Hello, I am running methylseq pipeline on several EM-seq samples and encountered an error (in .command.log)

[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Set --bwa-options="-K #" to produce compatible pair-ended results with previous versions of
fq2bam or BWA MEM.
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for EM_seq/scripts/work/9a/e820b2b96ed2671177b4bf47fbf62c/LIB-15-0321_T1-reseq_1_val_1.fq.gz and /EM_seq/scripts/work/9a/e820b2b96ed2671177b4bf47fbf62c/LIB-15-0321_T1-
reseq_2_val_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:2332FMLT3.4\tLB:lib1\tPL:bar\tSM:sample\tPU:2332FMLT3.4
[Parabricks Options Mesg]: Using --low-memory reduces the number of reads sent to GPU per batch in fq2bam_meth.
[Parabricks Options Mesg]: Using --low-memory sets the number of streams in bwa mem to 1.
[PB Info 2026-Aug-11 15:55:11] ------------------------------------------------------------------------------
[PB Info 2026-Aug-11 15:55:11] ||                 Parabricks accelerated Genomics Pipeline                 ||
[PB Info 2026-Aug-11 15:55:11] ||                              Version 4.3.2-1                             ||
[PB Info 2026-Aug-11 15:55:11] ||                      GPU-PBBWA mem, Sorting Phase-I                      ||
[PB Info 2026-Aug-11 15:55:11] ------------------------------------------------------------------------------
[PB Info 2026-Aug-11 15:55:11] Mode = pair-ended-gpu
[PB Info 2026-Aug-11 15:55:11] Running with 1 GPU(s), using 1 stream(s) per device with 16 worker threads per GPU
[PB ESC[31mErrorESC[0m 2026-Aug-11 15:55:11][src/internal/bwa_reference.cpp:71] Unable to read file: EM_seq/scripts/work/26/5d249fac96c681a807f8798af80feb/BwamethIndex/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.bwameth.c2t.bwt. Check that file exists, and check read permissions. Please ensure reference has been indexed, exiting.
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Exiting...
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Could not run fq2bam_meth
Exiting pbrun ...

The command I used to run the pipeline is

module load singularity/3.11.0

nextflow run nf-core-methylseq_4.1.0/4_1_0 -profile singularity,gpu \
         -c nf-core-methylseq_4.1.0/4_1_0/conf/nf-core-slurm/nfcore_custom.config \
         --input controls_sheet.csv \
         --outdir ../healthy_controls_processed_data \
         --fasta reference_genome/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta  \
         --fasta_index reference_genome/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.fai \
         --aligner bwameth \
         --use_mem2 true \
         --em_seq true

The mextflow version is 24.10.5 and methylseq version is 4.1.0. I checked the work dir and the file the command was looking for was not there (end with bwameth.c2t.bwt). I am not sure if this is an issue with bwa-mem2. Below is what the work dir contains:

GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta                   GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.bwameth.c2t.ann
GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.bwameth.c2t       GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.bwameth.c2t.bwt.2bit.64
GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.bwameth.c2t.0123  GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.bwameth.c2t.pac
GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.bwameth.c2t.amb

Could be due to : "--use_mem2 true". Try withot this