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shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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Long reads support #113

Open owenkuo-TW opened 2 weeks ago

owenkuo-TW commented 2 weeks ago

Hi,

Already complete the test. But failed with path to pacbio hifi.fastq.gz and also a tsv noted sample/file path. Would encounter error like below "Error in rule pool_paired_unmapped_R2: jobid: 9". Please kindly provide option to proceed. Thanks!

beardymcjohnface commented 2 weeks ago

Hi, sorry it might not be that obvious. Run Hecatomb like so: hecatomb run --trim filtlong ... I would probably also use --assembly cross if you dont have too many samples, but for hifi reads you might want to try an assembler and parameters better tuned for hifi reads.

owenkuo-TW commented 2 weeks ago

Thanks for the reply. Can I apply contigs to conduct partial hecatmob pipeline?

beardymcjohnface commented 2 weeks ago

Sure! If you just want the read-annotations without the assembly, just add 'read_annotations' to specify the target output files: hecatomb run read_annotations ...

owenkuo-TW commented 1 week ago

Thanks for the reply! Just complete the read_annotations option, but can I apply assembled contigs into hecatomb process?

beardymcjohnface commented 1 week ago

Not easily. It would probably be easier to manually run mmseqs searches of the contigs against the secondary databases.