Local test failure

[tkchafin]

Description of the bug

SAMTOOLS_SORT is failing in local tests (-profile test, docker), but working on farm (-profile test,sanger,singularity):

ERROR ~ Error executing process > 'SANGERTOL_VARIANTCALLING:VARIANTCALLING:INPUT_MERGE:SAMTOOLS_SORT (icCanRufa1_cram_T1)'

Caused by:
  Process `SANGERTOL_VARIANTCALLING:VARIANTCALLING:INPUT_MERGE:SAMTOOLS_SORT (icCanRufa1_cram_T1)` terminated with an error exit status (1)


Command executed:

  samtools cat \
      GCA_947369205.1.unmasked.pacbio.icCanRufa1_0_3.cram \
  | \
  samtools sort \
       \
      -T icCanRufa1_cram_T1 \
      --threads 2 \
      --reference GCA_947369205.1_OX376310.1_CANBKR010000003.1.fasta.gz \
      -o icCanRufa1_cram_T1.bam \
      -
  
  cat <<-END_VERSIONS > versions.yml
  "SANGERTOL_VARIANTCALLING:VARIANTCALLING:INPUT_MERGE:SAMTOOLS_SORT":
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  [main_cat] ERROR: input is not BAM or CRAM
  [W::hts_set_opt] Cannot change block size for this format
  samtools sort: failed to read header from "-"

Command used and terminal output

No response

Relevant files

No response

System information

No response

[tkchafin]

Not high priority. It is some sort of arm incompatibility -- works fine if I run a terminal with rosetta emulation