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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Error Unknown method #3

Closed Magisterh1 closed 2 years ago

Magisterh1 commented 2 years ago

Hi! I tried to use nextNEOpi and received the following error:

Unknown method div on ConfigObject type

My code: nextflow run nextNEOpi.nf --readsTumor /work/Projects/Neoantigens_nextNEOpi/testdata/Tumor_ERR8313719_1.fastq /work/Projects/Neoantigens_nextNEOpi/testdata/Tumor_ERR8313719_2.fastq --readsNormal /work/Projects/Neoantigens_nextNEOpi/testdata/Normal_ERR8313721_1.fastq /work/Projects/Neoantigens_nextNEOpi/testdata/Normal_ERR8313721_2.fastq -config conf/params.config --outputDir /data/results/nextNEOpi/myResults --trim_adapters true --use_NetChop false -profile conda,cluster -resume

Can you please help me to solve this issue?

Thank you!! Best, GH

riederd commented 2 years ago

Please try to use the following format to provide paired end reads on the command line, as it si explained in the Readme under "FASTQ raw reads:":

--readsTumor /work/Projects/Neoantigens_nextNEOpi/testdata/Tumor_ERR8313719_{1,2}.fastq --readsNormal /work/Projects/Neoantigens_nextNEOpi/testdata/Normal_ERR8313721_{1,2}.fastq

alternatively, you may use a batch file to pass on the reads (which will be the only way in future versions anyway).

Hope this helps

Magisterh1 commented 2 years ago

Thank you! I tried to run nextNEOpi.nf using the batch file and using your recommendation from above with and without quotes. However, I always end up with "Unknown method div on ConfigObject type". Do you have an other suggestion for me? THX

riederd commented 2 years ago

Can you send me the .nextflow.log file

Magisterh1 commented 2 years ago

nextflow.log

riederd commented 2 years ago

Thanks, can you also post the /work/Projects/Neoantigens_nextNEOpi/nextNEOpi/conf/params.config file.

riederd commented 2 years ago

..and please check also the cluster profile settings in /work/Projects/Neoantigens_nextNEOpi/nextNEOpi/conf/profiles.config as you are specify -profile conda,cluster . You might need to adjust the cluster profile to match your environment . See also the Profiles: cluster section in the Readme

Magisterh1 commented 2 years ago

yes, here are the params: params.config.txt

I am working on a Ubuntu 18.04.5 LTS. Using "-profile conda" without cluster did not change the error

riederd commented 2 years ago

Hmmm, can you try to update nextflow to the current version? either by: nextflow self-update or: curl -s https://get.nextflow.io | bash

Magisterh1 commented 2 years ago

ok, done, unfortunately only the wording of the error changed: Unknown method invocation div on ConfigObject type

riederd commented 2 years ago

There is one more thing that I spotted in your params.config: You need to put the path for the resourcesBaseDir under quotes, e.g. resourcesBaseDir = "/work/Projects/Neoantigens_nextNEOpi/resources"

Please check all paths that you changed in the config files.

Magisterh1 commented 2 years ago

OK, what worked so far: 1. update nextflow, 2. add quotes to paths in params.config. Now I have to solve some conda problems... THX for your help!!

riederd commented 2 years ago

Glad, I could help. BTW we recommend using singularity instead of conda. But either should work.