Error in `fasterq_dump`

[sarahMIRI]

The following error occurs in rule fasterq_dump

The control file data associated with this error is: SRR13055334,Treg_S2R2,SE,total
Another dataset with an error similar to this one is: SRR13055335,Treg_S2R3,SE,total

Using restart-times: 3 in ~/.config/snakemake/slurm/config.yml profile fixed the issue. It successfully dumped the SRA data on the subsequent execution

Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 40
Rules claiming more threads will be scaled down.
Select jobs to execute...

[Fri Apr 14 13:40:32 2023]
checkpoint fasterq_dump:
    input: results/temp/prefetch/Treg/Treg_S2R3/Treg_S2R3.sra
    output: results/data/Treg/raw/Treg_S2R3_S.fastq.gz
    jobid: 0
    benchmark: benchmarks/Treg/fasterq_dump/Treg_S2R3_S.benchmark
    wildcards: tissue_name=Treg, tag=S2R3, PE_SE=S
    threads: 40
    resources: mem_mb=25600, disk_mb=256000, tmpdir=/tmp, time_min=45
Downstream jobs will be updated after completion.


            command='fasterq-dump --force --progress --threads 40 --temp /scratch --outdir /scratch'
            
            # Set the split/concatenate based on paired end or single end data
            if [[ "False" == "True" ]]; then
                command+=' --split-files'
            else
                command+=' --concatenate-reads'
            fi
            
            # Add the SRA file path to the command
            command+=' results/temp/prefetch/Treg/Treg_S2R3/Treg_S2R3.sra'
            
            echo $command
            eval $command
        
            # gzip the output
            pigz --synchronous --processes 40 /scratch/Treg_S2R3.fastq
        
            mv /scratch/Treg_S2R3.fastq.gz results/data/Treg/raw/Treg_S2R3_S.fastq.gz
            
Activating conda environment: /lustre/work/helikarlab/saghamiri2/FastqToGeneCounts/.snakemake/conda/ae87d42240ae7094f66a487b198441d3
2023-04-14T18:40:33 fasterq-dump.2.11.0 err: extract_acc2( 'results/temp/prefetch/Treg/Treg_S2R3/Treg_S2R3.sra' ).VFSManagerExtractAccessionOrOID() -> RC(rcVFS,rcPath,rcConstructing,rcParam,rcIncorrect)
lookup :|  0.00%2023-04-14T18:40:35 fasterq-dump.2.11.0 warn: database incorrect while opening manager within database module - can't open NC_012920.1 as a RefSeq or as a WGS
2023-04-14T18:40:35 fasterq-dump.2.11.0 err: cmn_iter.c cmn_read_String( #11294389 ).VCursorCellDataDirect() -> RC(rcDB,rcMgr,rcOpening,rcDatabase,rcIncorrect) 
2023-04-14T18:40:35 fasterq-dump.2.11.0 err: sorter.c get_from_raw_read_iter( 11294389 ) -> RC(rcDB,rcMgr,rcOpening,rcDatabase,rcIncorrect)
2023-04-14T18:40:35 fasterq-dump.2.11.0 warn: database incorrect while opening manager within database module - can't open NC_012920.1 as a RefSeq or as a WGS
2023-04-14T18:40:35 fasterq-dump.2.11.0 err: cmn_iter.c cmn_read_String( #11608122 ).VCursorCellDataDirect() -> RC(rcDB,rcMgr,rcOpening,rcDatabase,rcIncorrect) 
2023-04-14T18:40:35 fasterq-dump.2.11.0 warn: database incorrect while opening manager within database module - can't open NC_012920.1 as a RefSeq or as a WGS
2023-04-14T18:40:35 fasterq-dump.2.11.0 err: cmn_iter.c cmn_read_String( #12235588 ).VCursorCellDataDirect() -> RC(rcDB,rcMgr,rcOpening,rcDatabase,rcIncorrect) 
2023-04-14T18:40:36 fasterq-dump.2.11.0 warn: database incorrect while opening manager within database module - can't open CM000685.1 as a RefSeq or as a WGS
2023-04-14T18:40:36 fasterq-dump.2.11.0 err: cmn_iter.c cmn_read_String( #10980656 ).VCursorCellDataDirect() -> RC(rcDB,rcMgr,rcOpening,rcDatabase,rcIncorrect) 
2023-04-14T18:40:37 fasterq-dump.2.11.0 err: sorter.c run_producer_pool().join_and_release_threads -> RC(rcExe,rcProcess,rcExecuting,rcProcess,rcCanceled)

2023-04-14T18:40:37 fasterq-dump.2.11.0 err: sorter.c execute_lookup_production() -> RC(rcExe,rcProcess,rcExecuting,rcProcess,rcCanceled)
merge  : 
2023-04-14T18:40:37 fasterq-dump.2.11.0 err: fasterq-dump.c produce_lookup_files() -> RC(rcExe,rcProcess,rcExecuting,rcProcess,rcCanceled)
fasterq-dump quit with error code 3
[Fri Apr 14 13:40:37 2023]
Error in rule fasterq_dump:
    jobid: 0
    output: results/data/Treg/raw/Treg_S2R3_S.fastq.gz
    conda-env: /lustre/work/helikarlab/saghamiri2/FastqToGeneCounts/.snakemake/conda/ae87d42240ae7094f66a487b198441d3
    shell:
        
            command='fasterq-dump --force --progress --threads 40 --temp /scratch --outdir /scratch'
            
            # Set the split/concatenate based on paired end or single end data
            if [[ "False" == "True" ]]; then
                command+=' --split-files'
            else
                command+=' --concatenate-reads'
            fi
            
            # Add the SRA file path to the command
            command+=' results/temp/prefetch/Treg/Treg_S2R3/Treg_S2R3.sra'
            
            echo $command
            eval $command
        
            # gzip the output
            pigz --synchronous --processes 40 /scratch/Treg_S2R3.fastq
        
            mv /scratch/Treg_S2R3.fastq.gz results/data/Treg/raw/Treg_S2R3_S.fastq.gz
            
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

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