Ecosyste.ms: Issues

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GitHub / nanoporetech/ont_fast5_api issues and pull requests

#84 - Unable to copy object (file read failed) on parallel FS

Issue - State: open - Opened by matzmz 2 months ago

#83 - fast5_compress error:

Issue - State: open - Opened by sahoo2000 6 months ago

#82 - compress_fast5 command

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

#80 - Directly cast dataset into desired type instead of using it as a cont…

Pull Request - State: open - Opened by nileshpatra 9 months ago - 1 comment

#79 - similar API for pod5?

Issue - State: open - Opened by assafgrw 10 months ago - 2 comments

#77 - error when converting single read to multi read

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

#75 - fast5_subset to take list of .fast5 files

Issue - State: closed - Opened by MustafaElshani over 1 year ago - 1 comment

#74 - Some problem of multi_to_single_fast5

Issue - State: closed - Opened by Bin-Ma over 1 year ago - 6 comments

#73 - WARNING:Fast5Filter:xxx reads not found!

Issue - State: open - Opened by markme123 almost 2 years ago - 8 comments

#71 - compress_fast5 not compressing?

Issue - State: closed - Opened by mawa86 over 2 years ago - 2 comments

#70 - The labels in the "end_reason" data type get lost when using compress_fast5

Issue - State: closed - Opened by hasindu2008 over 2 years ago - 7 comments

#69 - multi_to_single_fast5 problem

Issue - State: closed - Opened by FerchoHQ over 2 years ago - 3 comments

#68 - demultiplexing generates additional - folder

Issue - State: closed - Opened by Fatihlrcfs over 2 years ago - 3 comments

#67 - subset obtained with fast5_subset does not work for guppy

Issue - State: closed - Opened by ndierckx over 2 years ago - 3 comments

#66 - demux_fast5 resume list

Issue - State: open - Opened by SkabbiVML over 2 years ago - 1 comment

#65 - multi_to_multi_fast5

Issue - State: open - Opened by nick-youngblut over 2 years ago - 2 comments

#64 - vbz compression compatibility with guppy_basecaller

Issue - State: closed - Opened by nick-youngblut over 2 years ago - 2 comments

#63 - Multi to single fast5 goes into sleep

Issue - State: closed - Opened by kaltinel over 2 years ago - 7 comments

#62 - fast5_subset OSError

Issue - State: closed - Opened by ndierckx over 2 years ago - 4 comments

#61 - Issues attempting to duplicate reads

Issue - State: closed - Opened by CodingKaiser over 2 years ago - 8 comments

#60 - 'demux_fast5' (and 'fast5_subset') for single read fast5s

Issue - State: closed - Opened by AAnnan almost 3 years ago - 5 comments

#59 - --filename_base behaves differently in 'fast5_subset'

Issue - State: open - Opened by AAnnan almost 3 years ago - 2 comments

#58 - --sanitize can't be used with --in_place with compress_fast5

Issue - State: closed - Opened by mattloose almost 3 years ago - 2 comments

#57 - ERROR:ont_fast5_api.conversion_tools.multi_to_single_fast5:Unable to open file

Issue - State: closed - Opened by 123chenshixin almost 3 years ago - 1 comment

#56 - filesize increased reconverting vbz compressed fast5 back to gzip compression

Issue - State: closed - Opened by biolene about 3 years ago - 13 comments

#55 - multi_to_single_fast5 generated only 4000 single fast5

Issue - State: closed - Opened by Johnsonzcode about 3 years ago - 13 comments

#54 - Guppy default modified base calling configuration file doesn't exist

Issue - State: closed - Opened by JayVaz18 about 3 years ago - 1 comment

#52 - mounting error

Issue - State: closed - Opened by xj-Liang-Olga about 3 years ago - 2 comments

#51 - fast5_subset failing mid-run

Issue - State: closed - Opened by irenenewton over 3 years ago - 6 comments

#50 - fast5_subset is missing?

Issue - State: closed - Opened by kaykay202 over 3 years ago - 1 comment

#49 - [M]: add tombo resquiggle

Pull Request - State: closed - Opened by loganylchen over 3 years ago - 5 comments

#48 - Update LICENSE.txt URL schemes: http -> https

Pull Request - State: closed - Opened by thequicksort over 3 years ago - 1 comment

#47 - Metadata from multifast5

Issue - State: open - Opened by usamec over 3 years ago - 1 comment

#46 - Error when running compress_fast5 but seems to complete

Issue - State: closed - Opened by callumparr over 3 years ago - 3 comments

#45 - Question: subset by barcode

Issue - State: closed - Opened by JWDebler over 3 years ago - 10 comments

#44 - Decompression

Issue - State: closed - Opened by jamez-eh almost 4 years ago - 10 comments

#43 - multi_to_single_fast5 hanging

Issue - State: closed - Opened by fbrennen almost 4 years ago - 1 comment

#42 - no space left on device [errno28]

Issue - State: closed - Opened by cyber-ux almost 4 years ago - 9 comments

#41 - multi_to_single_fast5 command give syntax error

Issue - State: closed - Opened by aman21392 about 4 years ago - 5 comments

#39 - Check if the Fast5 is multi-read or single-read

Issue - State: closed - Opened by akk01 about 4 years ago - 1 comment

#38 - single_to_multi_fast5 compression is not working ?

