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jts / nanopolish

Signal-level algorithms for MinION data
MIT License
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Nanopolish index error #287

Closed jonhultqvist closed 6 years ago

jonhultqvist commented 6 years ago

Hi,

I have been attempting to use nanopolish index on a 1D nanopore dataset (FLOMIN-107) basecalled using Albacore 2.1.3. The run crashed with a core dump and the error message displayed below. I have not seen anyone report this specific error previously. Any suggestions on what may be causing it?

My command was the following

nanopolish index -d /scratch2/jon/MINION_DATA_STORAGE/170829_PCE/reads/ \ /scratch2/jon/MinION/PCE/albacore_basecall_2.0/FASTQ/PCE_MinION_albacore_2.1.3_ALL.fq

and I got the following error message with a core dump

` [readdb] num reads: 717143, num reads with path: 714123 HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 47086235801600:

000: H5O.c line 246 in H5Oopen(): unable to open object

major: Symbol table
minor: Can't open object

001: H5O.c line 1357 in H5O_open_name(): object not found

major: Symbol table
minor: Object not found

002: H5Gloc.c line 430 in H5G_loc_find(): can't find object

major: Symbol table
minor: Object not found

003: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed

major: Symbol table
minor: Object not found

004: H5Gtraverse.c line 755 in H5G_traverse_real(): component not found

major: Symbol table
minor: Object not found

terminate called after throwing an instance of 'hdf5_tools::Exception' what(): /Raw/Reads//Signal_Pack/params/read_id: error in H5Oopen /var/spool/gridengine/execd/perun14/job_scripts/3626018: line 9: 35177 Aborted (core dumped) nanopolish index.........`

jts commented 6 years ago

Are you using the latest version of nanopolish? A few weeks ago I changed it to catch and ignore these HDF5 issues.

jonhultqvist commented 6 years ago

Thanks for replying so swiftly. I'm on v0.8.4. I will update to the latest committed code and see if that helps.

jonhultqvist commented 6 years ago

Okey, I can confirm that it is working now. Seems there was an invalid fast5-file (platform QC-derived) in the directory.

Thanks for the speedy fix.