nanoporetech/pod5-file-format issues and pull requests

#133 - pod5 breaks with new numpy 2.0.0

Issue - State: open - Opened by Psy-Fer 16 days ago - 6 comments

#132 - Pod5 convert to_fast5 is losing signal data

Issue - State: open - Opened by ssomalra 20 days ago

#132 - Pod5 convert to_fast5 is losing signal data

Issue - State: closed - Opened by ssomalra 20 days ago

#131 - pod5 merge hangs indefinitely at 99-100%(the last 20 pod5 have not been merged)

Issue - State: open - Opened by kir1to455 25 days ago

#130 - Is it possible to repack pod5 files with a specific read number?

Issue - State: closed - Opened by Shians about 1 month ago - 4 comments
Labels: question

#129 - pod5 convert fast5 doesn't finish for a set of files

Issue - State: open - Opened by KristinaGagalova about 1 month ago - 11 comments

#128 - Lost signal data

Issue - State: closed - Opened by atongmuuu about 1 month ago - 3 comments

#127 - Support for sampling rates larger than int16 when writing pod5 files

Issue - State: closed - Opened by shadowk29 about 1 month ago

#126 - Split Read IDs Cause Missing Read Error?

Issue - State: closed - Opened by peradastra about 2 months ago - 1 comment

#125 - pod5 convert fast5 is stalling

Issue - State: closed - Opened by sahuno about 2 months ago - 4 comments

#124 - pod5 filter get killed

Issue - State: closed - Opened by yinyuanmtu 2 months ago - 5 comments

#123 - error：XX.fast5 is not a multi-read fast5 file

Issue - State: closed - Opened by moxqiang 2 months ago - 2 comments

#122 - Troubleshooting Conversion of Fast5 Files to Pod5 Format

Issue - State: closed - Opened by biozzq 3 months ago - 12 comments

#121 - pod5 convert fast5 warning: Failed to read key read_XXX

Issue - State: closed - Opened by creaturemoon 3 months ago - 2 comments

#120 - No documentation regarding multi-file pod5 dependency

Issue - State: closed - Opened by VasLem 4 months ago - 2 comments

#119 - Missing conda pod5 package

Issue - State: open - Opened by Salome-Brunon 4 months ago - 2 comments

#118 - Getting the signal chunk size of a pod5 file

Issue - State: closed - Opened by hiruna72 4 months ago - 1 comment

#117 - MantaControl': Unable to read fast5 file at /path/: HDF5 exception",

Issue - State: closed - Opened by franztastic 4 months ago - 2 comments

#116 - getrandom error with pod5 convert fast5

Issue - State: open - Opened by cocvincent 4 months ago - 14 comments

#115 - Reader class attributes immutable (Cannot edit "sample_id" field of mutable read object)

Issue - State: closed - Opened by jennifergribble-nanopore 4 months ago - 1 comment

#114 - Cannot install pod5 through pip on ARM due to dependency issues

Issue - State: open - Opened by hasindu2008 5 months ago - 11 comments

#113 - error with pod5 convert to_fast5

Issue - State: closed - Opened by mocherry 5 months ago - 1 comment

#112 - pod5 subset/filter in preparation for dorado duplex is slow

Issue - State: closed - Opened by wilsonte-umich 5 months ago - 5 comments

#111 - Semaphore hissy fit at the end of subset run

Issue - State: open - Opened by mp15 5 months ago - 1 comment

#110 - Scratch/tmp pod5 problem

Issue - State: open - Opened by Macdot3 5 months ago - 21 comments

#109 - option to split pod5 by size/read number

Issue - State: open - Opened by olawa 5 months ago - 3 comments

#108 - pod5 webserver memory error

Issue - State: closed - Opened by ranitori 6 months ago - 2 comments

#107 - pod5 view does not work for some data since version 0.3.0

Issue - State: open - Opened by davidsilvapires 6 months ago - 6 comments

#106 - V0.3.6 pod5 view "Error while processing"

Issue - State: closed - Opened by roo-weed 6 months ago - 3 comments

#105 - pod5 filter/ subset failed with TypeError: enable_string_cache() missing 1 required positional argument: 'enable'

