Error 256

[KFWins2022]

I updated to the new version of shovill and I am still having a 256 error. I cleared my cache, I have nothing else running, I updated everything. I don't know what the issue is.

Here is my spades log:
System information:
SPAdes version: 3.13.0
Python version: 3.11.0
OS: Linux-3.10.0-1160.76.1.el7.x86_64-x86_64-with-glibc2.17

Output dir: /home/user/Documents/Unpacked/SE111
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF

Dataset parameters:
Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
Reads:

Here is my bash log before it crashes:
Running: spades.py --pe1-1 flash.notCombined_1.fastq.gz --pe1-2 flash.notCombined_2.fastq.gz --s2 flash.extendedFrags.fastq.gz --only-assembler --threads 16 --memory 8 -o . --tmp-dir /tmp -k 31,55,79,103,127 >> /dev/null 2>&1
Error 256 running command

[jrudar]

I tried this and it worked:

ablab/spades#873

[mcolpus]

I think this has now been resolved by spades 3.15.4+, which you should get if you conda install shovill now

[fgonzalez3]

I also encountered Error 256 when Spades tried running even though I had the latest Spades version. My workaround was to create a Shovill conda environment manually following the GitHub instructions and then activate it as I did below in Snakemake:

import pandas as pd

configfile: "config/AMR.yaml"

samples_df = pd.read_csv("tsv/isolates.tsv", sep="\t")
SAMPLES = samples_df["sample_id"].tolist()
READS = {row.sample_id: {"r1": row.r1, "r2": row.r2} for row in samples_df.itertuples()}

rule all:
input:
expand("results/{genera}/shovill/{sample}/contigs.fa", sample=SAMPLES, genera=config["genera"]),
expand("results/{genera}/shovill/{sample}/contigs.gfa", sample=SAMPLES, genera=config["genera"]),
expand("results/{genera}/shovill/{sample}/shovill.corrections", sample=SAMPLES, genera=config["genera"]),
expand("results/{genera}/shovill/{sample}/shovill.log", sample=SAMPLES, genera=config["genera"]),
expand("results/{genera}/shovill/{sample}/spades.fasta", sample=SAMPLES, genera=config["genera"])

rule shovill:
"""
Assemble reads using Shovill
"""
input:
fwd=lambda wildcards: READS[wildcards.sample]["r1"],
rev=lambda wildcards: READS[wildcards.sample]["r2"]
output:
"results/{genera}/shovill/{sample}/contigs.fa",
"results/{genera}/shovill/{sample}/contigs.gfa",
"results/{genera}/shovill/{sample}/shovill.corrections",
"results/{genera}/shovill/{sample}/shovill.log",
"results/{genera}/shovill/{sample}/spades.fasta"
params:
genera=config["genera"]
shell:
"""
source activate /home/flg9/.conda/envs/shovill
shovill --outdir results/{params.genera}/shovill/{wildcards.sample} --R1 {input.fwd} --R2 {input.rev} --force
"""