Core dump with Python 3.9

[tnn111]

I did a fresh install of flye with micromamba. Python is 3.9.

I get a core dump on the minimap2 step. Any suggestions?

Thanks!

less /Spawn/Isolates/LT001001/results_flye_correct/10-consensus/minimap.stderr
[samfaipath] build FASTA index...
flye-samtools: bgzf.c:305: bgzf_open: Assertion compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE' failed. [M::mm_idx_gen::0.061*1.01] collected minimizers flye-samtools: bgzf.c:351: bgzf_hopen: Assertion compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE' failed.
[M::mm_idx_gen::0.0765.21] sorted minimizers
[M::main::0.0765.21] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.0844.82] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.0894.62] distinct minimizers: 634261 (89.75% are singletons); average occurrences: 1.133; average spacing: 5.364; total length: 3854817
/bin/bash: line 1: 512917 Broken pipe flye-minimap2 '/Spawn/Isolates/LT001001/results_flye_correct/00-assembly/draft_assembly.fasta' '/Spawn/Isolates/LT001001/LT001001_correct_nano.fasta.gz' -x map-ont -t 32 -a -p 0.5 -N 10 --sam-hit-only -L -K 1G -z 1000 -Q --secondary-seq -I 64G
512918 Aborted (core dumped) | flye-samtools view -T '/Spawn/Isolates/LT001001/results_flye_correct/00-assembly/draft_assembly.fasta' -u -
512919 Aborted (core dumped) | flye-samtools sort -T '/Spawn/Isolates/LT001001/results_flye_correct/10-consensus/sort_240826_133759' -O bam -@ 4 -l 1 -m 1G -o '/Spawn/Isolates/LT001001/results_flye_correct/10-consensus/minimap.bam'

[mikolmogorov]

@tnn111 sorry for the late response! Looks like an internal error in minimap2. It is possible that something is inconsistent in your conda environment, likely to do with different versions of libz. I would try reinstalling into a fresh environment. If that does not solve the issue, I would try building from source or using the docker container. If that works - it is likely conda that causing the problem.