Issue running DIA-NN: Errors out with "command not found"

usegalaxy.eu support
,
1

Hello,
I am trying to run a dataset of DIA data through DIA-NN. The tool gives me a “command not found” error. Below is the command which it runs and the error produced:

mkdir ./input_data && mkdir ./tmp &&  ln -s '/data/dnb09/galaxy_db/files/2/4/a/dataset_24a41ce2-079d-4ec4-bae4-893829868c10.dat' './input_data/191023JAT12_4_Mix_3_1ug_pOT_30k_390_1010_12.raw' && ln -s '/data/dnb09/galaxy_db/files/f/7/b/dataset_f7bda34f-ded0-44b5-bd73-c8eda435e3ad.dat' './input_data/191023JAT11_3_Mix_1_1ug_pOT_30k_390_1010_12.raw' && ln -s '/data/dnb09/galaxy_db/files/0/9/5/dataset_09577774-b359-4c6d-9c39-ef7a90882d8b.dat' './input_data/191023JAT10_2_Mix_4_1ug_pOT_30k_390_1010_12.raw' && ln -s '/data/dnb09/galaxy_db/files/8/6/6/dataset_866480a6-14d1-487a-8ce0-4e46a5becddd.dat' './input_data/191023JAT03_1_Mix_2_1ug_pOT_30k_390_1010_12%.raw' &&   diann '--f ./input_data/191023JAT12_4_Mix_3_1ug_pOT_30k_390_1010_12.raw--f ./input_data/191023JAT11_3_Mix_1_1ug_pOT_30k_390_1010_12.raw--f ./input_data/191023JAT10_2_Mix_4_1ug_pOT_30k_390_1010_12.raw--f ./input_data/191023JAT03_1_Mix_2_1ug_pOT_30k_390_1010_12%.raw' --dir ./ --lib '/data/dnb09/galaxy_db/files/7/a/3/dataset_7a34d44d-cdca-4f3f-aac9-46a68073595c.dat' --out ./report.tsv --threads ${GALAXY_SLOTS:-1} --temp ./tmp        '--fasta /data/dnb09/galaxy_db/files/2/e/6/dataset_2e65db42-2e63-4486-b2aa-f9c419c45838.dat '       --relaxed-prot-inf   --peak-center --no-ifs-removal  --smart-profiling    --cut 'K*,R*' --missed-cleavages '1' --met-excision --min-pep-len '7' --max-pep-len '30' --min-pr-mz '300' --max-pr-mz '1800' --min-pr-charge '1' --max-pr-charge '4' --min-fr-mz '200' --max-fr-mz '1800'            --unimod4                               --matrices --qvalue 0.01   --verbose '1'  && cp ./report.tsv '/data/jwd05e/main/063/748/63748624/outputs/dataset_574b73bd-b8bf-470b-9afb-b6cfde5281c7.dat'

Error

/data/jwd05e/main/063/748/63748624/tool_script.sh: line 9: diann: command not found

I have run that dataset through EncyclopeDIA tool and it works fine in giving me an output as expected. I have submitted a bug report but would appreciate any help w.r.t resolving the issue.

Thanks

2

Hi @prao123

The tool might need an update. Sending in a bug report was the correct option.

The EU team gets many bug reports. I’m running a test, and will get back to you here with the result. I wait in the queue, too, so will be later today.

1 Like
3

I have identified the problem and deployed a fix. @prao123 can you please test it in a few hours?

Thanks.

2 Likes
4

Hello @bjoern.gruening
I tested it again with my data and diann completed without any errors. That leads me to another issue:
We have our own Galaxy server instance and the error (command not found) still persists on my server (downloaded the tool again after you deployed the fix). Does it not update on the toolshed?

Thank you

5

Cool, glad it works now for you.

The tools needs a container. So you would need to configure Galaxy and your job_conf.yml file to support containers.