apcamargo/genomad issues and pull requests

#43 - Issues running genomad

Issue - State: open - Opened by david1ibarra over 1 year ago - 1 comment

#42 - Assistance Needed: Unexpected Error and Output Truncation During geNomad Tool Execution

Issue - State: open - Opened by david1ibarra over 1 year ago - 4 comments

#41 - Error: prokka: Failed to download resource "aragorn"

Issue - State: closed - Opened by AnnaaaaaaaaV over 1 year ago - 7 comments

#40 - Understanding Inputs and Outputs

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

#39 - Possibility to include NAs in taxonomy csv format for easier parsing?

Issue - State: closed - Opened by LanderDC over 1 year ago - 10 comments

#38 - enable-score-calibration option

Issue - State: closed - Opened by elozanoe over 1 year ago - 7 comments

#37 - Input file does not exist error

Issue - State: closed - Opened by Elle-ctricity over 1 year ago - 4 comments

#36 - aragorn package does not exist

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

#35 - question about nn-classification

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

#34 - mmseqs prefilter error: database has wrong type

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

#33 - Taxonomy changed when input contigs are different

Issue - State: closed - Opened by xwu35 over 1 year ago - 10 comments

#32 - FileNotFoundError

Issue - State: closed - Opened by chengzhongyi8 over 1 year ago - 5 comments

#31 - Provirus detection changes when more input is given

Issue - State: closed - Opened by nikolasbasler over 1 year ago - 3 comments

#30 - Is it safe to run genomad directly on nanopore R10.4.1 long reads?

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

#29 - Would there be a smaller database available to use for testing?

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

#28 - Is there a way to get the annotate outputs in a genbank format file?

Issue - State: open - Opened by liliancaesarbio over 1 year ago - 9 comments

#27 - nn-classification module uses all available CPUs instead of the limit set by --threads

Issue - State: closed - Opened by jamesck2 over 1 year ago - 9 comments

#26 - Is it better to run geNomad on single genome assemblies?

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

#25 - mmseqs2 prefilter failed: No k-mer could be extracted for the database genomad_db/genomad_db

Issue - State: closed - Opened by haleyhallowell over 1 year ago - 4 comments

#24 - Does prediction with no coordinates indicate the whole sequences is a viral sequence?

Issue - State: closed - Opened by shenwei356 over 1 year ago - 2 comments

#23 - How to organize the file structure of geNomad database

Issue - State: closed - Opened by shenwei356 over 1 year ago - 1 comment

#22 - Can genomad be applied to the metagenome bin?

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

#21 - mmseqs2 prefilter requires too much memory

Issue - State: closed - Opened by Bgi-zsy over 1 year ago - 3 comments

#20 - Long fasta headers with white spaces may interfere with downstream processing

Issue - State: closed - Opened by Werner0 almost 2 years ago - 4 comments

#19 - Difference between "Unclassified" and "Viruses" taxonomy?

Issue - State: closed - Opened by ecampbell50 almost 2 years ago - 7 comments

#18 - decrease in the number of hits with the new version

Issue - State: closed - Opened by kayanac almost 2 years ago - 20 comments

#17 - Too many threads used in numpy and tensorflow

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

#16 - Tenserflow error for nn-classification

Issue - State: closed - Opened by michoug almost 2 years ago - 4 comments

#15 - UnicodeEncodeError

Issue - State: closed - Opened by cody-mar10 almost 2 years ago - 3 comments

#14 - Processing many genomes

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

#13 - provirus info appears in find_proviruses/provirus.tsv but lost in summary/summary.tsv

Issue - State: closed - Opened by yumenghao2021 almost 2 years ago - 4 comments

#12 - AttributeError

Issue - State: closed - Opened by deminatanja almost 2 years ago - 6 comments

#11 - mmseqs2: returned non-zero exit status 1.

Issue - State: closed - Opened by MonicaSteffi almost 2 years ago - 19 comments

#10 - `OSError: Could not find/load shared object file: libllvmlite.so` from broken conda-forge package. Found fix with using numba channel.

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

#9 - Non-detailed taxonomy classification. Possibility of IMG/VR database integration

Issue - State: closed - Opened by poursalavati about 2 years ago - 10 comments

#8 - KeyError: 'provirus_names' when running genomad score_calibration

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

GitHub / apcamargo/genomad issues and pull requests