Question: Bowtie2 "--no-unal" option causes error
gravatar for TWV
10 months 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 10 months ago by Jennifer Hillman Jackson25k • written 10 months ago by TWV20
gravatar for Jennifer Hillman Jackson
10 months ago by
United States
Jennifer Hillman Jackson25k 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 10 months ago by Jennifer Hillman Jackson25k

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 10 months ago • written 10 months 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 10 months ago by Jennifer Hillman Jackson25k

Update: The latest tool version is ready to use at (or installed from the ToolShed for use in a local, docker, cloud Galaxy). It includes a fix to address this bug. Please let us know if any other issues come up!

Bowtie2 - map reads against reference genome (Galaxy Version

ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k

Dear Jennifer,

thanks a lot for your follow-up help. I have updated bowtie2 to the latest version and it does indeed work now.

With kind regards!

ADD REPLYlink written 8 months ago by TWV20
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