Issue - State: closed - Opened by svennd about 4 years ago - 5 comments

#37 - How to get info from fast5?

Issue - State: closed - Opened by renzilin about 4 years ago - 2 comments
Labels: question

#36 - Can I subsample Nanopore fast5/fastq with this tool?

Issue - State: closed - Opened by jolespin about 4 years ago - 7 comments

#35 - sequencing_summary.txt for fast5_subset output

Issue - State: closed - Opened by mmiladi about 4 years ago - 4 comments

#33 - fast5_subset on vbz compressed fast5 files

Issue - State: closed - Opened by Ganthark over 4 years ago - 4 comments

#32 - Type incompatibility in Fast5Info constructor

Issue - State: closed - Opened by lfearnley over 4 years ago - 4 comments

#31 - read_id does not exists in single fast5 reads

Issue - State: closed - Opened by usamec over 4 years ago - 2 comments

#30 - different filesize after "de-" compression

Issue - State: closed - Opened by svennd over 4 years ago - 3 comments

#29 - Add compression option in single_to_multi_fast5.py

Issue - State: closed - Opened by cgjosephlee over 4 years ago - 1 comment

#28 - --recursive in compress_fast5

Issue - State: closed - Opened by pterzian over 4 years ago - 2 comments

#27 - [bug report] single_to_multi_fast5 fail

Issue - State: closed - Opened by yipukangda over 4 years ago - 5 comments

#26 - "for for" in documentation

Issue - State: closed - Opened by Shians over 4 years ago - 2 comments

#25 - Following symlinks recursively

Issue - State: closed - Opened by wdecoster almost 5 years ago - 3 comments

#24 - fast5_subset take fastq as readID list

Issue - State: open - Opened by Kirk3gaard almost 5 years ago - 1 comment

#23 - '<' not supported between instances of 'str' and 'float'

Issue - State: closed - Opened by imet-k almost 5 years ago - 8 comments

#22 - Issue while converting single_to_multi_fast5

Issue - State: closed - Opened by andrese52 almost 5 years ago - 1 comment

#21 - ValueError: mpi4py.MPI.Status size changed, may indicate binary incompatibility.

Issue - State: closed - Opened by fbrennen almost 5 years ago - 3 comments

#19 - Write reads to a multi fast5?

Issue - State: closed - Opened by mrvollger almost 5 years ago - 7 comments

#18 - add option skip_analyses to remove fastq data during conversion

Pull Request - State: closed - Opened by tolot27 almost 5 years ago - 1 comment

#17 - fail to run fast5_subset

Issue - State: closed - Opened by limin321 about 5 years ago - 6 comments

#16 - multi_fast5_subset doesn't recognise the number of threads

Issue - State: closed - Opened by mattloose about 5 years ago - 6 comments

#15 - Select only subset of reads from multi_fast5

Pull Request - State: closed - Opened by lpryszcz about 5 years ago - 4 comments

#14 - multi_to_single_fast5 no output

Issue - State: closed - Opened by Shians about 5 years ago - 3 comments

#13 - multi_to_single_fast5 fails with no error

Issue - State: closed - Opened by pabloacera about 5 years ago - 4 comments

#12 - multi_to_single_fast5 stops converting after the first two files

Issue - State: closed - Opened by kychen37 about 5 years ago - 3 comments

#11 - `multi_to_single_fast5 ` producing a `file signature not found` error

Issue - State: closed - Opened by shaniAmare about 5 years ago - 3 comments

#10 - Unable to cobvert multi_to_single_fast5

Issue - State: closed - Opened by icedevil2001 over 5 years ago - 6 comments

#9 - AttributeError: 'ProgressBar' object has no attribute 'currval'

Issue - State: closed - Opened by hygine over 5 years ago - 7 comments

#8 - filename_mapping.txt gets overwritten

Issue - State: closed - Opened by mbhall88 over 5 years ago - 4 comments

#7 - albacore errors after multi_to_single_fast5.py

Issue - State: closed - Opened by lcoombe over 5 years ago - 20 comments

#6 - problem with duplicate name

Issue - State: closed - Opened by lfaino over 5 years ago - 1 comment

#5 - `--recursive` option do not search into symbolic links

Issue - State: closed - Opened by cgjosephlee over 5 years ago - 4 comments

#4 - Show a correct error message on file opening failure

Pull Request - State: closed - Opened by hyeshik over 5 years ago - 2 comments

#3 - Update for compatibility with multi file fast5s

Issue - State: closed - Opened by mattloose over 5 years ago - 4 comments

#2 - feature request : add tar as input format for single_to_multi_fast5

Issue - State: closed - Opened by svennd over 5 years ago - 3 comments

#1 - fast5 validator

Issue - State: closed - Opened by mattloose almost 6 years ago - 3 comments