Samtool sort or indexing aborted due to an "unexpected error"

[FranBonath]

Description of the bug

pipeline stops with the somewhat undescript error "Execution aborted due to an unexpected error"
I couldn't figure out whether the issue lies within samtools sort or samtools index, but it seems a .bai file is created while .csi and .crai are missing. If this is by design or not, I am not sure.

Command used and terminal output

$nextflow run /vulpes/ngi/staging/220908.aadcfe0/sw/nanoseq/workflow/ -profile uppmax \ -c /vulpes/ngi/staging/220908.aadcfe0/conf//nextflow_miarka_sthlm.config \ -c /vulpes/ngi/staging/220908.aadcfe0/conf//nanoseq_sthlm.config --input samplesheet_v2.csv --protocol directRNA --kit SQK-LSK109 --skip_basecalling --skip_demultiplexing --outdir /proj/ngi2016003/nobackup/fran/analysis/nanopore/projects/P25605/results/nanoseq_RNA2/ -resume --skip_fusion_analysis --skip_differential_analysis

terminal output:
Monitor the execution with Nextflow Tower using this url https://ngi-tower.scilifelab.se/orgs/NGI/workspaces/NGI-Stockholm/watch/266swhDov0hekG
Monitor the execution with Nextflow Tower using this url https://ngi-tower.scilifelab.se/orgs/NGI/workspaces/NGI-Stockholm/watch/266swhDov0hekG
Monitor the execution with Nextflow Tower using this url https://ngi-tower.scilifelab.se/orgs/NGI/workspaces/NGI-Stockholm/watch/266swhDov0hekG
[43/057fed] process > NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_v2.csv)                                     [100%] 1 of 1, cached: 1 ✔
[dd/3921bb] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT (P25605_101_CII_R1)                                   [100%] 4 of 4, cached: 4 ✔
[cd/fb90cc] process > NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:FASTQC (P25605_102_CII_SF3B1_WT_OE_shSF3B1_1_R1)               [100%] 4 of 4, cached: 4 ✔
[96/ddf0e8] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GET_CHROM_SIZES (genome.fa)                                             [100%] 1 of 1, cached: 1 ✔
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:GTF2BED                                                                 -
[da/c72cdc] process > NFCORE_NANOSEQ:NANOSEQ:PREPARE_GENOME:SAMTOOLS_FAIDX (genome.fa)                                              [100%] 4 of 4, cached: 4 ✔
[37/819191] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_INDEX (genome.fa)                                              [100%] 1 of 1, cached: 1 ✔
[dc/daa322] process > NFCORE_NANOSEQ:NANOSEQ:ALIGN_MINIMAP2:MINIMAP2_ALIGN (P25605_101_CII_R1)                                      [100%] 4 of 4, cached: 4 ✔
[58/2766db] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_VIEW_BAM (P25605_104_HG3SF3B1_MUT_OEshSF3B1-1_R1)     [100%] 4 of 4, cached: 4 ✔
[5b/2ab78c] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_SORT (P25605_104_HG3SF3B1_MUT_OEshSF3B1-1_R1)         [100%] 4 of 4, cached: 4 ✔
[e5/d81f52] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:SAMTOOLS_INDEX (P25605_101_CII_R1)                             [100%] 4 of 4, cached: 4 ✔
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS                              [  0%] 0 of 4
[fa/959feb] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (P25605_104_HG3SF3B1_M... [ 25%] 1 of 4, cached: 1
[de/4c7ddf] process > NFCORE_NANOSEQ:NANOSEQ:BAM_SORT_INDEX_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (P25605_104_HG3SF3B1_M... [ 25%] 1 of 4, cached: 1
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:BEDTOOLS_GENOMECOV                                                [  0%] 0 of 4
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGWIG:UCSC_BEDGRAPHTOBIGWIG                                             -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:BEDTOOLS_BAMBED                                                   [  0%] 0 of 4
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BEDTOOLS_UCSC_BIGBED:UCSC_BED12TOBIGBED                                                -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:BAMBU                                                                                  [  0%] 0 of 1
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:RNA_MODIFICATION_XPORE_M6ANET:NANOPOLISH_INDEX_EVENTALIGN                              -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:RNA_MODIFICATION_XPORE_M6ANET:XPORE_DATAPREP                                           -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:RNA_MODIFICATION_XPORE_M6ANET:XPORE_DIFFMOD                                            -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:RNA_MODIFICATION_XPORE_M6ANET:M6ANET_DATAPREP                                          -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:RNA_MODIFICATION_XPORE_M6ANET:M6ANET_INFERENCE                                         -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:CUSTOM_DUMPSOFTWAREVERSIONS                                                            -
[-        ] process > NFCORE_NANOSEQ:NANOSEQ:MULTIQC                                                                                -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/nanoseq] Pipeline completed with errors-
Execution aborted due to an unexpected error

 -- Check script '/vulpes/ngi/production/v22.09/sw/nanoseq/workflow/./workflows/../subworkflows/local/../../modules/local/nanopolish_index_eventalign.nf' at line: 2 or see '.nextflow.log' file for more details

Relevant files

nextflow.log

System information

N E X T F L O W ~ version 21.10.6
Hardware - HPC (Uppmax)
Executor - Slurm
container - Docker/Singularity
nanoseq version: nf-core/nanoseq v3.0.0