Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / mossmatters/HybPiper issues and pull requests

#127 - Issue with distribute_reads_to_targets.py

Issue - State: open - Opened by Kedraous over 1 year ago - 1 comment

#126 - exonerate_contigs issue and less genes with seqs in v2.1.5?

Issue - State: open - Opened by joyceem over 1 year ago - 3 comments

#124 - should --run_intronerate be on by default?

Issue - State: open - Opened by mossmatters over 1 year ago - 4 comments

#123 - Overflow error in gene_recovery_heatmap

Issue - State: closed - Opened by mossmatters over 1 year ago - 12 comments

#122 - Much lower recovery from HybPiper 2.1 than 1.3

Issue - State: open - Opened by V-Z over 1 year ago - 14 comments

#121 - Exonerate multiprocessing timeout error

Issue - State: open - Opened by mossmatters over 1 year ago

#120 - option in Hybpiper 1.3 not in Hybpiper 2.1

Issue - State: open - Opened by veronicamb over 1 year ago - 14 comments

#119 - Question about the --timeout flag

Issue - State: closed - Opened by Eremus007 over 1 year ago - 1 comment

#118 - Issues installing hybpiper

Issue - State: closed - Opened by veronicamb over 1 year ago - 2 comments

#117 - fasta headers don't have gene name

Issue - State: open - Opened by GavSmy over 1 year ago - 2 comments

#116 - Adding to bioconda

Issue - State: closed - Opened by TomHarrop over 1 year ago - 5 comments

#115 - Using fix_targetfile messes up with the target file

Issue - State: open - Opened by josh3397 over 1 year ago - 3 comments

#111 - Flag/Subparser to specify output path suggestion

Issue - State: open - Opened by Eremus007 almost 2 years ago

#110 - exonerate() raised: [Errno 24] Too many open files

Issue - State: open - Opened by Alicia-Talavera almost 2 years ago - 11 comments

#109 - Spades assembly failes on test-dataset and real dataset

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

#107 - check_dependencies error

Issue - State: closed - Opened by dianzhiyong almost 2 years ago - 1 comment

#106 - Stop codons in the final assembly

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

#105 - hybpiper assemble error

Issue - State: open - Opened by dianzhiyong almost 2 years ago - 5 comments

#103 - issue with exon sequences

Issue - State: open - Opened by annietaylor107 about 2 years ago

#102 - Problem with hybpiper check_dependencies 2.0.1

Issue - State: closed - Opened by antonambroa about 2 years ago - 1 comment

#101 - Locus sequence depth

Issue - State: open - Opened by andycrowl about 2 years ago - 1 comment

#100 - hybpiper.assemble - assemble - ERROR - ERROR: No genes with reads, exiting!

Issue - State: open - Opened by XiaoTW123 about 2 years ago - 10 comments

#99 - verions 2.0.1 tag/release

Issue - State: closed - Opened by pur80a about 2 years ago - 3 comments

#98 - Minimal outputs functionality

Issue - State: open - Opened by BenKuhnhaeuser about 2 years ago - 2 comments

#97 - ValueError: No records found in handle; stats and paralog_retriever

Issue - State: closed - Opened by SethMusker about 2 years ago - 5 comments

#96 - Very slow I/O?

Issue - State: closed - Opened by SethMusker about 2 years ago - 5 comments

#95 - Running in cluster

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

#94 - Issue with recovery_heatmap

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

#93 - Problem with get_inframe_targetfile.py.gz

Issue - State: closed - Opened by LuoChen2 over 2 years ago - 2 comments

#92 - Combining different hybpiper runs together?

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

#91 - Simplify heatmap width and height computation

Pull Request - State: closed - Opened by LPDagallier over 2 years ago - 1 comment

#90 - conda install with an bug report

Issue - State: closed - Opened by Fzhao89 over 2 years ago - 4 comments

#89 - Subprocess module fails when default shell is dash

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

#88 - Hybpiper run stuck at 'Potential paralogs detected' step

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

#87 - Running exonerate_hits for 387 genes.... One of them reported an error

Issue - State: closed - Opened by wudongyi534 over 2 years ago - 5 comments

#86 - the outputfile is not complete,FNA file is empty

Issue - State: open - Opened by Armeniacavulgaris over 2 years ago - 3 comments

#85 - hybpiper retrieve_sequences in directory without write permission

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

#84 - Error running the the dataset (HybPiper2 in macOS Monterey 12.4, chip M1)

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

#83 - hybpiper_stats.tsv file not generated with BLASTx hybpiper_assemble?

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

#81 - Hybpiper stats fails when namelist contains failed sample

Issue - State: closed - Opened by mossmatters over 2 years ago - 1 comment

#80 - Stitched contig and 'N' characters

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

#79 - Comments HybPiper v2

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

#78 - Fail to call Biopython 1.8

Issue - State: closed - Opened by hyyuu over 2 years ago - 6 comments

#77 - pyqt error_unable to create graphs

Issue - State: closed - Opened by abedoya250 over 2 years ago - 3 comments

#76 - spades - DEBUG - Deleting SPAdes assembly folder for gene gene002.

