Question: Bowtie2 "--no-unal" option causes error
gravatar for TWV
4 weeks ago by
TWV20 wrote:

When trying to run bowtie2 on a fastqsanger file with any reference genome, enabling the "Suppress SAM records for reads that failed to align" option (--no-unal, in order not to get multi-gigabyte SAM files) leads to a tool error.

The following error is displayed:

cannot find 'sam' while searching for 'analysis_type.sam_options.sam'

Any help with solving this issue would be greatly appreciated.

ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson24k • written 4 weeks ago by TWV20
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson24k wrote:


I am not able to reproduce this error with an earlier version of the tool, but the most recent version could have a bug. I will do some testing and create an issue report against the tool if I can reproduce this with the current Galaxy release 17.09 and Bowtie2 More feedback about that once done.

If you have time, please reply with the Galaxy release you are using (17.09? Local or Docker or Cloudman?) and the Bowtie2 tool version ( to aid with testing.

Short-term workaround: use Bowtie2 as this function is known to work with Galaxy release 17.09.

Galaxy Main does not have the most current version ( installed yet. A ticket to update the server has been created here and includes notes about the potential bug:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 4 weeks ago by Jennifer Hillman Jackson24k

The Galaxy version is 17.09 Local, the Bowtie2 version was

I have also tested the 2.3.4 version and have the same error.

It seems to work with the version as you suggested. So now what is left is seeing why the newer versions don't work.


ADD REPLYlink modified 29 days ago • written 29 days ago by TWV20

Hello - I was also able to reproduce the issue. Both in and the newly published version 2.3.4. Using version is the recommended workaround.

Please follow the issue ticket here for updates:

Thanks for reporting the problem and for the followup!

ADD REPLYlink written 29 days ago by Jennifer Hillman Jackson24k
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