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Xinglab / TideHunter

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
https://github.com/yangao07/TideHunter
MIT License
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Numbers of reads in fasta/fastq file #11

Open DamarisLa opened 2 years ago

DamarisLa commented 2 years ago

Hi Yan, I ran the test scenario and I ran your test script and I ran the tool on a fasta that contains only one fasta-record with an assembled chr22. Both lead to outputs. (is am interested in results in tabular format). I was glad that the tests ran.

However when I run it with da fasta-file that contains reads from the whole genome (6mio reads/records) its doesn't even start to analyze, I always immediately stops. My system calls it "illegal instructions" (even though it's the same instructions used in the successful test case.

I there a limitation to the size of a fasta-file or the number of reads by your tools?

Best regards Damaris

yangao07 commented 2 years ago

TideHunter was designed to detect tandem repeats from sequencing long reads, instead of assemblies. For your case, the total length of chr22 is too long for TideHunter to deal with.

Yan

DamarisLa commented 2 years ago

Hi, Thank you so much for your response. Yeah, I was aware of that. Sorry, I described my issue wrongly. The chr22 did actually work, but a full genome with sequencing long reads did not work. Your test case has one record. When I failed with the normal genome sequencing long reads (6mio reads), I wondered if I can only assign a fasta file with a smaller amount of sequencing long reads?

I basically want to know if there is a limitation of how many sequencing long reads can be in the fasta file?

Sorry for putting it wrongly.

Best regards.

PS: I will not analyse the output of my Chr22 run. I am aware that TideHunter is not designed for that. It was only to test my system and the installation, as I struggled with the sequence long read file..

yangao07 commented 2 years ago

The number of input sequences should have no limitation. Which version of TideHunter are you using? Did you use the latest v1.5.1? A bug in v1.5.0 was fixed recently.

Yan

DamarisLa commented 2 years ago

Thank you. A then I can rule out that. I have version 1.5.1. But I'll continue to debug, maybe it's after all sth internal. Thanks so much for your quick response. Damaris