tombo resquiggle 0%|
Li-Rui091 opened this issue · comments
Hi,
I run resquiggle on my test data ,the command as follows:
thread=2
params_fast5=/public211/lirui/m6Adection/data/GCP1/test
params_ref=/public211/lirui/m6Adection/data/reference/Arabidopsis_thaliana.TAIR10.cdna.all.fa
tombo resquiggle --rna --processes ${thread} --corrected-group RawGenomeCorrected_000 --basecall-group Basecall_1D_000
--include-event-stdev --overwrite --ignore-read-locks ${params_fast5} ${params_ref}
However, the log shows that the process has been 0% for more than 24 hours:
[17:41:53] Loading minimap2 reference.
[17:42:02] Getting file list.
[17:42:02] Re-squiggling reads (raw signal to genomic sequence alignment).
0%| | 0/2 [00:00<?, ?it/s]
Any advice for me to fix it is appreciated.
@Li-Rui091
This happened to me and I realized I didn't have the hdf5 plugin. Check to see if you have it already by typing
h5repack
. If the usage is displayed then you have it. If not, follow the install instructions below. This is installation instructions for Linux.
wget https://github.com/nanoporetech/vbz_compression/releases/download/v1.0.1/ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
tar xvzf ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
export HDF5_PLUGIN_PATH=/tools/ont-vbz-hdf-plugin-1.0.1-Linux/usr/local/hdf5/lib/plugin
h5repack
I have the same issue of resquiggle being stuck at 0%. I checked hdf5 and do have it installed. Any other suggestions to get tombo resquiggle to work? Thanks.