Scaffold_curation:minimap2_align receives empty? or truncated file.

[mahesh-panchal]

samtools sort receives a truncated file in the pipe of the MINIMAP2_ALIGN process.

  [M::mm_idx_gen::51.363*1.39] collected minimizers
  [M::mm_idx_gen::57.010*1.83] sorted minimizers
  [WARNING] For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.
  [M::main::57.011*1.83] loaded/built the index for 81 target sequence(s)
  [M::mm_mapopt_update::57.919*1.82] mid_occ = 500
  [M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 81
  [M::mm_idx_stat::58.535*1.81] distinct minimizers: 98935066 (78.29% are singletons); average occurrences: 4.217; average spacing: 9.640; total length: 4022375851
  [E::sam_parse1] no SQ lines present in the header
  [W::sam_read1_sam] Parse error at line 3
  samtools sort: truncated file. Aborting
  [main_samview] fail to read the header from "-".

command

  minimap2 \
      --MD -x map-hifi \
      -t 6 \
      "Austropotamobius_torrentium_hifiasm-scaffolded-default_scaffolds_final.fa" \
      "m84045_240208_231139_s4.hifi_reads.fasta.gz" \
       \
       \
      -a | samtools sort | samtools view -@ 6 -b -h -o hifiasm-scaffolded-default_m84045_240208_231139_s4.hifi_reads.bam