Return no data during current difference

[SorenHeidelbach]

Hi, when trying to calculate current difference i keep get "No data for chunk #xx" for all chunks in stdout. I have checked the coverage of my contigs and they are all suitably high (>10 WGA and >100 NAT).

[1] "2021-12-16 07:52:37 CET" [1] " Prepare index for zymo_wga." [1] " Extract read mapped on chunks for zymo_wga." [1] " Link fast5 to fasta for zymo_wga." [1] " Prepare index for zymo_nat." [1] " Extract read mapped on chunks for zymo_nat." [1] " Link fast5 to fasta for zymo_nat." [1] "2021-12-16 07:53:17 CET" [1] "Processing chunk #115" [1] " Preparing zymo_wga input data for chunk #115" [1] " Preparing zymo_nat input data for chunk #115" [1] " Correcting mapping." [1] " No data for chunk #115" [1] " Remove temporary files." [1] "Processing chunk #116" [1] " Preparing zymo_wga input data for chunk #116" [1] " Preparing zymo_nat input data for chunk #116" [1] " Correcting mapping." [1] " No data for chunk #116" [1] " Remove temporary files." [1] "2021-12-16 07:54:42

The fast5 is in multiread format and was basecalled using guppy v. 5.0.7 and assembled using flye v. 2.9

[touala]

Hi @SorenHeidelbach,

It's possible that you're facing the same issue than in #26 where the .fast5 compression methods (vbz) is not compatible with nanopolish instalation I set up in the current nanodisco version (v1.0.3). Please let me know if this is it.

Thank you,

Alan

[SorenHeidelbach]

It is very likely, the fast5 is vbz compressed. I will return once i have tried running it on gzip compressed fast5, using the compression conversion you mentioned in the other issue

Thanks

[SorenHeidelbach]

Change compression format solved the issue.

Thanks