Comments (3)
After 2 days of hectic debugging, I think I found the issue. The data type for the Events group as given by h5dump is as follows,
GROUP "BaseCalled_template" {
DATASET "Events" {
DATATYPE H5T_COMPOUND {
H5T_IEEE_F64LE "mean";
H5T_IEEE_F64LE "start";
H5T_IEEE_F64LE "stdv";
H5T_IEEE_F64LE "length";
H5T_STRING {
STRSIZE 5;
STRPAD H5T_STR_NULLPAD;
CSET H5T_CSET_ASCII;
CTYPE H5T_C_S1;
} "model_state";
H5T_STD_I64LE "move";
H5T_IEEE_F32LE "weights";
**H5T_IEEE_F32LE "p_model_state**";
For p_model_state the data type is H5T_IEEE_F32LE. However, in fast5.hpp:393 it is declared as double instead of float as below.
struct Basecall_Event
{
double mean;
double stdv;
double start;
double length;
**double p_model_state**;
long long move;
The Bus error dissappeared after I did this change.
from fast5.
Hi @hasindu2008,
Thanks for looking into this. I don't have access to an ARM development machine so I have limited ability to help.
This issue may have been caused by changes to ONT's fast5 file format (the internal data types have changed a few times in the past). Can you let me know which dataset caused the problem?
Thanks,
Jared
from fast5.
Hi @jts
The dataset that I used was downloaded from (https://github.com/nanopore-wgs-consortium/NA12878/blob/master/Genome.md) under the FAST5 (Signal Level files) section. I am attaching one of those fast5 files here for your convenience. After I changed the data type for p_model_state from double to float, now things are working perfectly.
from fast5.
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from fast5.