jtamames/SqueezeMeta issues and pull requests

#892 - SQMtools v1.6.3 incompatibility with SqueezeMeta v1.6.5

Issue - State: closed - Opened by itirg 15 days ago - 2 comments

#891 - Problems with filtering the host genome

Issue - State: open - Opened by neokie-sun 24 days ago - 3 comments

#890 - SQMtools for functional analysis

Issue - State: closed - Opened by Alexa2279 about 1 month ago - 2 comments

#889 - Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

Issue - State: open - Opened by AntonioPuriel about 1 month ago - 14 comments

#888 - Contradictory results after sequential and coassembly modes comparison

Issue - State: closed - Opened by Selucote82 about 1 month ago - 2 comments

#887 - Stopping in STEP1 Died at /home/user/miniconda3/envs/squeezemeta/bin/SqueezeMeta.pl line 941

Issue - State: closed - Opened by MSJennyLee about 1 month ago - 2 comments

#886 - stopped at step 14

Issue - State: closed - Opened by Ayush09-cmd about 1 month ago - 6 comments

#885 - Error in loading SQM - version conflict

Issue - State: closed - Opened by Whitehouse2610 about 1 month ago - 4 comments

#884 - Projects cannot been loaded in SQMtools

Issue - State: closed - Opened by Selucote82 about 2 months ago - 3 comments

#883 - Missing dependencies with Conda installation

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

#882 - --restart is not running

Issue - State: closed - Opened by AntonioPuriel about 2 months ago - 16 comments

#881 - Dereplication step after sequential mode with long reads

Issue - State: closed - Opened by Selucote82 about 2 months ago - 5 comments

#880 - stop in step10

Issue - State: open - Opened by mingxues2024 about 2 months ago - 7 comments

#879 - SqueezeMeta manual unavailable

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

#878 - cores and ram allocated to Squeezemeta

Issue - State: closed - Opened by Alexa2279 about 2 months ago - 2 comments

#877 - Metagenomics

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

#876 - Died at line 941

Issue - State: closed - Opened by Selucote82 about 2 months ago - 5 comments

#875 - Option to continue making database

Issue - State: closed - Opened by Harpreet525 2 months ago - 5 comments

#874 - died at line 969

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

#873 - Assembly error or real contig?

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

#872 - For the results from sqm2table

Issue - State: closed - Opened by mingxues2024 2 months ago - 2 comments

#871 - Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

Issue - State: closed - Opened by Ayush09-cmd 2 months ago - 6 comments

#870 - Can't open conf file

Issue - State: closed - Opened by mingxues2024 2 months ago - 3 comments

#869 - sqm2tables.py

Issue - State: closed - Opened by mingxues2024 2 months ago - 4 comments

#868 - Error: Stopping in STEP10 -> 10.mapsamples.pl. File Sample1/intermediate/10.Sample1.mapcount is empty!

Issue - State: closed - Opened by eoinoh91 3 months ago - 15 comments

#867 - SqueezeMeta stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally

Issue - State: closed - Opened by ankurnaqib 3 months ago - 3 comments

#866 - sqm_reads.pl appears to be stuck while running

Issue - State: closed - Opened by mycomira 3 months ago - 3 comments

#865 - running the program from data on a hardrive

Issue - State: closed - Opened by gene-pool-CY 3 months ago - 6 comments

#864 - Metagenome Assembly and SqueezeMeta Configuration

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

#863 - Stopping in STEP4 -> 04.rundiamond.pl. Program finished abnormally

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

#862 - For running specific step

Issue - State: closed - Opened by mingxues2024 3 months ago - 2 comments

#861 - GPU accelerated

Issue - State: closed - Opened by gene-pool-CY 3 months ago - 1 comment

#860 - Error Encountered in SqueezeMeta with PacBio data

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

#859 - Normalization of abundances

Issue - State: closed - Opened by inej90 3 months ago - 2 comments

#858 - Issue using combineSQM

Issue - State: closed - Opened by Whitehouse2610 3 months ago - 2 comments

#857 - SqueezeMeta_conf.pl

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

#856 - test_install.pl: Error with minimap2 and kmer-db

Issue - State: closed - Opened by Selucote82 3 months ago - 6 comments

#855 - metaFlye

Issue - State: closed - Opened by athavars 4 months ago - 6 comments

#854 - Taxonomy abundance from SQM object

Issue - State: closed - Opened by Vincev454 4 months ago - 1 comment

#853 - RESTART SEQUENTIAL MODE

Issue - State: open - Opened by EorgeKit 4 months ago - 9 comments

#852 - How to combine the results analized by 'sequential mode'

Issue - State: closed - Opened by mingxues2024 4 months ago - 3 comments

#851 - antimicrobial function SQMlite

Issue - State: closed - Opened by inej90 4 months ago - 2 comments

#850 - Ways to speed up runtime

Issue - State: closed - Opened by Vincev454 4 months ago - 9 comments

#849 - Metadata connections SQMtools

Issue - State: open - Opened by inej90 4 months ago - 1 comment
Labels: enhancement

