bbduk error?

[pck00]

Hello, Testing out illumina files and running into this error:

(metacerberus) pck@LSE315-PK:~/metagenome_seq$ metacerberus.py --prodigal ~/metagenome_seq/ --illumina --meta --dir_out test HMM: 'KOFam_all'

Starting MetaCerberus Pipeline

Checking for external dependencies: fastqc /home/pck/anaconda3/envs/metacerberus/bin/fastqc flash2 /home/pck/anaconda3/envs/metacerberus/bin/flash2 fastp /home/pck/anaconda3/envs/metacerberus/bin/fastp porechop /home/pck/anaconda3/envs/metacerberus/bin/porechop bbduk.sh /home/pck/anaconda3/envs/metacerberus/bin/bbduk.sh FragGeneScanRs /home/pck/anaconda3/envs/metacerberus/lib/python3.10/site-packages/meta_cerberus/FGS/FragGeneScanRsprodigal /home/pck/anaconda3/envs/metacerberus/bin/prodigal prodigal-gv NOT FOUND, must be defined in config file as EXE_PRODIGAL-GV: phanotate.py NOT FOUND, must be defined in config file as EXE_PHANOTATE: hmmsearch /home/pck/anaconda3/envs/metacerberus/bin/hmmsearch countAssembly.py /home/pck/anaconda3/envs/metacerberus/bin/countAssembly.py Initializing RAY 2024-02-07 13:23:18,236 INFO worker.py:1612 -- Started a local Ray instance. View the dashboard at 127.0.0.1:8265 Started RAY single node Running RAY on 1 node(s) Using 16 CPUs per node

STEP 1: Loading sequence files: Processing 2 fastq sequences Processing 0 fasta sequences Processing 0 protein sequences Processing 0 rollup files

STEP 3: Trimming fastq files Trimming: prodigal_SRR9161505_2 /home/pck/metagenome_seq/SRR9161505_2.fastq Trimming: prodigal_SRR9161505_1 /home/pck/metagenome_seq/SRR9161505_1.fastq

STEP 4: Decontaminating trimmed files

STEP 5b: Reformating FASTQ files to FASTA format

(rayWorkerThread pid=1356) Command '['/home/pck/anaconda3/envs/metacerberus/bin/bbduk.sh', '-Xmx1g', 'in=/home/pck/metagenome_seq/test/step_03-trim/prodigal_SRR9161505_2/trimmed_prodigal_SRR9161505_2.fastq', 'out=/home/pck/metagenome_seq/test/step_04-decontaminate/prodigal_SRR9161505_2/decon-prodigal_SRR9161505_2.fastq', 'qin=30', 'qtrim=r', 'minlen=50', 'k=31', 'ref=default', 'hdist=1', 'stats=/home/pck/metagenome_seq/test/step_04-decontaminate/prodigal_SRR9161505_2/stats.txt']' returned non-zero exit status 1. (rayWorkerThread pid=1356) ERROR: Failed to execute: (rayWorkerThread pid=1356) ['/home/pck/anaconda3/envs/metacerberus/bin/bbduk.sh', '-Xmx1g', 'in=/home/pck/metagenome_seq/test/step_03-trim/prodigal_SRR9161505_2/trimmed_prodigal_SRR9161505_2.fastq', 'out=/home/pck/metagenome_seq/test/step_04-decontaminate/prodigal_SRR9161505_2/decon-prodigal_SRR9161505_2.fastq', 'qin=30', 'qtrim=r', 'minlen=50', 'k=31', 'ref=default', 'hdist=1', 'stats=/home/pck/metagenome_seq/test/step_04-decontaminate/prodigal_SRR9161505_2/stats.txt']

STEP 7: ORF Finder

STEP 8: HMMER Search

STEP 8: Filtering HMMER results

STEP 9: Parse HMMER results

STEP 10: Creating Reports Saving Statistics Creating Rollup Tables Creating Count Tables NOTE: PCA Tables created only when there are at least four sequence files.

NOTE: Pathview created only when there are at least four sequence files.

Creating combined sunburst and bargraphs

Finished Pipeline (rayWorkerThread pid=1346) Command '['/home/pck/anaconda3/envs/metacerberus/bin/bbduk.sh', '-Xmx1g', 'in=/home/pck/metagenome_seq/test/step_03-trim/prodigal_SRR9161505_1/trimmed_prodigal_SRR9161505_1.fastq', 'out=/home/pck/metagenome_seq/test/step_04-decontaminate/prodigal_SRR9161505_1/decon-prodigal_SRR9161505_1.fastq', 'qin=30', 'qtrim=r', 'minlen=50', 'k=31', 'ref=default', 'hdist=1', 'stats=/home/pck/metagenome_seq/test/step_04-decontaminate/prodigal_SRR9161505_1/stats.txt']' returned non-zero exit status 1. (rayWorkerThread pid=1346) ERROR: Failed to execute: (rayWorkerThread pid=1346) ['/home/pck/anaconda3/envs/metacerberus/bin/bbduk.sh', '-Xmx1g', 'in=/home/pck/metagenome_seq/test/step_03-trim/prodigal_SRR9161505_1/trimmed_prodigal_SRR9161505_1.fastq', 'out=/home/pck/metagenome_seq/test/step_04-decontaminate/prodigal_SRR9161505_1/decon-prodigal_SRR9161505_1.fastq', 'qin=30', 'qtrim=r', 'minlen=50', 'k=31', 'ref=default', 'hdist=1', 'stats=/home/pck/metagenome_seq/test/step_04-decontaminate/prodigal_SRR9161505_1/stats.txt']

I've run into this problem with two different illumina SRA files, but no problems previously with long read seq data.

[raw-lab]

Good afternoon,

Thank you for using MetaCereberus.

Can you provide: OS info (linux, mac, etc) OS version info (e.g., Ubuntu 20.4) MetaCerberus version: (e.g., 1.2)

Many thanks, RAW

[pck00]

Distributor ID: Ubuntu Description: Ubuntu 22.04.2 LTS Release: 22.04 Codename: jammy

MetaCerberus: version: 1.2 September 2023

[raw-lab]

Update with 1.2.1 this bug was fixed in that. Let us know if you have any other issue and we can reopen this. Closing for now.