I’m trying to use MimodD variant calling for the first time with default settings in galaxy.eu and I’m getting the following error: /data/jwd02f/main/062/368/62368537/tool_script.sh: line 27: mimodd: command not found
Reads are aligned with BWA-MEM2, and other downstream calling variants tools like bcftools mpileup are able to call the variants.
I read that there were some problems earlier this summer with MimodD but that they got resolved, I was wondering whether others are having problems again or whether something I’m doing wrong is causing this error?
I was first using galaxy.org and got a similar error, therefore I tried at galaxy.eu.
Are you getting the same error at both servers? Could you share more details about those errors? The server and tool version will matter for each.
A shared history link would be great, or you can post back the contents of the job details page (“i” icon). See Troubleshooting errors. At the same time, you can submit a bug report at the ORG server – please include a link to this topic in the report comment section, so we can link the two and make sure to be reviewing the same problem. If you already did that, please submit again with the update comments.
Let’s start there. Agree that this could be a configuration problem but let’s double check not usage first.
Thank you very much for the follow-up! Errors are not exactly the same, but also tool version is different, so maybe this makes it hard to compare (see details below). An extra difference between the two is that I used the build-in Arabidopsis TAIR10 reference genome for mapping in case of usegalaxy.eu, which was not an option on usegalaxy.org, so over there I used a TAIR10 reference genome from history. In the meantime I’ve also tried to perform the mapping with MiModD Read Alignment. This is now running on usegalaxy.org to check if I get a similar error when mapping is performed with MiModD itself, however on usegalaxy.eu I’m already getting an error at step 1 when trying to make the annotation file required for the read alignment (added info below as well).
UPDATE: got it working on usegalaxy.org, both with the BWA-MEM mapped reads and Mimodd mapped reads. I had to edit the attributes (set database/build = Arabidopsis TAIR) for the BWA-MEM data and then it worked fine.