Issue - State: closed - Opened by hmqmuyang over 2 years ago - 5 comments

#75 - hybpiper cannot locate python packages.

Issue - State: closed - Opened by sun-jiao over 2 years ago - 5 comments

#74 - Missing Bio.Alphabet with Python 3.6, HybPiper 1.3

Issue - State: closed - Opened by V-Z over 2 years ago - 1 comment

#73 - The program ends early when SPAdes.py is executed

Issue - State: closed - Opened by RY970709 over 2 years ago - 6 comments

#72 - error with exonerate in new HybPiper version

Issue - State: closed - Opened by MareikeJaniak over 2 years ago - 10 comments

#71 - Problems executing spades.py

Issue - State: closed - Opened by RY970709 over 2 years ago - 2 comments

#70 - Develop

Pull Request - State: closed - Opened by chrisjackson-pellicle over 2 years ago

#69 - Issue with BWA

Issue - State: closed - Opened by sagesteppe over 2 years ago - 6 comments

#68 - Array HPC job

Issue - State: closed - Opened by isgilman about 3 years ago - 2 comments

#66 - How is the FAA document translated

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

#65 - get_seq_lengths.py and hybpiper_stats.py issues

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

#64 - hybpiper_stats.py can't locate .bam file issue

Issue - State: open - Opened by mdgn15 over 3 years ago - 4 comments

#63 - CPU and memory consumption

Issue - State: closed - Opened by mdgn15 over 3 years ago - 2 comments

#62 - Errors in coding sequences output by exonerate?

Issue - State: open - Opened by MareikeJaniak over 3 years ago

#59 - having a problem when using --unpaired

Issue - State: closed - Opened by PiraMew almost 4 years ago - 4 comments

#58 - spades not running on all genes for some samples

Issue - State: closed - Opened by willyard almost 4 years ago - 3 comments

#57 - depth_calculator.py working for some samples but not all??

Issue - State: closed - Opened by santosmalia about 4 years ago

#56 - distribute_reads_to_targets_bwa.py error

Issue - State: open - Opened by markusruhsam about 4 years ago - 4 comments

#55 - Add Dockerfile

Pull Request - State: open - Opened by nathanweeks over 4 years ago

#54 - problem with SpAdes

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

#53 - Fix shebang

Pull Request - State: open - Opened by joelnitta over 4 years ago

#52 - spades. py --cov-cutoff 8, is it possible to change this

Issue - State: closed - Opened by Deco313 over 4 years ago - 2 comments

#51 - Problem with reads_first.py

Issue - State: open - Opened by gubrins over 4 years ago - 1 comment

#50 - /bin/sh: 1: time: not found

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

#49 - exonerate_hits.py pauses at last gene

Issue - State: open - Opened by Paul-Donat almost 5 years ago - 4 comments

#48 - intronerate error

Issue - State: open - Opened by andycrowl almost 5 years ago - 3 comments

#47 - Running multiple samples on a server with a UNIX loop - BWA error

Issue - State: open - Opened by Ranhini almost 5 years ago - 3 comments

#46 - Hybpiper "sticking"

Issue - State: closed - Opened by tomwells-oxf almost 5 years ago - 2 comments

#45 - skip orientation...not enough pairs...names not identical

Issue - State: open - Opened by mforthman about 5 years ago - 1 comment

#44 - Number of files produced

Issue - State: closed - Opened by Jasmine0198 over 5 years ago - 2 comments

#43 - issue running get_seq_lengths.py

Issue - State: open - Opened by angelajmcd over 5 years ago - 6 comments

#42 - Error in distributing reads to gene directories

Issue - State: open - Opened by EBIshengoma over 5 years ago

#41 - intronerate IndexError: list index out of range error

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

#40 - ValueError: Sequence and quality captions differ

Issue - State: closed - Opened by ryansfuller about 6 years ago - 7 comments

#39 - Issue with distribute_targets.py

Issue - State: closed - Opened by Ptero64 about 6 years ago - 2 comments

#38 - exonerate_hits.py returning reverse-complement sequences

Issue - State: open - Opened by mossmatters over 6 years ago

#37 - jobs stopping (or going real slow) while spades running

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

#36 - distribute_reads_to_targets_bwa.py: progress meter

Issue - State: closed - Opened by biomendi over 6 years ago - 1 comment

#35 - SPAdes assembly ERROR due to low coverage

Issue - State: open - Opened by biomendi over 6 years ago - 10 comments

#34 - Heat map cleanup

Issue - State: closed - Opened by Wolflab about 7 years ago - 3 comments
Labels: enhancement

#33 - Run hanging in while loop

Issue - State: closed - Opened by akijarl about 7 years ago - 5 comments

#32 - distribute_targets.py ignores unpaired reads

Issue - State: closed - Opened by mossmatters about 7 years ago - 1 comment

#31 - Trouble with test dataset

Issue - State: closed - Opened by TARobison about 7 years ago - 2 comments

#29 - get_seq_lengths.py: unnecessary float -> string -> float conversions

Issue - State: closed - Opened by jttkim over 7 years ago - 1 comment

#28 - exonerate_hits.py: Hard-coded percent sequence identity threshold

Issue - State: closed - Opened by jttkim over 7 years ago - 1 comment