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lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
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wrong FASTA/FASTQ record. Continue anyway. #609

Open rebeelouise opened 4 years ago

rebeelouise commented 4 years ago

So for some reason, 2 out of many many many fastq are coming up with this error. I am not very bioinformatics savy. So may need some help solving this error.

This error means I cannot sort my file with samtools and do further downstream analysis!

Any help appreciated

Thanks

minimap2 -ax map-ont ../../../../references/ref.fasta ../fastq/barcode01.fastq > alignment.sam [M::mm_idx_gen::0.002*49.06] collected minimizers [M::mm_idx_gen::0.003*26.32] sorted minimizers [M::main::0.003*26.07] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.004*24.08] mid_occ = 3 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.004*22.84] distinct minimizers: 5587 (99.93% are singletons); average occurrences: 1.004; average spacing: 5.332 [WARNING] wrong FASTA/FASTQ record. Continue anyway. [WARNING] wrong FASTA/FASTQ record. Continue anyway. [M::worker_pipeline::4.410*2.19] mapped 587661 sequences [M::worker_pipeline::4.411*2.19] mapped 247 sequences [M::worker_pipeline::6.806*2.18] mapped 340000 sequences [M::main] Version: 2.17-r941 [M::main] CMD: minimap2 -ax map-ont ../../../../references/ref.fasta ../fastq/barcode01.fastq [M::main] Real time: 6.808 sec; CPU: 14.849 sec; Peak RSS: 0.641 GB

lunky-zao commented 1 year ago

I have the same problem with you. Have you solved it?