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s4hts / HTStream

A high throughput sequence read toolset using a streaming approach facilitated by Linux pipes
https://s4hts.github.io/HTStream/
Apache License 2.0
49 stars 9 forks source link

hts_Primers - error message #241

Closed adamerum closed 3 years ago

adamerum commented 3 years ago

Hello, I am trying (for the first time) to use hts_Primers to remove primers to which diversity spacers have been added to create sequence diversity for amplicon sequencing, using the following command: hts_Primers -1 X_R1.fastq.gz -2 X_R2.fastq.gz -P Fprimer.fasta -Q Rprimer.fasta

However, I receive the following error: image Do you have any idea what could be causing this? Thank you in advance.

msettles commented 3 years ago

Hmm, so you've likely found an edge case bug we haven't seen yet and need to address. Of the top of my head I'd say your primer is longer than the read? Anyway you could isolate that read and pass it on, OR if you could provide the whole dataset I can find it. Also with diversity spacers you want to use the -l option so if your primer is say ACTGATAT and you have 1-4 diversity basepair proceeding your primer then you'd use -l 4

samhunter commented 3 years ago

Hi @adamerum also could you let us know what version of HTStream you are using? If it isn't v1.3.3 please try updating. I don't remember the exact error, but we found a little bug in reading fasta files with spaces in the sequence name. That got fixed recently and the fix is present in the latest release (https://github.com/s4hts/HTStream/releases/tag/v1.3.3)

adamerum commented 3 years ago

Hi @msettles and @samhunter, thank you both for your fast and helpful feedback. I can confirm after modifying the command to include -l and updating to v1.3.3 hts_Primers is running smoothly, so I believe as you anticipated it was an issue with reading the fasta file. Thank you again for your help!

samhunter commented 3 years ago

Hi @adamerum it sounds like I should close this issue, thanks for the followup!