Question: NGS mapping via Bowtie on paired end trimmed files is failing
1
gravatar for prandad1
9 months ago by
prandad110
prandad110 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.

mapping genome bowtie fasta custom • 320 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by prandad110
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k 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 9 months ago • written 9 months ago by Jennifer Hillman Jackson25k
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