Error when running uncalled map

[ncolaian]

Hi,

I am currently getting an error when trying to run uncalled map.

uncalled map nif_data/NifH_data/uncalled_cdhit_ref/5k_nifH nanopore_data/single_fast5/0/8384d558-af58-4306-b661-34ed2ec7e3b7.fast5

Loading fast5s Mapping HDF5-DIAG: Error detected in HDF5 (1.8.21) thread 140484998567744:

000: H5Dio.c line 223 in H5Dread(): can't read data

major: Dataset
minor: Read failed

001: H5Dio.c line 605 in H5D__read(): can't read data

major: Dataset
minor: Read failed

002: H5Dchunk.c line 2093 in H5D__chunk_read(): unable to read raw data chunk

major: Low-level I/O
minor: Read failed

003: H5Dchunk.c line 3123 in H5D__chunk_lock(): data pipeline read failed

major: Data filters
minor: Filter operation failed

004: H5Z.c line 1311 in H5Z_pipeline(): required filter 'vbz' is not registered

major: Data filters
minor: Read failed

005: H5PL.c line 380 in H5PL_load(): search in paths failed

major: Plugin for dynamically loaded library
minor: Can't get value

006: H5PL.c line 738 in H5PL__find(): can't open directory: /usr/local/hdf5/lib/plugin

major: Plugin for dynamically loaded library
minor: Can't open directory or file

Traceback (most recent call last): File "/home/ubuntu/.local/bin/uncalled", line 341, in map_cmd(conf, args) File "/home/ubuntu/.local/bin/uncalled", line 157, in map_cmd for p in mapper.update(): RuntimeError: /Raw/Reads/Read_137128/Signal: error in H5Dread terminate called without an active exception Aborted (core dumped)

Here is the file version: HDF5 "8384d558-af58-4306-b661-34ed2ec7e3b7.fast5" { ATTRIBUTE "file_version" { DATATYPE H5T_IEEE_F64LE DATASPACE SCALAR DATA { (0): 2 } } }

and the listing of the fast5 groups

/ Group /Analyses Group /Analyses/Basecall_1D_000 Group /Analyses/Basecall_1D_000/BaseCalled_template Group /Analyses/Basecall_1D_000/BaseCalled_template/Fastq Dataset {SCALAR} /Analyses/Basecall_1D_000/Summary Group /Analyses/Basecall_1D_000/Summary/basecall_1d_template Group /Analyses/Segmentation_000 Group /Analyses/Segmentation_000/Summary Group /Analyses/Segmentation_000/Summary/segmentation Group /Raw Group /Raw/Reads Group /Raw/Reads/Read_137128 Group /Raw/Reads/Read_137128/Signal Dataset {14750/Inf} /UniqueGlobalKey Group /UniqueGlobalKey/channel_id Group /UniqueGlobalKey/context_tags Group /UniqueGlobalKey/tracking_id Group

Do you have any ideas why this may be failing?

Thanks!

[skovaka]

Try installing the VBZ compression plugin: https://github.com/nanoporetech/vbz_compression ONT recently changed their compression format, which didn't cause any problems when I tested it, but it looks like you might need to install it manually. Let me know if that works and I'll working on automating that, or at least add a note to the readme

[ncolaian]

Thanks for the quick response!

Unfortunately this didn't work for me. I am still getting the same error. I'm thinking that maybe it has to do with my file, however I'm not sure what's the hang-up.

Would you mind quickly testing or looking at this file? It is from a multi-read-fast5 file where I split it into single read files. The multi read file was downloaded from the pass directory saved by the Mk1C nanopore.

Thanks

https://pivotbio-my.sharepoint.com/:u:/p/ncolaianni/EfXpVVzJBq9BqHl9a0GQcXoB1Xf1ICBeUVybiGDYT1P4kQ?e=PeFWJC

[skovaka]

Thanks for sharing! Looks like it's the same issue reported here: https://github.com/nanoporetech/vbz_compression/issues/5 If you're on Linux (and maybe Mac too) try running export HDF5_PLUGIN_PATH=/usr/local/hdf5/lib/plugin, then run uncalled map. "/usr/local/hdf5/lib/plugin" should contain a file called "libvbz_hdf_plugin.so". If that command doesn't work and you don't see that file, you'll need to figure out where the VBZ installer put the plugin library. Hope that helps!

[ncolaian]

Ah, the last piece! It worked like a charm. Thanks a lot!

[skovaka]

No problem, glad it worked!