Question: Enhanced bowtie mapper
0
gravatar for Dendi Nugraha
9 months ago by
Osaka, Japan
Dendi Nugraha30 wrote:

Hi all,

I use tool called 'Enhanced Bowtie Mapper', and want to map my input file which is FASTQ collapser output (.fasta file). After I set all the parameters, the work was unsuccessful. It says this following error:

Settings: Output files: "/var/folders/3s/9x0zlc3d13g1ddx_r341p7dh0000gn/T/tmpwqQBwQ/tmpk1tpC7.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max buc

I have re-tried but still not working. What is going to be wrong? Thanks in advance

ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by Dendi Nugraha30
1
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There might be an incompatibility between the tool wrapper (last updated 8/2016) and the current Galaxy distribution 17.09). This could involve the tool wrapper itself, how it installs, or other potential bugs or just buggy behavior.

Options:

  1. The tool author would be the best person to help determine the root problem. Log into the Tool Shed (create an account if needed), go to the tool repository, and from the Repository Actions menu (upper right corner) choose to contact the repo author. A quick note explaining the problem can be sent for feedback.

  2. Contact the administrators of the Galaxy server where you are working to find out if this is a known problem or if others can reproduce it. This tool is not included at Galaxy Main https://usegalaxy.org.

  3. Try to eliminate usage/input format factors as contributing to the failure - see the Support FAQs for common problems that can cause trigger errors/odd results across tools.

  4. For Bowtie2, the recommended wrapped version is here if you want to try an alternative. Find and use this instead (if it is installed on the target public server - this tool is at Galaxy Main) or install it into your own load/cloud Galaxy. If it also fails, then the problem is almost certainly with the inputs. Errors produce at Galaxy Main can be sent in with a bug report for feedback if you cannot determine the problem.

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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