could not open image Script8C84027CBF0BFB90846176A9D9C58EDE@30624c7

[hrydbeck]

Description of the bug

WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /cfs/klemming/home/h/halfdan/nfc_rd/test_full/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location WARN: Input tuple does not match input set cardinality declared by process NFCORE_RAREDISEASE:RAREDISEASE:SMNCOPYNUMBERCALLER -- offending value: [father:, mother:, probands:[hugelymodelbat], upd_children:[], id:justhusky] WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:PREPARE_REFERENCES:TABIX_PBT (nf-core)'

Caused by: Process NFCORE_RAREDISEASE:RAREDISEASE:PREPARE_REFERENCES:TABIX_PBT (nf-core) terminated with an error exit status (255)

Command executed:

bgzip --threads 1 -c target.bed > nf-core.bed.gz tabix nf-core.bed.gz

cat <<-END_VERSIONS > versions.yml "NFCORE_RAREDISEASE:RAREDISEASE:PREPARE_REFERENCES:TABIX_PBT": tabix: $(echo $(tabix -h 2>&1) | sed 's/^.Version: //; s/ .$//') END_VERSIONS

Command exit status: 255

Command output: (empty)

Command error: FATAL: While checking image: could not open image Script8C84027CBF0BFB90846176A9D9C58EDE@30624c7: failed to retrieve path for Script8C84027CBF0BFB90846176A9D9C58EDE@30624c7: lstat Script8C84027CBF0BFB90846176A9D9C58EDE@30624c7: no such file or directory

Command used and terminal output

nextflow run nf-core/raredisease \
    -revision 2.0.1 -profile test_full,singularity,pdc_kth  \
    --skip_germlinecnvcaller \
    --variant_consequences_snv https://github.com/nf-core/test-datasets/blob/raredisease/reference/variant_consequences_v2.txt \
    --vep_filters https://github.com/nf-core/test-datasets/blob/raredisease/reference/hgnc.txt \
    --mobile_element_svdb_annotations /cfs/klemming/home/h/halfdan/nfc_rd/references/svdb_querydb_files.csv \
    --vep_plugin_files /cfs/klemming/home/h/halfdan/nfc_rd/references/vep_plugin_files.csv \
    --outdir out_test_full \
    --project naiss2024-22-481

Relevant files

.nextflow.log

System information

N E X T F L O W ~ version 23.10.1 HPC Dardel PDC slurm Singularity SUSE Linux Enterprise Server 15 SP3 revision 2.0.1