GraphMap2_Align Crash

[DrOllyGomez]

Check Documentation

I have checked the following places for your error:

• [X] nf-core website: troubleshooting
• [X] nf-core/nanoseq pipeline documentation

Description of the bug

Piepline crashes at the Grapmap2_Align stage

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:

nextflow run nf-core/nanoseq --monochrome_logs --input /mnt/blah-blah-blah/samplesheet.csv --outdir /home/mike.harbourblah-blah-blah --protocol directRNA --skip_basecalling --skip_demultiplexing --aligner graphmap2 --quantification_method bambu -profile singularity --skip_bigbed --skip_bigwig --skip_pycoqc --skip_nanoplot --skip_fastqc --skip_multiqc --skip_qc

3. See error: "Execution aborted due to an unexpected error -- Check script '.nextflow/assets/nf-core/nanoseq/./workflows/../subworkflows/local/../../modules/local/graphmap2_align.nf' at line: 8 or see '.nextflow.log' file for more details "

Expected behaviour

Graphmap2 pipeline stage to complete and for pipeline to continue.

Log files

Have you provided the following extra information/files:

• [X] The command used to run the pipeline (see point 1 above)
• [X] The .nextflow.log file

System

• Hardware: internal server Kernel Linux 5.4.0-105-generic x86_64
• Executor: local
• OS: Ubuntu
• Version Release 20.04.3 LTS (Focal Fossa) 64-bit

Nextflow Installation

• Version: 1.10.6 build 5661

Container engine

• Engine: Singularity
• version: 3.6.3

Additional context

nextflow.log

[DrOllyGomez]

samplesheet.csv

[DrOllyGomez]

the command run and err files from task 7b/9df27c7d8e536a2517d8b6555064f5, if they are relevant. eg the err file complains about some oddities

from_7b_slash_9df_etc.zip