WGLab
Aborted (core dumped) error when running with fast5 files
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
