NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN: corruption of 638 bytes: Error in middle of record #950
Description
Description of the bug
Due to memory limitations, I had to resume the pipeline multiple times.
Each time, the execution restarts from the process NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN because of the recurring error:
“corruption of 638 bytes: Error in middle of record”
Although the pipeline does not crash completely, every resume forces it to restart from the same previous stage instead of continuing from where it left off.
(base) user@user-System-Product-Name:/media/user/Petros/mag$ nextflow run nf-core/mag -r 5.2.0 -profile singularity --save_trimmed false --save_unfiltered_contigs false --save_alignments false --save_binning_intermediates false --save_process_intermediates false --input samplesheet.csv --outdir /media/user/Petros/no_sample/merge/mag --gtdb_db /media/user/Petros/metagenomics/databases/gtdbtk_r226/gtdbtk_r226_data.tar.gz --validate_params false -c filtlong_override.config -resume
Nextflow 25.10.2 is available - Please consider updating your version to it
N E X T F L O W ~ version 25.04.2
Launching `https://github.com/nf-core/mag` [dreamy_goldberg] DSL2 - revision: 99859fc04c [5.2.0]
corruption of 638 bytes: Error in middle of record
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|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/mag 5.2.0
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Input/output options
input : samplesheet.csv
outdir : /media/user/Petros/no_sample/merge/mag
Generic options
validate_params : false
trace_report_suffix : 2025-12-02_08-49-52
Taxonomic profiling options
gtdb_db : /media/user/Petros/metagenomics/databases/gtdbtk_r226/gtdbtk_r226_data.tar.gz
gtdbtk_min_completeness : 50.0
gtdbtk_max_contamination: 10.0
Bin quality check options
run_busco : true
Core Nextflow options
revision : 5.2.0
runName : dreamy_goldberg
containerEngine : singularity
launchDir : /media/user/Petros/mag
workDir : /media/user/Petros/mag/work
projectDir : /home/user/.nextflow/assets/nf-core/mag
userName : user
profile : singularity
configFiles : /home/user/.nextflow/assets/nf-core/mag/nextflow.config, /media/user/Petros/mag/filtlong_override.config
!! Only displaying parameters that differ from the pipeline defaults !!
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* The pipeline
https://doi.org/10.1093/nargab/lqac007
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/mag/blob/main/CITATIONS.md
executor > local (1)
executor > local (1)
executor > local (1)
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW -
executor > local (1)
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW -
executor > local (1)
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW -
executor > local (1)
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW -
executor > local (1)
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW -
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP -
executor > local (1)
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW -
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP -
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD -
executor > local (1)
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_RAW -
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTP -
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_BUILD -
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:BOWTIE2_PHIX_REMOVAL_ALIGN -
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:FASTQC_TRIMMED -
[- ] process > NFCORE_MAG:MAG:SHORTREAD_PREPROCESSING:CAT_FASTQ -
[9a/838eef] process > NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_RAW (sample14) [100%] 14 of 14, cached: 14 ✔
[bd/aaab30] process > NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:PORECHOP_ABI (sample14) [100%] 14 of 14, cached: 14 ✔
[62/f22fbb] process > NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOLYSE (sample09) [100%] 14 of 14, cached: 14 ✔
[07/bbf064] process > NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:FILTLONG (sample14) [100%] 14 of 14, cached: 14 ✔
