Aborted (core dumped) error when running with fast5 files

[Moretta1]

Hi，

I'm trying to detect 5mC with deepmod2, with input files in fast5 format and basecalling with guppy.

The basecalling cmd is:

guppy_basecaller -i /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/single_fast5_pass/dir_00/ -s /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/hg002.guppy/ -c ~/nanopore_methods/ont-guppy/data/dna_r10.4.1_e8.2_400bps_5khz_hac.cfg --bam_out --moves_out --recursive -x 'cuda:0'

then
find . -type f -name "*.bam" | samtools cat -b - -o ../all_pass.bam

and
samtools fastq all_pass.bam -T "*" | minimap2 -ax map-ont ~/reference_fa/hg19/Homo_sapiens.GRCh38.dna.primary_assembly.fa - -y | samtools sort -o aligned.sorted.bam

and then I tried deepmod2 cmd:
python deepmod2 detect --input /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/single_fast5_pass/dir_00/ --bam /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/hg002.guppy/all_pass.bam --file_type fast5 --output hg002_output --threads 8 --model bilstm_r10.4.1_5khz_v4.3 --seq_type dna --device cuda:0

I got the following error:

(deepmod2) rlwang@dell-tower-server:~/nanopore_methods/DeepMod2/DeepMod2-main$ python deepmod2 detect --input /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/single_fast5_pass/dir_00/ --bam /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/hg002.guppy/all_pass.bam --file_type fast5 --output hg002_output --threads 8 --model bilstm_r10.4.1_5khz_v4.3 --seq_type dna --device cuda
2025-07-14 10:52:10.608800: Starting DeepMod2.

2025-07-14 10:52:10.609198:
Command: python deepmod2 detect --input /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/single_fast5_pass/dir_00/ --bam /data/fast5_data/5mC/giab_fast5_data/hg002/20221109_1654_5A_PAG65784_f306681d/hg002.guppy/all_pass.bam --file_type fast5 --output hg002_output --threads 8 --model bilstm_r10.4.1_5khz_v4.3 --seq_type dna --device cuda

/home/rlwang/.conda/envs/deepmod2/lib/python3.8/site-packages/h5py/init.py:36: UserWarning: h5py is running against HDF5 1.10.4 when it was built against 1.14.3, this may cause problems
_warn(("h5py is running against HDF5 {0} when it was built against {1}, "
Warning! HDF5 library version mismatched error
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.14.3, library is 1.10.4
SUMMARY OF THE HDF5 CONFIGURATION
=================================

General Information:

               HDF5 Version: 1.10.4
              Configured on: Mon, 13 Apr 2020 12:15:08 +0000
              Configured by: Debian
                Host system: x86_64-pc-linux-gnu
          Uname information: Debian
                   Byte sex: little-endian
         Installation point: /usr
	    Flavor name: serial

Compiling Options:

                 Build Mode: production
          Debugging Symbols: no
                    Asserts: no
                  Profiling: no
         Optimization Level: high

Linking Options:

                  Libraries: static, shared

Statically Linked Executables:
LDFLAGS: -Wl,-Bsymbolic-functions -Wl,-z,relro
H5_LDFLAGS: -Wl,--version-script,$(top_srcdir)/debian/map_serial.ver
AM_LDFLAGS:
Extra libraries: -lpthread -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: x86_64-linux-gnu-ranlib

Languages:

                          C: yes
                 C Compiler: /usr/bin/gcc
                   CPPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2
                H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API
                AM_CPPFLAGS: 
                    C Flags: -g -O2 -fdebug-prefix-map=$(top_srcdir)=. -fstack-protector-strong -Wformat -Werror=format-security
                 H5 C Flags:  -std=c99  -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -O
                 AM C Flags: 
           Shared C Library: yes
           Static C Library: yes


                    Fortran: yes
           Fortran Compiler: /usr/bin/gfortran
              Fortran Flags: -g -O2 -fdebug-prefix-map=$(top_srcdir)=. -fstack-protector-strong
           H5 Fortran Flags:  -pedantic -Wall -Wextra -Wunderflow -Wimplicit-interface -Wsurprising -Wno-c-binding-type  -s -O2
           AM Fortran Flags: 
     Shared Fortran Library: yes
     Static Fortran Library: yes

                        C++: yes
               C++ Compiler: /usr/bin/g++
                  C++ Flags: -g -O2 -fdebug-prefix-map=$(top_srcdir)=. -fstack-protector-strong -Wformat -Werror=format-security
               H5 C++ Flags:   -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O
               AM C++ Flags: 
         Shared C++ Library: yes
         Static C++ Library: yes

                       Java: yes
              Java Compiler: /usr/bin/java (openjdk 11.0.7-ea 2020-04-14)

Features:

               Parallel HDF5: no

Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Threadsafety: yes
Default API mapping: v18
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE: no
Direct VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Metadata trace file: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
Bye...
Aborted (core dumped)

I have checked my conda environment:

hdf5 1.14.3 nompi_h2d575fe_109 conda-forge
lib-pod5 0.3.23 pypi_0 pypi
pod5 0.3.23 pypi_0 pypi

Is there any suggestions on how to fix it?

Best regards
Rulan