Issue - State: closed - Opened by jkh00 6 months ago - 3 comments

#104 - pod5 view fails with polars.exceptions.ColumnNotFoundError: not_set

Issue - State: closed - Opened by janpb 7 months ago - 2 comments

#103 - Segmentation fault (core dumped) when trying to run pod5 convert fast5

Issue - State: closed - Opened by DepledgeLab 7 months ago - 9 comments

#102 - Undefined references to libarrow symbols when using the libpod5.a

Issue - State: closed - Opened by hiruna72 7 months ago - 4 comments

#101 - Failed requirement 'flatbuffers/2.0.0@nanopore/testing' from 'conanfile.py

Issue - State: open - Opened by hiruna72 7 months ago - 3 comments

#100 - Metadata editing in pod5 files

Issue - State: open - Opened by DCossey 7 months ago - 10 comments
Labels: question

#99 - fast5 > pod5 conversion is very slow when input and output are on the same physical HDD?

Issue - State: closed - Opened by ItokawaK 7 months ago - 2 comments

#98 - pod5 inspect to work with multiple pod5s

Issue - State: closed - Opened by Kirk3gaard 7 months ago - 3 comments

#97 - fast5 to pod5 conversion issue

Issue - State: closed - Opened by HalfPhoton 7 months ago - 11 comments

#96 - Update documentation for subset from inspect reads

Issue - State: closed - Opened by Kirk3gaard 7 months ago - 2 comments

#95 - pod5 filter freeze

Issue - State: open - Opened by diego-rt 7 months ago - 3 comments

#94 - Can't install on arm

Issue - State: closed - Opened by Psy-Fer 7 months ago - 4 comments

#93 - Q: `pod5 subset <..> --threads` takes a lot of resources

Issue - State: open - Opened by sklages 7 months ago - 2 comments

#92 - Pod 5 subsets

Issue - State: open - Opened by Jeff-Field 7 months ago - 1 comment

#91 - Mysterious freeze in pod5 convert

Issue - State: closed - Opened by maximus-sci 7 months ago - 6 comments

#90 - assets are missing in the latest release

Issue - State: closed - Opened by hiruna72 7 months ago - 1 comment

#89 - Unable to set relative path --one-to-one directory

Issue - State: closed - Opened by RenscoHogers 8 months ago - 8 comments

#88 - ModuleNotFoundError: No module named 'lib_pod5.pod5_format_pybind'

Issue - State: closed - Opened by yoeHuuui 8 months ago - 5 comments

#88 - ModuleNotFoundError: No module named 'lib_pod5.pod5_format_pybind'

Issue - State: closed - Opened by yoeHuuui 8 months ago - 5 comments

#87 - pod5 subset job with double free or corruption error

Issue - State: closed - Opened by antoinefelden 8 months ago - 12 comments

#86 - fast5 to pod5 error : "can't locate attribute: 'median_before"

Issue - State: closed - Opened by Toinax 8 months ago

#86 - fast5 to pod5 error : "can't locate attribute: 'median_before"

Issue - State: closed - Opened by Toinax 8 months ago

#85 - ModuleNotFoundError: No module named '_version'

Issue - State: closed - Opened by npavlovikj 8 months ago - 6 comments

#84 - Fast5 to pod5 failure

Issue - State: open - Opened by pilaralv 8 months ago - 1 comment

#84 - Fast5 to pod5 failure

Issue - State: closed - Opened by pilaralv 8 months ago - 1 comment

#83 - [errno 30] Read-only file system

Issue - State: closed - Opened by zalibke 8 months ago - 1 comment

#82 - memory error

Issue - State: open - Opened by aCoalBall 8 months ago - 13 comments

#81 - Is fast5 converted form pod5 different from the fast5 saved by the sequencer?

Issue - State: closed - Opened by onkar2470 8 months ago - 1 comment

#80 - Pod5 install error

Issue - State: closed - Opened by keenhl 8 months ago - 3 comments

#79 - pod5 convert to_fast5 aborts with Errno 11, flags=13, o_flags=242

Issue - State: closed - Opened by hartnegg 9 months ago - 1 comment

#78 - Python 3.12 Installation error with lib-pod5 version conflicts

Issue - State: closed - Opened by zg404 9 months ago - 5 comments

#77 - Get the set of raw signal files from a pod5 dataset given a list of read ids.

