ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS'

[BaderddineSaleh]

hello everyone,

i have the following ERROR in this command:

nextflow run nf-core/sarek -r 3.5.0 \
   -profile docker \
   --genome GATK.GRCh38 \
   --input samplesheet.csv \
   --outdir results

i encounter the following ERROR:

[bf/877d1b] NFCORE_SAREK:SAREK:FASTQC (ERR4383817-17)                                          [100%] 2 of 2 ✔
[5c/8e2b4a] NFCORE_SAREK:SAREK:FASTP (ERR4383812-12)                                           [100%] 2 of 2 ✔
[26/71bdd3] NFC…_SAREK:SAREK:FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM (ERR4383817) [100%] 24 of 24 ✔
[7a/bc7d40] NFCORE_SAREK:SAREK:BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES (ERR4383817)            [100%] 2 of 2 ✔
[6d/0e4271] NFC…SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS (ERR4383817) [100%] 2 of 2 ✔
[3b/d8e25d] NFC…SAREK:SAREK:BAM_MARKDUPLICATES:CRAM_QC_MOSDEPTH_SAMTOOLS:MOSDEPTH (ERR4383817) [ 50%] 1 of 2
[bd/e92c04] NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_BASERECALIBRATOR (ERR4383817)        [ 78%] 33 of 42
[e5/007fd9] NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383812)       [100%] 1 of 1, failed: 1
Plus 20 more processes waiting for tasks…
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/sarek] Pipeline completed with errors-
WARN: Killing running tasks (10)
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383812)'

ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_BASERECALIBRATOR:GATK4_GATHERBQSRREPORTS (ERR4383812)'

[FriederikeHanssen]

To help you we require more information why this task failed. Please attach the .nextflow.log

[BaderddineSaleh]

this is the .nextflow.log file for this run

nextflow.log

this is the content of my config file:

process {
    executor = 'local'
    cpus = 32
    memory = '100 GB'
}
aws {
    client {
        anonymous = true
    }


}
withName:'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR|GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS'{
        cpus   = { 20    * task.attempt }
        memory = { 40.GB * task.attempt }
    }

also my samplesheet.csv if needed

patient,sample,lane,fastq_1,fastq_2
ERR4383812,ERR4383812_L001,L001,data/ERR4383812_L001_R1.fastq.gz,data/ERR4383812_L001_R2.fastq.gz
ERR4383817,ERR4383817_L001,L001,data/ERR4383817_L001_R1.fastq.gz,data/ERR4383817_L001_R2.fastq.gz