The pipeline seems to be running an BISMARK_ALIGN step for the first sample as many times as the total number of samples, instead of a separate BISMARK_ALIGN step for each sample.
The BISMARK_ALIGN step says it cannot find the mm10.fa reference file. But it was definitely configured correctly and the file is present:
Error:
-[nf-core/methylseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (M1)'
Caused by:
Process `NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN (M1)` terminated with an error exit status (2)
Command executed:
bismark \
-1 M1_1_val_1.fq.gz -2 M1_2_val_2.fq.gz \
--genome BismarkIndex \
--bam \
--bowtie2 --maxins 1000 --multicore 4
cat <<-END_VERSIONS > versions.yml
"NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN":
bismark: $(echo $(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*$//')
END_VERSIONS
Command exit status:
2
Command output:
(empty)
Command error:
Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.4.5])
Output format is BAM (default)
Alignments will be written out in BAM format. Samtools found here: '/usr/local/bin/samtools'
Reference genome folder provided is BismarkIndex/ (absolute path is '/gpfs/scratch/user/methylation/work/17/9f7fe2cc089132a7e63fbc29c8d339/BismarkIndex/)'
FastQ format assumed (by default)
Input files to be analysed (in current folder '/gpfs/scratch/user/methylation/work/58/93334847cd4de313854a32d6a7333a'):
M1_1_val_1.fq.gz
M1_2_val_2.fq.gz
Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!)
Summary of all aligner options: -q --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 1000
Running Bismark Parallel version. Number of parallel instances to be spawned: 4
Current working directory is: /gpfs/scratch/user/methylation/work/58/93334847cd4de313854a32d6a7333a
Now reading in and storing sequence information of the genome specified in: /gpfs/scratch/user/methylation/work/17/9f7fe2cc089132a7e63fbc29c8d339/BismarkIndex/
Failed to read from sequence file mm10.fa No such file or directory
Work dir:
/gpfs/scratch/user/methylation/work/58/93334847cd4de313854a32d6a7333a
But file is present:
$ ls /gpfs/scratch/user/methylation/work/17/9f7fe2cc089132a7e63fbc29c8d339/BismarkIndex/
Bisulfite_Genome mm10.fa
Description of the bug
Hi, in the dev version there are multiple issues:
The pipeline seems to be running an BISMARK_ALIGN step for the first sample as many times as the total number of samples, instead of a separate BISMARK_ALIGN step for each sample.
The BISMARK_ALIGN step says it cannot find the mm10.fa reference file. But it was definitely configured correctly and the file is present:
Error:
But file is present:
Command used and terminal output
No response
Relevant files
No response
System information
Nextflow 23.04.4
Executor: slurm