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kzeglinski / nabseq_nf

Nextflow pipeline for NAb-seq (analyses nanopore sequencing data from hybridomas and single B cells)
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pipeline failed at annotation_grouping_pre_consensus :igblast #2

Closed jagos01 closed 1 year ago

jagos01 commented 1 year ago

Hello, I am trying to run this workflow on my local computer. I used the following command: nextflow run ./nabseq_nf/main.nf --fastq_dir /home/scott/Data_Raw/mAbs_June1/20230601_1623_MC-111382_FAW58338_807354c1/fastq_pass/ --organism mouse --sample_sheet /home/scott/Data_Analysis/mAb_test/sample_sheet.csv -profile standard

I received the following error message:

Command error: BLAST query/options error: Germline annotation database mouse/mouse_V could not be found in [internal_data] directory Please refer to the BLAST+ user manual.

Any help resolving this is appreciated. Thanks, Scott

kzeglinski commented 1 year ago

Hi Scott!

A couple of things here:

  1. If you are running the latest version of NAb-seq, we now require the organism to be specified in the sample sheet rather than as a command line parameter (sorry for the confusion! I should probably add an error message flagging this change). We made this change to allow the running of a batch of samples from different organisms at once. So the sample sheet should look like: barcode,sample_name,species,report_group barcode18,15-14-7H9-19-1,mouse,1 For more information please see the tutorial: https://kzeglinski.github.io/nab-seq/new_tutorial.html

  2. The error message you're receiving I think probably relates to file mounting in containers. I believe that -profile standard in nextflow usually uses docker. In this case, you might want to add the following to the docker section of the nextflow config: runOptions= "-v $HOME:$HOME" (or you can replace $HOME with the path of where the nabseq_nf folder is located). I'm not sure why nextflow doesn't mount these paths automatically, but a few people have had this issue now so I might add a note in the documentation on it.

Hopefully this helps! Happy to answer any questions & help troubleshoot further if needed ☺️

jagos01 commented 1 year ago

Hello, Thank you for your quick reply. I removed the organism from the command line (sample sheet was formatted correctly) and added the docker mount path in nexflow config. Works perfectly now. Thanks again, Scott

kzeglinski commented 1 year ago

No worries! Glad to hear it is working 😄