Unable to create a properly formatted BAM file

[grbot]

I've been struggling with winnowmap and suspect that my input files might be incorrectly formatted, although they appear to be fine on inspection. Despite this, I'm unable to generate a properly formatted BAM file.

If anyone has encountered a similar issue or has any insights into what might be going wrong, I’d greatly appreciate your guidance.

+winnowmap -W repetitive_k15.txt -a -x map-pb --eqx --cs -Y -L -y -t16 asm.sorted.fa /cromwell-executions/HMMFlaggerEndToEndWithMapping/4b630494-74b4-4a92-bc9e-14e4c57383c5/call-alignmentTask/longReadAlignmentScattered/deee1c4e-7927-4261-8792-19a28fe85eb1/call-alignment/shard-0/inputs/807686892/AXH0D.fq.gz
+ samtools view -h -b
[M::mm_idx_gen::0.044*0.91] reading downweighted kmers
[M::mm_idx_gen::0.090*0.86] collected downweighted kmers, no. of kmers read=67424
[M::mm_idx_gen::0.090*0.86] saved the kmers in a bloom filter: hash functions=2 and size=969400 
[M::mm_idx_gen::171.855*1.16] collected minimizers
[M::mm_idx_gen::172.696*1.23] sorted minimizers
[WARNING] For a multi-part index, no @SQ lines will be outputted. Please use --split-prefix.
[M::main::172.696*1.23] loaded/built the index for 1363 target sequence(s)
[M::main::172.696*1.23] running winnowmap in SV-aware mode
[M::main::172.696*1.23] stage1-specific parameters minP:1000, incP:1.99, maxP:8000, sample:1000, min-qlen:10000, min-qcov:0.5, min-mapq:5, mid-occ:5000
[M::main::172.696*1.23] stage2-specific parameters s2_bw:1000, s2_zdropinv:25
[M::mm_idx_stat] kmer size: 15; skip: 50; is_hpc: 0; #seq: 1363
[M::mm_idx_stat::172.894*1.23] distinct minimizers: 23608244 (28.59% are singletons); average occurrences: 6.838; average spacing: 25.024
[E::sam_parse1] no SQ lines present in the header
[W::sam_read1_sam] Parse error at line 2
samtools view: error reading file "-"
ln: failed to access '/cromwell-executions/HMMFlaggerEndToEndWithMapping/4b630494-74b4-4a92-bc9e-14e4c57383c5/call-alignmentTask/longReadAlignmentScattered/deee1c4e-7927-4261-8792-19a28fe85eb1/call-alignment/shard-0/execution/*.sorted.bam': No such file or directory

[mobinasri]

@grbot Is your asm.sorted.fa a diploid assembly? if yes I recommend using -I8gfor winnowmap.