Closed kazumaxneo closed 6 months ago
Hello Kazuma,
I'm very glad to see you like GenomeTailor. If I understand well this issue is in the wrong repository and concerns GenomeTailor alone ? (the GenomeTailor version packed with HairSplitter should not have these problems)
Thank you for bringing up the issue with raven, it was a compatibility issue with different versions of raven that should be corrected now.
The repository of GenomeTailor was a bit messy since I did not realize anyone actually used it except me, sorry for that. I cleaned it up, now it should work better. You were absolutely right about the test instance, I added it.
Keep in mind that GenomeTailor is in beta version , that the reassembly module does not work very well for now and that I am actively developing it. I hope to have a significantly improved version by the end of next week. Nevertheless, all you comments are welcome to help improve GenomeTailor :smiley:, if you desire a particular feature it is the best time to say so!
Hi RolandFaure
Thank you ! I had a little concerned and cloned GenomeTailor repo. independently. That would caused this problem. When I used GenomeTailor enclosed with HairSplitter as you commented, the problem did not happen (job finished successfully).
I noticed one another thing : "samtools consensus" commnad looks introduced from samtools v1.16. So I think it would be better to use samtools > v1.16 in the install section of README (currently 1.19 is the latest).
Take care.
Hello Kazuma, Glad to hear the problem is solved. You are absolutely right for the samtools version, thank you very much for bringing it up :smile: Do not hesitate if you have more questions, problems or suggestions
Hi.
This is a great implementation. When running Hairsplitter, however, it fails on the raven reassemblies after a while (attached picture).
$python hairsplitter.py -f SRR27955205.fastq -i metaflye_assembly.fasta -x ont -o outdir -t 20
I am not sure what the cause is, so I would appreciate it if you could include tiny dataset in the repository or write an example of some public data run if possible.
Kazuma Uesaka