Join mismatch

[zbaida-achraf]

Hello,
I am encountering an error when running the nf-core/sarek pipeline version 3.5.0 with Nextflow. Below is the command I used and the corresponding error message.

nextflow run nf-core/sarek -r 3.5.0 \
  -profile docker \
  --fasta /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta \
  --bwa /home/ec2-user/SageMaker/Nextflow/references/BWAIndex \
  --igenomes_ignore true \
  --input /home/ec2-user/SageMaker/Nextflow/samplesheet.csv \
  --outdir /home/ec2-user/SageMaker/Nextflow/results \
  --step mapping variant_calling annotate \
  --aligner bwa-mem \
  --tools haplotypecaller,snpeff \
  --dbsnp /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz \
  --dbsnp_tbi /home/ec2-user/SageMaker/Nextflow/reference_aws/references/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi \
  --snpeff_db GRCh38.105 \
  --snpeff_cache /home/ec2-user/anaconda3/envs/JupyterSystemEnv/share/snpeff-5.2-1/data \
  -c nextflow.config \
  -resume

Error

ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details
Join mismatch for the following entries: key=[patient:ERR4383812, sample:ERR4383812, sex:NA, status:0, n_fastq:12, data_type:cram, id:ERR4383812] values=

[FriederikeHanssen]

Hi! This error is 9/10 a red herring. Could you share the .nextflow.log of that run?

[zbaida-achraf]

Hi! Thanks for the response. Sure, I’ll share the .nextflow.log from that run.

log.txt

[FriederikeHanssen]

I think this is the more relevant error: org.broadinstitute.hellbender.exceptions.GATKException: there is no usable data in any input file. You could start inspecting the files that are staged into that process