jtamames/SqueezeMeta issues and pull requests

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

Issue - State: closed - Opened by Shivabrahmam about 1 month ago - 11 comments

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

Issue - State: open - Opened by Biotrinf about 1 month ago - 1 comment

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

Issue - State: open - Opened by AntonioPuriel about 1 month ago - 4 comments

#843 - Understanding KEGG pathways output

Issue - State: open - Opened by da-shanmugapriya about 1 month ago - 3 comments

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

Issue - State: open - Opened by vmevada102 about 2 months ago - 4 comments

#841 - nrdmnd database issue

Issue - State: closed - Opened by abhirajnair2002 about 2 months ago - 1 comment

#840 - Issue with SQMtools

Issue - State: open - Opened by mradz19 about 2 months ago - 6 comments

#839 - SQMtools run in R

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

#838 - Is low taxonomic resolution to be expected?

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

#837 - loadSQM does not let me load the project

Issue - State: open - Opened by inej90 2 months ago - 1 comment

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

Issue - State: closed - Opened by mradz19 2 months ago - 15 comments

#835 - server not reachable

Issue - State: closed - Opened by abhirajnair2002 2 months ago - 3 comments

#834 - Program ending abruptly

Issue - State: closed - Opened by abhirajnair2002 2 months ago - 1 comment

#833 - restarting from step 10

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

#832 - Issue with download of database

Issue - State: closed - Opened by abhirajnair2002 2 months ago - 1 comment

#831 - Assembly error

Issue - State: open - Opened by abhirajnair2002 2 months ago - 11 comments

#830 - unable to down load databases

Issue - State: open - Opened by zuriashm 2 months ago - 2 comments

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

Issue - State: closed - Opened by MicroSeq 2 months ago - 8 comments

#828 - SQM_LONGREADS.PL died at line 933

Issue - State: open - Opened by inej90 3 months ago - 1 comment

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

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

#826 - Step 14 Not Progressing

Issue - State: closed - Opened by giovrosin 3 months ago - 9 comments

#825 - Workflow, tool version outline

Issue - State: open - Opened by s-junguy 3 months ago - 7 comments
Labels: enhancement

#824 - link to kegg database

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

#823 - Abundant phylum not being classified

Issue - State: closed - Opened by Manso002 3 months ago - 28 comments

#822 - Error in installation

Issue - State: closed - Opened by jmpe77 3 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: open - Opened by mojiefei 3 months ago - 4 comments

#820 - the sample file!

Issue - State: closed - Opened by Khattab2022 3 months ago

#819 - External database - CAZy Annotations missing.

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

#818 - Error when in step 1 Assembly with megahit

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

#817 - SQM for genomics

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

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

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

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

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

#814 - Question on diamond, block and ram usage

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

#813 - sqm2zip has stopped working?

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

#812 - Error in step 10

Issue - State: closed - Opened by cmaltec 4 months ago - 21 comments

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

Issue - State: closed - Opened by mingxues2024 4 months ago - 11 comments

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

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

#809 - -binners, just do maxbin

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

#808 - Missing file at step 10

Issue - State: closed - Opened by mradz19 4 months ago - 2 comments

#807 - cazy -extdb

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

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

Issue - State: closed - Opened by DioufMouss0 4 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 4 months ago - 6 comments

#804 - error for assembly

Issue - State: closed - Opened by laibinhuang 4 months ago - 15 comments

#803 - add databse erro

Issue - State: closed - Opened by Panda-smile 4 months ago

#802 - Can't open /home/lbhuang/Moore/results_2021/CA2021/results/01.CA2021.fasta

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

#801 - Assemble stopped abnormally.

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

#800 - sqm2itol.pl Died at sqm2itol.pl line 147.

Issue - State: closed - Opened by DioufMouss0 4 months ago - 8 comments

#799 - SQM with Flye assembly

Issue - State: closed - Opened by inej90 4 months ago - 5 comments

#798 - sqmitols.py erro

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

#797 - repeat lca assigment with custom diamond file

Issue - State: closed - Opened by bresyd 4 months ago - 4 comments

#796 - SQMTOOLS selection

Issue - State: closed - Opened by Panda-smile 4 months ago - 4 comments

#795 - exportKrona error

Issue - State: closed - Opened by diegorojasa 5 months ago - 11 comments

#794 - Python and R interpreter not found

Issue - State: closed - Opened by sakcham 5 months ago - 15 comments

#793 - rna sqmtools erro

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

#792 - Some SqueezeMeta dependencies could not be found

Issue - State: closed - Opened by Manso002 5 months ago - 5 comments

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

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

#790 - Error running Sequential mode with external assemblies

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

#789 - error running Merging contigs with minimus2

Issue - State: closed - Opened by DioufMouss0 5 months ago - 6 comments

#788 - How to group samples of the same treatments?

