use custom snpeff database, such as Candian.aruis #1654
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Command used: Terminal output: Launching WARN: Access to undefined parameter |\ | |__ __ / nf-core/sarek v3.4.4Core Nextflow options Input/output options Main options executor > local (83) Caused by: Command executed: snpEff cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: view the complete command output by changing to the process work dir and entering the command -- Check '.nextflow.log' file for details -- Check '.nextflow.log' file for details executor > local (83) Caused by: Command executed: snpEff cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: view the complete command output by changing to the process work dir and entering the command -- Check '.nextflow.log' file for details -- Check '.nextflow.log' file for details executor > local (83) Caused by: Command executed: snpEff cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: view the complete command output by changing to the process work dir and entering the command -- Check '.nextflow.log' file for details -- Check '.nextflow.log' file for details |
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I think that the problem is that the "genome" for snpeff is set to AFAIKT, it means that the value of Looking at the snpeff-cache that you downloaded, you might be able to figure out what appropriate values for |
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According to snpEff.config, Candida auris database is below:
How do I set snpeff_genome and snpeff_db? |
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Hi @ybdong919, The first column is the info that I used to make the In some cases there's no snpeff_db, and I don't think sarek handles that for now. I'll try to have a more in depth look and see how to deal with that within sarek. |
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Thanks, @maxulysse. With the command So perhaps it would work if @ybdong919 set (Notice a dot ( Or something like that? |
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@asp8200 I made the change from . to _ in the line you mentioned. However, it does not work. According to the log, it looks like more places that need to be changed from ( . ) to ( _ ). The command is : The termianl output is: Launching WARN: Access to undefined parameter |\ | |__ __ / nf-core/sarek v3.4.4Core Nextflow options Input/output options Main options Reference genome options Generic options !! Only displaying parameters that differ from the pipeline defaults !!If you use nf-core/sarek for your analysis please cite:
[- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - [- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - |
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It looks to me like you haven't made the change I mentioned above. The pipeline is looking for a directory named |
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I did change. See my line 877 below: |
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Very strange 🤔 Could you just - as a sanity check - try something like and rerun your nf-command. Then I would expect that you get an error message like If you indeed get that, then perhaps just hardcode the snpeff-argument for now, that is, try Given the problems your facing with getting this to work for "Candian aruis", I think we might try to improve on the setup of the snpeff-cache (and possibly the vep-cache) in Sarek in a future release. |
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@ybdong919 : Okay, so I've been trying to reproduce the error and it turns out that you also need to change a dot to an underscore here. |
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@ybdong919 : On this dev-branch, I tried solving the problem you encountered by retiring |
It did not work. See below: Command: nextflow run ./sarek -profile singularity --input samplesheet.csv --outdir ./Candida --tools 'snpeff' --step annotate --genome null --igenomes_ignore --skip_tools baserecalibrator --snpeff_cache //nf-core/sarek/data --snpeff_db _candida_aurisgca_001189475 Output of terminal: Launching WARN: Access to undefined parameter |\ | |__ __ / nf-core/sarek v3.4.4Core Nextflow options Input/output options Main options Reference genome options Generic options !! Only displaying parameters that differ from the pipeline defaults !!If you use nf-core/sarek for your analysis please cite:
[- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - |
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@ybdong919 : Could you try running your command using the version of Sarek from my branch modify_snpeff_cache_setup? |
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Yes, I did. but not work. I think more places need to be debugged. |
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Hmmm ... That is strange 🤔 @maxulysse just merged my PR to the dev-branch of the nf-core/sarek-repo, and I just ran the following test on that branch: Here the folder Works fine for me: 
And it produces |
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How and where should the pipeline scripts be changed if I want to use it to analyze other microbe genomes? |
This is my running log according to your command: N E X T F L O W ~ version 24.04.4 Launching WARN: Access to undefined parameter |\ | |__ __ / nf-core/sarek v3.5.0devCore Nextflow options Input/output options Main options Reference genome options Generic options !! Only displaying parameters that differ from the pipeline defaults !!If you use nf-core/sarek for your analysis please cite:
[- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - [- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - [- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - [- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - [- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - [- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - [- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - [- ] NFC…EPARE_GENOME:BWAMEM1_INDEX - executor > local (1) executor > local (1) Caused by: Command executed: snpEff cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command -- Check '.nextflow.log' file for details executor > local (1) Caused by: Command executed: snpEff cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command -- Check '.nextflow.log' file for details -- Check '.nextflow.log' file for details executor > local (1) Caused by: Command executed: snpEff cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command -- Check '.nextflow.log' file for details -- Check '.nextflow.log' file for details executor > local (1) Caused by: Command executed: snpEff cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command -- Check '.nextflow.log' file for details -- Check '.nextflow.log' file for details |
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Would you share the version 5.0 or 5.1 of Candida auris? The two versions are not available when I try to download them by "snpeff --download Candida auris" : [dongyibo@login9 nf-core]$ snpeff -download Candida_auris |
Description of the bug
How can I use a custom snpeff reference database, such as candida.auris, in Sarek. This snpeff reference did not included in Sarek. I tried --snpeff_cache, but not work.
Can you show me how to do it?
Command used and terminal output
No response
Relevant files
No response
System information
No response
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