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nanoporetech / ont_fast5_api

Oxford Nanopore Technologies fast5 API software
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demux_fast5: `python3.9(20125,0x7ff84e0ee640) malloc: *** error for object 0x1110417b0: pointer being freed was not allocated` #78

Open richardstoeckl opened 1 year ago

richardstoeckl commented 1 year ago

Hi,

I am trying to demultiplex the fast5 files of a Flongle sequencing run which I basecalled afterwards using guppy 6.5.7+ca6d6af.

I am using the following command:

# ont-fast5-api version 4.1.1 installed using pip
demux_fast5 --recursive -t 4 \
--input path/to/original/sequencing/run/ \
--save_path demultiplexed/ \
--summary_file path/to/basecalled/directory/sequencing_summary.txt

However, on a Ubuntu 20.04 system I get the following errors:

free(): invalid pointer########################################################################################                                                                                                       | 47% ETA:  0:00:17
free(): invalid pointer#########################################################################################################################################################################                      | 88% ETA:  0:00:04
free(): invalid pointer
free(): invalid pointer#################################################################################################################################################################################              | 93% ETA:  0:00:03

And the process stops at different pecentages, when I restart the command.

On a macOS Ventura 13.4.1 System, I get the following errors:

python3.9(20125,0x7ff84e0ee640) malloc: *** error for object 0x1110417b0: pointer being freed was not allocated                                                                                                       | 32% ETA:  0:01:01
python3.9(20125,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20127,0x7ff84e0ee640) malloc: *** error for object 0x10738d300: pointer being freed was not allocated######################################                                                                 | 66% ETA:  0:00:32
python3.9(20127,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20155,0x7ff84e0ee640) malloc: *** error for object 0x1053a3490: pointer being freed was not allocated###########################################################                                            | 77% ETA:  0:00:23
python3.9(20155,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20171,0x7ff84e0ee640) malloc: *** error for object 0x10e398210: pointer being freed was not allocated############################################################                                           | 78% ETA:  0:00:23
python3.9(20171,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20128,0x7ff84e0ee640) malloc: *** error for object 0x111800620: pointer being freed was not allocated#########################################################################                              | 85% ETA:  0:00:16
python3.9(20128,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20175,0x7ff84e0ee640) malloc: *** error for object 0xcf2c74b16bcc87a8: pointer being freed was not allocated######################################################################                          | 87% ETA:  0:00:15
python3.9(20175,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20178,0x7ff84e0ee640) malloc: *** error for object 0x108b35750: pointer being freed was not allocated
python3.9(20178,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20182,0x7ff84e0ee640) malloc: *** error for object 0x10a1294b0: pointer being freed was not allocated##############################################################################                         | 87% ETA:  0:00:15
python3.9(20182,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20126,0x7ff84e0ee640) malloc: *** error for object 0x109a8be70: pointer being freed was not allocated###############################################################################                        | 87% ETA:  0:00:15
python3.9(20126,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20181,0x7ff84e0ee640) malloc: *** error for object 0x10c643f90: pointer being freed was not allocated###############################################################################                        | 88% ETA:  0:00:15
python3.9(20181,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20187,0x7ff84e0ee640) malloc: *** error for object 0x10a55de90: pointer being freed was not allocated##########################################################################################             | 93% ETA:  0:00:08
python3.9(20187,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20179,0x7ff84e0ee640) malloc: *** error for object 0x6165722901100100: pointer being freed was not allocated
python3.9(20179,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug
python3.9(20202,0x7ff84e0ee640) malloc: *** error for object 0x103a1057c2e6400: pointer being freed was not allocated#####################################################################################            | 94% ETA:  0:00:08
python3.9(20202,0x7ff84e0ee640) malloc: *** set a breakpoint in malloc_error_break to debug

Again, the software stops at different percentages, usually around 94-96%.

Any idea what could cause this?