Bismark soft clip --local_alignment True keeps L,value,value

[ioannagare]

Description of the bug

Hello community! I have been trying to run the option --local_alignment as True to enable soft clipping and get this error: In Bowtie 2 --local mode, the option '--score_min ' needs to be in the format <G,value,value>. Please consult "setting up functions" in the Bowtie 2 manual for further information.

When I look at the error folder the command.sh I see: bismark
-1 file_1_val_1.fq.gz -2 file_2_val_2.fq.gz
--genome Genome_directory_runs
--bam
--bowtie2 --score_min L,0,-0.6 --local --maxins 1000 --multicore 4

The manual of bowtie2 says this for the case of local mode the --score_min needs to be changed: --score-min | Sets a function governing the minimum alignment score needed for an alignment to be considered "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying L,0,-0.6 sets the minimum-score function f to f(x) = 0 + -0.6 * x, where x is the read length. See also: setting function options. The default in --end-to-end mode is L,-0.6,-0.6 and the default in --local mode is G,20,8. https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#setting-function-options

I suspect there might be an issue because in the browser when I create the options for local mode I am not able to change this to G,value,value and the default leaves the L,value,value which breaks the process. Best, Ioanna

Command used and terminal output

#!/bin/bash

#SBATCH --clusters=cluster
#SBATCH --partition=partition
#SBATCH --cpus-per-task=3
#SBATCH --mem-per-cpu=4763mb
#SBATCH --time=240:00:00
#SBATCH --mail-user=mail
#SBATCH -J default_1
#SBATCH -o path/slurm/%J-%x.out

echo "start";hostname;  date 

nextflow run nf-core/methylseq -r 2.7.1 -name default_1 -profile conda -resume -params-file /bismark/soft_clip_true/0_setup/nf-params.json

echo "finish";hostname;  date

output is
Command exit status:
  255

Command output:
  (empty)

Command error:
  Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.5.4])
  Output format is BAM (default)
  Alignments will be written out in BAM format. Samtools found here: 'bismark/soft_clip_true/0_setup/work/conda/env-c3ffa047973ad1f3-4f74706f8ceae196cb2b8d70176e5af1/bin/samtools'
  Reference genome folder provided is Genome_directory_runs/	(absolute path is '/Genome_directory_runs/)'
  FastQ format assumed (by default)
  In Bowtie 2 --local mode, the option '--score_min <func>' needs to be in the format <G,value,value>. Please consult "setting up functions" in the Bowtie 2 manual for further information

Work dir:
/bismark/soft_clip_true/0_setup/work/7f/45ae44f2199faefb390cc483c42c33

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

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

Relevant files

No response

System information

N E X T F L O W version 24.10.1 build 5930 created 18-11-2024 12:21 UTC (13:21 CEST) cite doi:10.1038/nbt.3820 http://nextflow.io HPC slurm Conda nextflow run nf-core/methylseq -r 2.7.1

[sateeshperi]

hi @ioannagare is this still an issue? or have you found a fix ?