Issue - State: closed - Opened by hiruna72 9 months ago - 4 comments

#76 - Signal and record compression methods

Issue - State: closed - Opened by hiruna72 9 months ago - 9 comments

#75 - input file 'is not a multi-read fast5'

Issue - State: closed - Opened by yanchunzhang 9 months ago - 1 comment

#74 - pod5 subset incorrect usage line

Issue - State: closed - Opened by cfblaeb 10 months ago - 6 comments

#73 - remove incorrect information regarding threads

Pull Request - State: open - Opened by cfblaeb 10 months ago

#72 - pod5 subset cannot shard a large aggregate pod5 file

Issue - State: open - Opened by billytcl 10 months ago - 6 comments

#71 - 'Argument list too long' for 'pod5 convert fast5' command

Issue - State: closed - Opened by Flower9618 10 months ago - 4 comments

#70 - is there option for threading for pod5 convert?

Issue - State: closed - Opened by sahuno 10 months ago - 3 comments

#69 - is there option for threading?

Issue - State: closed - Opened by sahuno 10 months ago - 2 comments

#68 - pod5 convert fast5 does not gracefully exit after an error when using "strict"

Issue - State: open - Opened by billytcl 10 months ago - 1 comment

#67 - how much information you loose when you convert fast5 to pod5 and back to fast5?

Issue - State: closed - Opened by sahuno 10 months ago - 2 comments

#66 - pod5 don't seem to save much space on short reads

Issue - State: open - Opened by billytcl 10 months ago - 7 comments

#65 - Q: --recursive only for POD5 input?

Issue - State: closed - Opened by sklages 10 months ago - 4 comments

#64 - customising read ids, UUIDs

Issue - State: closed - Opened by harikaurel 11 months ago - 11 comments

#63 - Getrandom runtime error

Issue - State: closed - Opened by j0hnn0 11 months ago - 6 comments

#62 - More info on some read table values

Issue - State: open - Opened by Psy-Fer 12 months ago - 9 comments

#61 - end_reason changelog or docs

Issue - State: closed - Opened by Psy-Fer 12 months ago - 4 comments

#60 - Add Conda Recipes

Pull Request - State: open - Opened by JannesSP 12 months ago

#59 - CMake Error CMake Error at CMakeLists.txt:5 (include):

Issue - State: closed - Opened by huicongyao 12 months ago - 3 comments

#58 - 'No progress in 600 seconds - quitting'

Issue - State: closed - Opened by lucky5sugar 12 months ago - 12 comments

#57 - filter

Issue - State: closed - Opened by HannahBenisty 12 months ago - 7 comments

#56 - Sample_id ERROR

Issue - State: closed - Opened by Vsd1106 almost 1 year ago - 3 comments

#55 - No way to demultiplex pod5 files.

Issue - State: closed - Opened by rjmat97 about 1 year ago - 3 comments

#54 - pod5: Identify multi fast5 error

Issue - State: closed - Opened by HITzhongyu about 1 year ago - 4 comments

#53 - pod5 subset killed

Issue - State: closed - Opened by SalvadorGJ about 1 year ago - 10 comments

#52 - Error:Unable to open the group "Raw": (Symbol table) Object not found

Issue - State: closed - Opened by Vsd1106 about 1 year ago - 13 comments

#51 - pod5 subset - terminate called without an active exception with slurm submissions

Issue - State: closed - Opened by bef22 about 1 year ago - 4 comments

#50 - pod5:Empty queue or timeout

Issue - State: closed - Opened by HITzhongyu about 1 year ago - 20 comments

#49 - pod5:Enqueueing exception with pod5 convert

Issue - State: closed - Opened by masohn about 1 year ago - 4 comments

#48 - Missing `pod5_format_export.h` ?

Issue - State: closed - Opened by huicongyao about 1 year ago - 1 comment

#47 - Support for parquet storage?

Issue - State: closed - Opened by willros about 1 year ago - 6 comments

#46 - Fast5 to pod5 - 5khz mode

Issue - State: closed - Opened by gwl2 about 1 year ago - 2 comments

#45 - Guppy v6.5.7 with pod5 uses tons of memory vs fast5

Issue - State: closed - Opened by billytcl about 1 year ago - 3 comments

GitHub / nanoporetech/pod5-file-format issues and pull requests