problem with the combine_annotations step

[ssvassiliev]

Hi! I am trying to run DRAM2 on an HPC cluster using the singularity_slurm profile.

The COMBINE_ANNOTATIONS step fails because the file .._sql_formatted_viral_hits.csv created at the previous stage SQL_VIRAL cannot be opened.

combine_annotations.log:

ERROR: Error loading DataFrame for sample Ecoli_strK-12_substrMG1655: [Errno 2] No such file or directory: '/scratch/user/DRAM2/work/78/157d7ff6a66e318a233c38477bd36b/Ecoli_strK_sql_formatted_viral_hits.csv'

However, this file exists at this location. Does anyone know how to fix this problem?

Using the annotation command --annotate --use_viral --use_vogdb

[SergVassiliev]

I resolved the issue by adding the necessary binding path to the singularity scope in nextflow.config. I am new to nextflow, so this might not be the best solution.

singularity { ... runOptions = "--bind /path_to_bind:/path_to_bind" }

[fjell-dev]

I resolved the issue by adding the necessary binding path to the singularity scope in nextflow.config. I am new to nextflow, so this might not be the best solution.

singularity { ... runOptions = "--bind /path_to_bind:/path_to_bind" }

I also ran into this issue. Could you clarify a bit about which path for binding that I need to change? Thank you.

[madeline-scyphers]

This is fixed in beta13, see #431 for more details