in the reference genome section. When I click on execute, however, I keep getting the same error:

Settings: Output files: "genome.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default

and ...

Settings: Output files: "genome.*.bt2"

S Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default

and ...

Settings: Output files: "genome.*.bt2" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 4 (one in 16) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default

I am unsure of how to untangle this error report - could you please provide feedback as to why these inputs are failing? I look forward to hearing back!

admin edit: remove email

Sincerely, Pranay Randad.

ADD COMMENTlink modified 10 weeks ago by Jennifer Hillman Jackson23k • written 10 weeks ago by prandad10
0
gravatar for Jennifer Hillman Jackson
10 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The original mapping job was run using a custom reference genome that was not in fasta format, triggering this failure. The newer mapping jobs use a fasta custom genome and have been successful.

However, the format of the custom genome may cause problems with downstream tools. Correct the format with the tool NormalizeFasta to remove the description line content. How to is explained here:

Support FAQs https://galaxyproject.org/support/#troubleshooting

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 105 users visited in the last hour