Facing error with minimap2 when running single cell long pipeline.py

[Aravind-sunda]

I am running the sc_long_pipeline.py as a rule in my snakemake workflow. The following is a command that I am using

    applications/flames/python/sc_long_pipeline.py \
    -a {params.annotation_gff3} \
    -i {input.flames_cb_matched} \
    -o {output.flames_isoform_dir} \
    -f {params.reference} \
    -c {params.config_file} \
    # -m {params.minimap_dir}

Log File Output
Activating conda environment: .snakemake/conda/3731e9db73179dc68eabd2b463b92ab3_
Use config file: reference/config_default.json
Parameters in configuration file:
comment : this is the default config for nanopore single cell long read data using 10X RNA-seq kit. use splice annotation in alignment.
pipeline_parameters
do_genome_alignment : True
do_isoform_identification : True
do_read_realignment : True
do_transcript_quantification : True
global_parameters
generate_raw_isoform : False
has_UMI : True
isoform_parameters
MAX_DIST : 10
MAX_TS_DIST : 120
MAX_SPLICE_MATCH_DIST : 10
min_fl_exon_len : 40
Max_site_per_splice : 3
Min_sup_cnt : 5
Min_cnt_pct : 0.001
Min_sup_pct : 0.2
strand_specific : 0
remove_incomp_reads : 4
random_seed : 666666
alignment_parameters
use_junctions : True
no_flank : False
seed : 2022
realign_parameters
use_annotation : True
transcript_counting
min_tr_coverage : 0.4
min_read_coverage : 0.4
output directory not exist, create one:
results/flames/t1_shCTRL/isoform
Input parameters:
gene annotation: reference/gencode.vM10.annotation.gff3
genome fasta: reference/GRCm38.p4.genome.fa
input fastq: results/flames/t1_shCTRL/t1_shCTRL_cb_matched.fastq.gz
output directory: results/flames/t1_shCTRL/isoform
directory contains minimap2:

align reads to genome using minimap2 2024-07-16 17:03:24

b''
Traceback (most recent call last):
File "applications/flames/python/sc_long_pipeline.py", line 240, in
sc_long_pipeline(args)
File "applications/flames/python/sc_long_pipeline.py", line 168, in sc_long_pipeline
seed=config_dict["alignment_parameters"]["seed"])
File "/condo/brannanlab/tmhaxs421/STAMP/Luiz-LongRead/applications/flames/python/minimap2_align.py", line 41, in minimap2_align
shell=True, stderr=subprocess.STDOUT))
File "/condo/brannanlab/tmhaxs421/STAMP/Luiz-LongRead/.snakemake/conda/3731e9db73179dc68eabd2b463b92ab3_/lib/python3.7/subprocess.py", line 411, in check_output
**kwargs).stdout
File "/condo/brannanlab/tmhaxs421/STAMP/Luiz-LongRead/.snakemake/conda/3731e9db73179dc68eabd2b463b92ab3_/lib/python3.7/subprocess.py", line 512, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['minimap2 -ax splice -t 12 --junc-bed results/flames/t1_shCTRL/isoform/tmp.splice_anno.bed12 --junc-bonus 1 -k14 --secondary=no --seed 2022 reference/GRCm38.p4.genome.fa results/flames/t1_shCTRL/t1_shCTRL_cb_matched.fastq.gz | samtools view -bS -@ 4 -m 2G -o results/flames/t1_shCTRL/isoform/tmp.align.bam - ']' returned non-zero exit status 127.

Can someone tell me why I am facing this error? I have tried a lot of alternatives. None seem to work.