# Input

nextflow run nf-core/rnavar -r 1.1.0 -resume \
    --input samplesheet.csv \
    --outdir RNAvar01/ \
    --fasta $SCRATCH/04.Ref/genome.fa.gz \
    --gtf $SCRATCH/04.Ref/genome.gtf \
    --bam_csi_index \
    -profile cropdiversityhpc \
    --skip_baserecalibration \
    --multiqc_title RNAvar01 \

# Output

ERROR ~ Error executing process > 'NFCORE_RNAVAR:RNAVAR:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (T06_2A)'

Caused by:
  Process `NFCORE_RNAVAR:RNAVAR:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX (T06_2A)` terminated with an error exit status (1)


Command executed:

  samtools \
      index \
      -@ 1 \
       \
      T06_2A.bam
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAVAR:RNAVAR:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  [E::hts_idx_check_range] Region 536967197..536967331 cannot be stored in a bai index. Try using a csi index
  [E::sam_index] Read 'LH00235:454:22TTTTLT4:1:2467:1307:1869' with ref_name='Chr1T', ref_length=575865044, flags=163, pos=536967198 cannot be indexed
  samtools index: failed to create index for "T06_2A.bam": Numerical result out of range