How to fix minimap2 -> samtools sort error (samtools sort: truncated file. Aborting)?

Question

[O.rka]

I'm trying to run the following pipeline: [minimap2] -> [samtools sort] && [samtools index]

In particular, here's the command I'm running:

( minimap2 -a -x map-ont -t 4 Genomes/E_crus-galli_v2.0/EC.fasta reads.nanofilt.fastq | samtools sort -T tmp -o sorted.bam && samtools index sorted.bam )

Here's the error I'm getting:

[M::mm_idx_gen::26.816*1.85] collected minimizers
[M::mm_idx_gen::32.482*2.22] sorted minimizers
[M::main::32.482*2.22] loaded/built the index for 2289 target sequence(s)
[M::mm_mapopt_update::33.938*2.17] mid_occ = 725
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 2289
[M::mm_idx_stat::34.924*2.14] distinct minimizers: 67972833 (48.03% are singletons); average occurrences: 3.694; average spacing: 5.339
[M::worker_pipeline::405.636*3.79] mapped 698957 sequences
[M::worker_pipeline::776.285*3.91] mapped 696720 sequences
[W::sam_read1] Parse error at line 3989404
samtools sort: truncated file. Aborting

Here is the exit code: 1

Here's my versions:

(f5c_env) -bash-4.1$ minimap2 --version
2.17-r941

(f5c_env) -bash-4.1$ samtools --version
samtools 1.10
Using htslib 1.10.2
Copyright (C) 2019 Genome Research Ltd.

[GenoMax]

This may apply : Modify query names longer than 252

Wonder if ONT has started outputting read names > 252 characters of late.

[John Marshall]

The htslib/samtools “QNAMEs limited to 252 characters instead of 254” bug was fixed in 1.10.

The absence of an additional [E::sam_parse1] query name too long error message is also indicative that this is not the problem.