minimap2: Stdin is empty

[vpeddu]

Hi,

I'm running nf-LO between hg38 and pantro6 using the minimap2 preset. The docker container used was built as suggested in the docs. I'm running this on a SLURM cluster launched via a login node. It looks like minimap2 fails but the .exitcode is still 0 so the downstream processes fail. I can confirm that the same files and settings work with lastz but not minimap2.

I've also noticed that only one minimap2 process spawns whereas a few hundred lastz processes typically spawn. It seems that splitsrc and splittgt each return a large single multifasta.

run script:

nextflow run evotools/nf-LO \
	-latest \
	-c phoenix.config \
	--outdir pantro6_to_hg38_nflo \
	--distance near \
	--aligner minimap2 \
	--max_cpus 32 \
	--max_memory 128.GB \
	-w work3 \
	--source panTro6_cleaned.fa \
	--target hg38_cleaned.fa \
	-with-tower \
	-profile docker -with-docker vpeddu/nflo:latest

process .command.error:

Got 30 lifts in source.lift
Lifting stdin
Got 328 lifts in target.lift
Lifting stdin
[M::mm_idx_gen::42.331*1.45] collected minimizers
[M::mm_idx_gen::68.360*2.79] sorted minimizers
[M::main::68.360*2.79] loaded/built the index for 30 target sequence(s)
[M::mm_mapopt_update::174.858*1.28] mid_occ = 121
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 30
[M::mm_idx_stat::259.800*0.94] distinct minimizers: 213075345 (92.73% are singletons); average occurrences: 1.328; average spacing: 10.079; total length: 2851453592
stdin is empty