Segmentation fault

[diego-rt]

Hello,

I've been trying to get winnowmap to align some HiFi reads to the axolotl genome (which is rather giant at 29G) but I keep getting some segmentation fault. Any help would be greatly appreciated!

The command is:

winnowmap -ay -t 16 -L genome_index.mmi Revio_FC011.part_005.fq.gz | samtools view -F 4 -bSu -o Revio_FC011.bam

The output:

[...]
@SQ SN:ptg000910l   LN:23331
@SQ SN:ptg000911l   LN:21101
@PG ID:Winnowmap    PN:Winnowmap    VN:2.03 CL:winnowmap -ay -t 16 -L genome_index.mmi Revio_FC011.part_005.fq.gz
[M::main::36.787*0.90] loaded/built the index for 911 target sequence(s)
[M::main::36.787*0.90] running winnowmap in SV-aware mode
[M::main::36.787*0.90] stage1-specific parameters minP:2000, incP:2.83, maxP:16000, sample:2000, min-qlen:10000, min-qcov:0.5, min-mapq:5, mid-occ:5000
[M::main::36.787*0.90] stage2-specific parameters s2_bw:2000, s2_zdropinv:25
[M::mm_idx_stat] kmer size: 15; skip: 50; is_hpc: 0; #seq: 911
[M::mm_idx_stat::38.317*0.90] distinct minimizers: 54141373 (21.73% are singletons); average occurrences: 21.624; average spacing: 25.188
Segmentation fault

This is the index generation command and output:

meryl count k=15 output merylDB Amex8.0.asm.bp.p_ctg.gfa.fa
meryl print greater-than distinct=0.9998 merylDB > repetitive_k15.txt

winnowmap -W repetitive_k15.txt -x map-pb -t 3 -I 100G -d genome_index.mmi Amex8.0.asm.bp.p_ctg.gfa.fa

[M::mm_idx_gen::0.028*0.56] reading downweighted kmers
[M::mm_idx_gen::0.056*0.72] collected downweighted kmers, no. of kmers read=105766
[M::mm_idx_gen::0.056*0.72] saved the kmers in a bloom filter: hash functions=2 and size=1520672 
[M::mm_idx_gen::1127.643*1.20] collected minimizers
[M::mm_idx_gen::1169.157*1.26] sorted minimizers
[M::main::1187.256*1.25] loaded/built the index for 911 target sequence(s)
[M::main::1187.256*1.25] running winnowmap in SV-aware mode
[M::main::1187.256*1.25] 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::1187.256*1.25] stage2-specific parameters s2_bw:1000, s2_zdropinv:25
[M::mm_idx_stat] kmer size: 15; skip: 50; is_hpc: 0; #seq: 911
[M::mm_idx_stat::1188.086*1.25] distinct minimizers: 54141373 (21.73% are singletons); average occurrences: 21.624; average spacing: 25.188
[M::main] Version: 2.03, pthreads=3, omp_threads=3
[M::main] CMD: winnowmap -W repetitive_k15.txt -x map-pb -t 3 -I 100G -d genome_index.mmi Amex8.0.asm.bp.p_ctg.gfa.fa
[M::main] Real time: 1189.460 sec; CPU: 1490.543 sec; Peak RSS: 35.782 GB