Issue - State: closed - Opened by DioufMouss0 5 months ago - 3 comments

#787 - erro in step 10

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

#786 - Error, fewer reads in file specified with -1 than in file specified with -2

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

#785 - erro in step1 coassembly~

Issue - State: closed - Opened by zhangbenbenchina 5 months ago - 25 comments

#784 - Installation Error

Issue - State: closed - Opened by RM9717 5 months ago - 4 comments

#783 - Stopped at Step 9/10, 29-01-24

Issue - State: closed - Opened by RM9717 5 months ago - 5 comments

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

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

#781 - SQMTools R upload Issue

Issue - State: closed - Opened by Whitehouse2610 5 months ago - 2 comments

#780 - Error in STEP 1 - 01.run_all_assemblies.pl.

Issue - State: closed - Opened by Manso002 5 months ago - 4 comments

#779 - test_install.pl I got many error

Issue - State: closed - Opened by fpeti11 5 months ago - 4 comments

#778 - itol

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

#777 - Mac installation of SqueezeMeta

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

#776 - SQMtools taxonomy output

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

#775 - Completeness and Contamination of bins are missing but the other parameters have values

Issue - State: closed - Opened by zcx970213 5 months ago - 2 comments

#774 - SqueezeMeta crashes when running on Ubuntu 22 virtualbox computer

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

#773 - PacBio data with minimap2 and flye

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

#772 - Issue with step 10 when submitting job on a condor server

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

#771 - Working with reads

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

#770 - Spades unequal amount of reads

Issue - State: closed - Opened by oyac 6 months ago - 10 comments
Labels: bug

#769 - Metatranscript

Issue - State: closed - Opened by zhangbenbenchina 6 months ago - 1 comment

#768 - Visualizar gráficos generados con R y SQMtools

Issue - State: closed - Opened by inej90 6 months ago - 5 comments

#767 - External bins

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

#766 - Illegal instruction (core dumped)

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

#765 - Error en los inputs (Please do not use blank spaces in the samples file)

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

#764 - SQMTools Error Error in subsetORFs

Issue - State: closed - Opened by johnbio12 7 months ago - 4 comments

#763 - Problem running the anvi-filter-sqm.py script SMQ2anvio

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

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

Issue - State: closed - Opened by gunj27 7 months ago - 13 comments

#761 - Problems with anvio-load-sqm (in the run-HMMs step)

Issue - State: closed - Opened by jahid10 7 months ago - 3 comments

#760 - Error creating taxid.db, please contact us!

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

#759 - Died at line 276 in sqm_longreads.pl

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

#758 - sqm_hmm_reads core dump error

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

#757 - 10.mapsamples.pl

Issue - State: closed - Opened by zhenzhao123 7 months ago - 3 comments

#756 - read counts

Issue - State: closed - Opened by zhenzhao123 7 months ago - 9 comments

#755 - "zip file is corrupt" when loading a zipped project into SQMtools

Issue - State: open - Opened by fpusan 8 months ago - 1 comment
Labels: bug, SQMtools

#754 - Benchmark data for HPC cluster

Issue - State: closed - Opened by fpeti11 8 months ago - 2 comments

#753 - i am facing the problem to analysing the Ion Torrent Reads.

Issue - State: closed - Opened by vmevada102 8 months ago - 11 comments

#752 - 01.run_all_assemblies.pl. Program finished abnormally

Issue - State: closed - Opened by zhenzhao123 8 months ago - 3 comments

#751 - 01.run_assembly.pl (megahit)

Issue - State: closed - Opened by zhenzhao123 8 months ago - 7 comments

#750 - Sample information problem

Issue - State: closed - Opened by zhenzhao123 8 months ago - 7 comments

#749 - The "tax" parameter of the "subsetTax" function could accept list of taxons

Issue - State: open - Opened by glenjasper 8 months ago - 3 comments
Labels: enhancement, SQMtools

#748 - Should unclassified and unmapped abundances be taken into account during gene abundance normalization?

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

#747 - Add the taxonomic category "Kingdom" for eukaryotes

Issue - State: open - Opened by glenjasper 8 months ago - 4 comments
Labels: enhancement, Taxonomic annotation

GitHub / jtamames/SqueezeMeta issues and pull requests