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Winnowmap doesn't throw a [Warning] or [Error] when -W is empty #50

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Isoris opened this issue Jan 31, 2025 · 0 comments
Open

Winnowmap doesn't throw a [Warning] or [Error] when -W is empty #50

Isoris opened this issue Jan 31, 2025 · 0 comments

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@Isoris
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Isoris commented Jan 31, 2025

Hello,

in Winnowmap
--version v.2.03 winnowmap does not throw any error or warning when [[-z ${-W repetitive_k15.txt} ]] is empty (0 bytes.).

`meryl print greater-than 0.998 merylDB > Hybrid_catfish_polished_12.fa_repetitive_k15.txt

Found 1 command tree.

PROCESSING TREE #1 using 128 threads.
opGreaterThan
merylDB
print to 0.998

Cleaning up.

Bye.
winnowmap -ax map-pb --MD -W Hybrid_catfish_polished_12.fa_repetitive_k15.txt -t 100 --secondary=no Hybrid_catfish_polished_12.fa ../../../00-reads/hifi/CG_F_HIFI_None_reads.fastq | samtools view -bhS -@ 100 -F4 | samtools sort -@ 100 - > winnow
map.hifi.sorted.bam
[M::mm_idx_gen::0.0013.94] reading downweighted kmers
[M::mm_idx_gen::0.002
3.56] collected downweighted kmers, no. of kmers read=0
[M::mm_idx_gen::0.0023.53] saved the kmers in a bloom filter: hash functions=2 and size=14384
[M::mm_idx_gen::61.592
1.13] collected minimizers
[M::mm_idx_gen::62.1871.29] sorted minimizers
[M::main::62.187
1.29] loaded/built the index for 55 target sequence(s)
[M::main::62.1871.29] running winnowmap in SV-aware mode
[M::main::62.187
1.29] 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::62.1871.29] stage2-specific parameters s2_bw:1000, s2_zdropinv:25
[M::mm_idx_stat] kmer size: 15; skip: 50; is_hpc: 0; #seq: 55
[M::mm_idx_stat::62.479
1.29] distinct minimizers: 19446918 (47.79% are singletons); average occurrences: 3.702; average spacing: 25.387
`

I am not sure if its normal or not. for instance if the file exists but is empty the programs still runs as usual.
Basically to replicate , the user makes a typo in the meryl print command, a file is generated for repetitive k15 but is empty. then Winnowmap runs perfectly fine.

With regards, Quentin.

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