[Internal] [Bug] Conda environment on scicomp: RepeatMasker::createLib(): Error

[jessicarowell]

ERROR ~ Error executing process > 'TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:REPEATMASKER (2)'

Caused by:
Process TOSTADAS_WORKFLOW:TOSTADAS:REPEATMASKER_LIFTOFF:REPEATMASKER (2) terminated with an error exit status (2)

Command executed:

echo IL0005.fasta
echo mpxv_repeats_lib.fasta
RepeatMasker -s IL0005.fasta -gff -lib mpxv_repeats_lib.fasta -s

Command exit status:
2

Command output:
IL0005.fasta
mpxv_repeats_lib.fasta
RepeatMasker version 4.1.5
Search Engine: NCBI/RMBLAST [ 2.14.1+ ]
Using Custom Repeat Library: mpxv_repeats_lib.fasta

Building general libraries in: /scicomp/scratch/ick4/conda/env-20ce62a14176755b741d472f92113882/share/RepeatMasker/Libraries//general

Command error:
IL0005.fasta
mpxv_repeats_lib.fasta
RepeatMasker version 4.1.5
Search Engine: NCBI/RMBLAST [ 2.14.1+ ]
Using Custom Repeat Library: mpxv_repeats_lib.fasta

Building general libraries in: /scicomp/scratch/ick4/conda/env-20ce62a14176755b741d472f92113882/share/RepeatMasker/Libraries//general
RepeatMasker::createLib(): Error invoking /scicomp/scratch/ick4/conda/env-20ce62a14176755b741d472f92113882/bin//makeblastdb on file /scicomp/scratch/ick4/conda/env-20ce62a14176755b741d472f92113882/share/RepeatMasker/Libraries//general.working/is.lib.

Work dir:
/scicomp/scratch/ick4/82/0a62db4cf533855a933b5d6e1c5ca7

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details

Place an ❌ in a Box that Best Matches the Bug's Importance:

• 1 - Most severe (a full-break in core function)
• [] 2-4 - Moderate (break for a particular aspect/feature) (how integral is the broken feature?)
• [] 5 - Least severe (non-functional issue, such as inconsitency / error in documentation or administrative in nature) 

Please Complete the Following Information:

• OS: [e.g. iOS]: scicomp
• Browser [e.g. chrome, safari]:
• Version [e.g. 22]:
• Run environment (container, cloud service, HPC, platform, etc.):

Please Outline Necessary Steps to Replicate Bug (Go to.. Click on... Install the following... etc.):
nextflow run main.nf -profile test,conda --species virus --submission --sra --biosample --genbank --output_dir test_ramiya --submission_config ~/02.scratch/submission_config.yaml

Any Additional Context or Information? Has There Been Any Progress Made So Far Towards this Request? Any Concrete Instructions to Resolve the Bug or Helpful Resources to Reference? Screenshots or Logs?

Activating the tostadas environment specified in the .nextflow.log and running .command.sh in the work directory works just fine and produces the following output:

IL0005.fasta
mpxv_repeats_lib.fasta
RepeatMasker version 4.1.2-p1
Search Engine: NCBI/RMBLAST [ 2.14.1+ ]
Using Custom Repeat Library: mpxv_repeats_lib.fasta

Building general libraries in: /scicomp/scratch/ick4/conda/tostadas-2e88a25c20f71533c926836063aee2de/share/RepeatMasker/Libraries//general

analyzing file IL0005.fasta

Checking for E. coli insertion elements
identifying Simple Repeats in batch 1 of 4
identifying matches to mpxv_repeats_lib.fasta sequences in batch 1 of 4
identifying Simple Repeats in batch 1 of 4

Checking for E. coli insertion elements
identifying Simple Repeats in batch 2 of 4
identifying matches to mpxv_repeats_lib.fasta sequences in batch 2 of 4
identifying Simple Repeats in batch 2 of 4

Checking for E. coli insertion elements
identifying Simple Repeats in batch 3 of 4
identifying matches to mpxv_repeats_lib.fasta sequences in batch 3 of 4
identifying Simple Repeats in batch 3 of 4

Checking for E. coli insertion elements
identifying Simple Repeats in batch 4 of 4
identifying matches to mpxv_repeats_lib.fasta sequences in batch 4 of 4
identifying Simple Repeats in batch 4 of 4
processing output:
cycle 1
cycle 2
cycle 3
cycle 4
cycle 5
cycle 6
cycle 7
cycle 8
cycle 9
cycle 10
Generating output...
masking
done