[5f/40488c] process > NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:NANOPLOT_FILTERED (sample14) [100%] 14 of 14, cached: 14 ✔
[- ] process > NFCORE_MAG:MAG:LONGREAD_PREPROCESSING:CAT_FASTQ_LONGREADS -
[- ] process > NFCORE_MAG:MAG:ASSEMBLY:POOL_LONG_READS -
[- ] process > NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:METASPADES -
[- ] process > NFCORE_MAG:MAG:ASSEMBLY:SHORTREAD_ASSEMBLY:MEGAHIT -
[- ] process > NFCORE_MAG:MAG:ASSEMBLY:HYBRID_ASSEMBLY:METASPADESHYBRID -
[18/94d57c] process > NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE (sample14) [100%] 14 of 14, cached: 14 ✔
[51/2d4295] process > NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:METAMDBG_ASM (sample14) [100%] 14 of 14, cached: 14 ✔
[- ] process > NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_SHORTREAD_ASSEMBLIES -
[e0/e68de0] process > NFCORE_MAG:MAG:ASSEMBLY:GUNZIP_LONGREAD_ASSEMBLIES (FLYE-sample11.assembly.fasta.gz) [100%] 28 of 28, cached: 28 ✔
[48/ff3660] process > NFCORE_MAG:MAG:QUAST (FLYE-sample11) [100%] 28 of 28, cached: 28 ✔
[33/4e49a3] process > NFCORE_MAG:MAG:PRODIGAL (sample11) [100%] 28 of 28, cached: 28 ✔
[- ] process > NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_BUILD -
[- ] process > NFCORE_MAG:MAG:BINNING_PREPARATION:SHORTREAD_BINNING_PREPARATION:BOWTIE2_ASSEMBLY_ALIGN -
[22/a408c5] process > NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_INDEX (28) [100%] 28 of 28, cached: 28 ✔
[ce/b5a4e2] process > NFCORE_MAG:MAG:BINNING_PREPARATION:LONGREAD_BINNING_PREPARATION:MINIMAP2_ASSEMBLY_ALIGN (sample11) [100%] 392 of 392, cached: 392 ✔
[e1/d40737] process > NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_LONGREAD (sample14) [100%] 28 of 28, cached: 28 ✔
[- ] process > NFCORE_MAG:MAG:BINNING:METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS_SHORTREAD -
[8b/1c6831] process > NFCORE_MAG:MAG:BINNING:CONVERT_DEPTHS (sample06) [100%] 28 of 28, cached: 28 ✔
[67/6be97e] process > NFCORE_MAG:MAG:BINNING:METABAT2_METABAT2 (sample14) [100%] 28 of 28, cached: 28 ✔
[87/a7fdff] process > NFCORE_MAG:MAG:BINNING:MAXBIN2 (sample06) [100%] 28 of 28, cached: 28 ✔
[4c/71ec0f] process > NFCORE_MAG:MAG:BINNING:ADJUST_MAXBIN2_EXT (FLYE-sample06) [100%] 28 of 28, cached: 28 ✔
[ac/c83289] process > NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CUTUPFASTA (sample14) [100%] 28 of 28, cached: 28 ✔
[fd/65ffc7] process > NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCTCOVERAGETABLE (sample14) [100%] 28 of 28, cached: 28 ✔
[a5/c4f913] process > NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_CONCOCT (sample14) [100%] 28 of 28, cached: 28 ✔
[8e/dd2040] process > NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_MERGECUTUPCLUSTERING (sample14) [100%] 28 of 28, cached: 28 ✔
[cd/3643f1] process > NFCORE_MAG:MAG:BINNING:FASTA_BINNING_CONCOCT:CONCOCT_EXTRACTFASTABINS (sample14) [100%] 28 of 28, cached: 28 ✔
[78/6e61c9] process > NFCORE_MAG:MAG:BINNING:COMEBIN_RUNCOMEBIN (sample12) [ 89%] 25 of 28, cached: 25
[e9/988ce3] process > NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_KMER (sample11) [100%] 28 of 28, cached: 28 ✔
[ec/58095c] process > NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_TOOSHORT (sample06) [100%] 28 of 28, cached: 28 ✔
[39/f7343d] process > NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_METABINNER (sample11) [100%] 28 of 28, cached: 28 ✔
[29/c44550] process > NFCORE_MAG:MAG:BINNING:BINNING_METABINNER:METABINNER_BINS (sample11) [100%] 28 of 28, cached: 28 ✔
[52/db8649] process > NFCORE_MAG:MAG:BINNING:SPLIT_FASTA (METAMDBG-MetaBinner-sample11) [100%] 84 of 84, cached: 84 ✔
[6a/d56530] process > NFCORE_MAG:MAG:BINNING:GUNZIP_UNBINS (FLYE-MetaBinner-sample09.unbinned.1.fa.gz) [100%] 1 of 1, cached: 1 ✔
[11/2a77dd] process > NFCORE_MAG:MAG:BIN_QC:BUSCO_BUSCO (FLYE-MetaBinner-sample09) [100%] 1 of 1, cached: 1
[42/5e8482] process > NFCORE_MAG:MAG:GTDBTK:GTDBTK_DB_PREPARATION (gtdbtk_r226_data.tar.gz) [100%] 1 of 1, cached: 1 ✔
[7d/377d43] process > NFCORE_MAG:MAG:PROKKA (FLYE-MetaBinner-sample09.unbinned.1) [100%] 1 of 1, cached: 1
Plus 12 more processes waiting for tasks…
Command used and terminal output
Relevant files
No response
System information
No response