#848 - Problem to load SQM project

Issue - State: closed - Opened by inej90 4 months ago - 3 comments

#847 - Stopping in STEP5

Issue - State: closed - Opened by guianrey 4 months ago - 5 comments

#846 - Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

Issue - State: closed - Opened by Shivabrahmam 4 months ago - 11 comments

#845 - Stopping in STEP4 -> 04.rundiamond.pl

Issue - State: closed - Opened by Biotrinf 4 months ago - 3 comments

#844 - Stopping in STEP1 -> 01.run_all_assemblies.pl. Program finished abnormally

Issue - State: closed - Opened by AntonioPuriel 5 months ago - 4 comments

#843 - Understanding KEGG pathways output

Issue - State: closed - Opened by da-shanmugapriya 5 months ago - 4 comments

#842 - Stopping in STEP10 -> 10.mapsamples.pl. Program finished abnormally Line no 18

Issue - State: closed - Opened by vmevada102 5 months ago - 5 comments

#841 - nrdmnd database issue

Issue - State: closed - Opened by abhirajnair2002 5 months ago - 1 comment

#840 - Issue with SQMtools

Issue - State: closed - Opened by mradz19 5 months ago - 9 comments

#839 - SQMtools run in R

Issue - State: closed - Opened by AntonioPuriel 5 months ago - 4 comments

#838 - Is low taxonomic resolution to be expected?

Issue - State: closed - Opened by chrismitbiz 5 months ago - 3 comments

#837 - loadSQM does not let me load the project

Issue - State: closed - Opened by inej90 5 months ago - 2 comments

#836 - Illegal division by zero in step 18.getbins.pl

Issue - State: closed - Opened by mradz19 5 months ago - 18 comments

#835 - server not reachable

Issue - State: closed - Opened by abhirajnair2002 5 months ago - 3 comments

#834 - Program ending abruptly

Issue - State: closed - Opened by abhirajnair2002 5 months ago - 1 comment

#833 - restarting from step 10

Issue - State: closed - Opened by timyerg 5 months ago - 4 comments

#832 - Issue with download of database

Issue - State: closed - Opened by abhirajnair2002 5 months ago - 1 comment

#831 - Assembly error

Issue - State: closed - Opened by abhirajnair2002 5 months ago - 12 comments

#830 - unable to down load databases

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

#829 - Binning Issues - Failure to generate outputs in intermediate/binners folder.

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

#828 - SQM_LONGREADS.PL died at line 933

Issue - State: closed - Opened by inej90 6 months ago - 2 comments

#827 - Died at /root/micromamba/envs/SqueezeMeta/bin/SqueezeMeta.pl line 239

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

#826 - Step 14 Not Progressing

Issue - State: closed - Opened by giovrosin 6 months ago - 9 comments

#825 - Workflow, tool version outline

Issue - State: open - Opened by s-junguy 6 months ago - 7 comments
Labels: enhancement

#824 - link to kegg database

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

#823 - Abundant phylum not being classified

Issue - State: closed - Opened by Manso002 6 months ago - 28 comments

#822 - Error in installation

Issue - State: closed - Opened by jmpe77 6 months ago - 8 comments

#821 - How to use data obtained from other software to start from the middle of the steps of SqueezeMeta and run the subsequent steps?

Issue - State: closed - Opened by mojiefei 6 months ago - 5 comments

#820 - the sample file!

Issue - State: closed - Opened by Khattab2022 6 months ago

#819 - External database - CAZy Annotations missing.

Issue - State: open - Opened by da-shanmugapriya 6 months ago - 7 comments
Labels: bug

#818 - Error when in step 1 Assembly with megahit

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

#817 - SQM for genomics

Issue - State: closed - Opened by inej90 7 months ago - 4 comments

#816 - How to set the output path of the Sequential mode?

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

#815 - Illegal division by zero in step 18.getbins.pl - at calculating coverage

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

#814 - Question on diamond, block and ram usage

Issue - State: closed - Opened by eperezv 7 months ago - 5 comments

#813 - sqm2zip has stopped working?

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

#812 - Error in step 10

Issue - State: closed - Opened by cmaltec 7 months ago - 21 comments

#811 - Can not open k141.final.contigs.fa. Now exit to system...'

Issue - State: closed - Opened by mingxues2024 7 months ago - 11 comments

#810 - 10.mapsamples.pl. Program finished abnormally

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

#809 - -binners, just do maxbin

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

#808 - Missing file at step 10

Issue - State: closed - Opened by mradz19 7 months ago - 2 comments

#807 - cazy -extdb

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

#806 - anvi-filter-sqm.py Config Error

Issue - State: closed - Opened by DioufMouss0 7 months ago - 5 comments

#805 - STEP4 -> HOMOLOGY SEARCH || Error: Database was built with a different version of Diamond and is incompatible

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

#804 - error for assembly

Issue - State: closed - Opened by laibinhuang 7 months ago - 15 comments

#803 - add databse erro

Issue - State: closed - Opened by Panda-smile 7 months ago

GitHub / jtamames/SqueezeMeta issues and pull requests