Error with Nanopolish

[oliveira-lab]

Hi Alan,

I installed nanodisco on the cluster and is working fine on your test dataset. However, upon running it in one of my datasets, I am getting all eventalign files empty (as below):

Warning messages: 1: In fread(path_fwd, header = T, sep = "\t", stringsAsFactors = TRUE, : File '/home/nanodisco/analysis/difference_subset/tmp.281.DDG_AAAA_ONT_1_FAR92030_A_WGA.fwd.eventalign' has size 0. Returning a NULL data.table. 2: In fread(path_rev, header = T, sep = "\t", stringsAsFactors = TRUE, : File '/home/nanodisco/analysis/difference_subset/tmp.281.DDG_AAAA_ONT_1_FAR92030_A_WGA.rev.eventalign' has size 0. Returning a NULL data.table. 3: In fread(path_fwd, header = T, sep = "\t", stringsAsFactors = TRUE, : File '/home/nanodisco/analysis/difference_subset/tmp.281.DDG_AAAA_ONT_1_FAR54859_A_NAT.fwd.eventalign' has size 0. Returning a NULL data.table. 4: In fread(path_rev, header = T, sep = "\t", stringsAsFactors = TRUE, : File '/home/nanodisco/analysis/difference_subset/tmp.281.DDG_AAAA_ONT_1_FAR54859_A_NAT.rev.eventalign' has size 0. Returning a NULL data.table.

When I look at one of the event align.err files they have the following error:

[readdb] num reads: 903, num reads with path to fast5: 903 nanopolish: src/nanopolish_squiggle_read.cpp:321: void SquiggleRead::load_from_raw(fast5_file&, uint32_t): Assertion `rt.n > 0' failed.

I was able to find this issue described in the nanopolish GitHub page:

https://github.com/jts/nanopolish/issues/403

And it seems to indicate that is a problem with nanopolish version. Do you confirm? I am using version 0.11.0

Still, I am still banging my head around this. Can you help ?

All the best, Pedro

[oliveira-lab]

Hi Alan,

I found the problem and solution. This arises because I was using VBZ compressed fast5 files. I converted them to GZIP, and it worked properly. You may close the issue! Thanks! Pedro

[touala]

Thank you Pedro for providing the solution.