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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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classify: Paired filename format missing # character #607

Open LiZhihua1982 opened 2 years ago

LiZhihua1982 commented 2 years ago

Hi Everyone， Because there are so many unclassified (>80%) reads, so I want to extract the unclassified reads using the code as below, it report error: classify: Paired filename format missing # character, How to slove? Thanks! (bracken) lizhihua@lizhihua-T640:/media/lizhihua/software/unclasssified_analysis$ kraken2 --db /media/lizhihua/software/Kraken2_Bracken/k2_pluspf_20210517 --threads 40 --paired fastp_out/HY35_1.fq.gz fastp_out/HY35_2.fq.gz --report Kraken2_out/HY35.report --unclassified-out HY35.unclassified.fq --output Kraken2_out/HY35.output Loading database information... done. Processed 10000 sequences (2970860 bp) ...classify: Paired filename format missing # character: HY35.unclassified.fq

LiZhihua1982 commented 2 years ago

I can solve this problem using HY35#.unclassified.fq instead of HY35.unclassified.fq

ichauchcc commented 5 months ago

This might sounds really ridiculous, but my error message is : kraken2: --paired requires positive and even number filenames And adding a "#" also solves it

Yaeeren commented 3 weeks ago

@ichauchcc Hi, there, I've met the same clue ’kraken2: --paired requires positive and even number filenames’ when Kraken2：-- paired is used, but I could't solve the error as you did before, have you got any newest idea about the problem? thank u a lot!!!