Error in rule LongRead_correct_allRead:

[herber4]

log
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 16
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job count min threads max threads

---

LongRead_correct_allRead 1 1 1
all 1 1 1
bwa_1 1 1 1
bwa_2 1 1 1
bwa_3 1 1 1
bwa_4 1 1 1
first_assemble 1 1 1
fq_to_fa 1 1 1
longread_polish 1 1 1
pilon_polish_1 1 1 1
pilon_polish_2 1 1 1
pilon_polish_3 1 1 1
pilon_polish_4 1 1 1
polish_round1 1 1 1
rearrange 1 1 1
select_longestContig 1 1 1
select_longread 1 1 1
short_to_long 1 1 1
total 18 1 1

Select jobs to execute...

[Thu Jul 28 06:57:53 2022]
rule LongRead_correct_allRead:
input: /data/lackey_lab/austin/peach/copper/B-assembler/test/1_nanopore.fast
q, /data/lackey_lab/austin/peach/copper/B-assembler/test/CuR_R1_clean.fastq.gz,
/data/lackey_lab/austin/peach/copper/B-assembler/test/CuR_R2_clean.fastq.gz
output: output/racon_polish_longread.fastq
jobid: 11
reason: Missing output files: output/racon_polish_longread.fastq
resources: tmpdir=/tmp

[Thu Jul 28 07:17:29 2022]
Error in rule LongRead_correct_allRead:
jobid: 11
output: output/racon_polish_longread.fastq
shell:

    cat /data/lackey_lab/austin/peach/copper/B-assembler/test/CuR_R1_clean.f

astq.gz /data/lackey_lab/austin/peach/copper/B-assembler/test/CuR_R2_clean.fastq
.gz > output/shortread.fq
minimap2 -ax sr /data/lackey_lab/austin/peach/copper/B-assembler/test/1_
nanopore.fastq /data/lackey_lab/austin/peach/copper/B-assembler/test/CuR_R1_clea
n.fastq.gz /data/lackey_lab/austin/peach/copper/B-assembler/test/CuR_R2_clean.fa
stq.gz > output/short_long.sam
racon output/shortread.fq output/short_long.sam /data/lackey_lab/austin/
peach/copper/B-assembler/test/1_nanopore.fastq > output/racon_polish_longread.fa
sta
scripts/fa2fq.pl output/racon_polish_longread.fasta > output/racon_polis
h_longread.fastq

    (one of the commands exited with non-zero exit code; note that snakemake

uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-07-28T065752.977498.snakemake.log

config:

DATA

longread: /data/XXXXX/austin/peach/copper/B-assembler/test/1_nanopore.fastq # Path to Nanopore or pacbio long reads, all long reads should be in a fastq file

illumina:
R1: /data/XXXXX/austin/peach/copper/B-assembler/test/CuR_R1_clean.fastq.gz # Path to Illumina R1 reads
R2: /data/XXXXXX/austin/peach/copper/B-assembler/test/CuR_R2_clean.fastq.gz # Path to Illumina R2 reads

REQUIREMENT

genomesize: 5200000 #extimate genome size in base pair

LONGREAD TYPE

readtype: ONT #nanopore:ONT, pacbio:pb

PATH

sourceDir: PathToSourceDir
outputDir: PathToOutputDir

command:

bash run_assembler.sh 16 Hybrid

any idea what's going on?