Ecosyste.ms: Issues

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

GitHub / jtamames/SqueezeMeta issues and pull requests

#792 - Some SqueezeMeta dependencies could not be found

Issue - State: closed - Opened by Manso002 8 months ago - 5 comments

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

Issue - State: closed - Opened by diegorojasa 8 months ago - 5 comments

#790 - Error running Sequential mode with external assemblies

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

#789 - error running Merging contigs with minimus2

Issue - State: closed - Opened by DioufMouss0 8 months ago - 6 comments

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

Issue - State: closed - Opened by DioufMouss0 8 months ago - 3 comments

#787 - erro in step 10

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

#785 - erro in step1 coassembly~

Issue - State: closed - Opened by zhangbenbenchina 8 months ago - 25 comments

#784 - Installation Error

Issue - State: closed - Opened by RM9717 8 months ago - 4 comments

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

Issue - State: closed - Opened by RM9717 8 months ago - 5 comments

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

Issue - State: closed - Opened by diegorojasa 8 months ago - 5 comments

#781 - SQMTools R upload Issue

Issue - State: closed - Opened by Whitehouse2610 8 months ago - 2 comments

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

Issue - State: closed - Opened by Manso002 8 months ago - 4 comments

#779 - test_install.pl I got many error

Issue - State: closed - Opened by fpeti11 8 months ago - 4 comments

#778 - itol

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

#777 - Mac installation of SqueezeMeta

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

#776 - SQMtools taxonomy output

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

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

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

#773 - PacBio data with minimap2 and flye

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

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

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

#771 - Working with reads

Issue - State: closed - Opened by inej90 9 months ago - 2 comments

#770 - Spades unequal amount of reads

Issue - State: closed - Opened by oyac 9 months ago - 10 comments
Labels: bug

#769 - Metatranscript

Issue - State: closed - Opened by zhangbenbenchina 9 months ago - 1 comment

#768 - Visualizar gráficos generados con R y SQMtools

Issue - State: closed - Opened by inej90 9 months ago - 5 comments

#767 - External bins

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

#766 - Illegal instruction (core dumped)

Issue - State: closed - Opened by rakeshkrpatra 9 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 10 months ago - 4 comments

#764 - SQMTools Error Error in subsetORFs

Issue - State: closed - Opened by johnbio12 10 months ago - 4 comments

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

Issue - State: closed - Opened by apazminov 10 months ago - 4 comments

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

Issue - State: closed - Opened by gunj27 10 months ago - 13 comments

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

Issue - State: closed - Opened by jahid10 10 months ago - 3 comments

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

Issue - State: closed - Opened by DeniRibicic 10 months ago - 4 comments

#759 - Died at line 276 in sqm_longreads.pl

Issue - State: closed - Opened by FloatingFloss 10 months ago - 5 comments

#758 - sqm_hmm_reads core dump error

Issue - State: closed - Opened by Tetrajf 10 months ago - 3 comments

#757 - 10.mapsamples.pl

Issue - State: closed - Opened by zhenzhao123 10 months ago - 3 comments

#756 - read counts

Issue - State: closed - Opened by zhenzhao123 11 months ago - 9 comments

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

Issue - State: open - Opened by fpusan 11 months ago - 1 comment
Labels: bug, SQMtools

#754 - Benchmark data for HPC cluster

Issue - State: closed - Opened by fpeti11 11 months ago - 2 comments

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

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

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

Issue - State: closed - Opened by zhenzhao123 11 months ago - 3 comments

#751 - 01.run_assembly.pl (megahit)

Issue - State: closed - Opened by zhenzhao123 11 months ago - 7 comments

#750 - Sample information problem

Issue - State: closed - Opened by zhenzhao123 11 months ago - 7 comments

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

Issue - State: open - Opened by glenjasper 11 months ago - 3 comments
Labels: enhancement, SQMtools

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

Issue - State: open - Opened by glenjasper 11 months ago - 4 comments
Labels: enhancement, Taxonomic annotation

#746 - STABLE VERSION REQUIRED!!! SQUEEZEMETA

Issue - State: closed - Opened by Michaelijesse 11 months ago - 1 comment

#745 - The pipeline stopped without finishing megahit

Issue - State: closed - Opened by feixiang1209 11 months ago - 2 comments

#744 - sqm_annot.pl fails at splitting Diamond file

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

#743 - Input error

Issue - State: closed - Opened by lam-c 11 months ago - 11 comments

#742 - Using sqm_annot.pl, died at line 223

Issue - State: closed - Opened by gracegyho 12 months ago - 2 comments

#741 - Problem with kmer-db installation

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

#740 - Can I obtain the latest version of the KEGG database using make.download.pl?

Issue - State: closed - Opened by Lafmas 12 months ago - 1 comment

#739 - sqm_longreads.pl taxonomy calls

Issue - State: closed - Opened by mscarbor 12 months ago - 3 comments

#738 - identify genenames annotated with one database with other.

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

#737 - minimap2 --version Segmentation fault

Issue - State: closed - Opened by jayramr 12 months ago - 3 comments

#736 - Incorporate MetaGeneMark in ORF prediction

Issue - State: closed - Opened by tboonf 12 months ago - 1 comment

#735 - anvio does not go until end

Issue - State: closed - Opened by Azimdine 12 months ago - 1 comment

#734 - problem with SqueezeMeta_conf.pl in anvio

Issue - State: closed - Opened by Azimdine almost 1 year ago - 7 comments

#733 - Issue with step 6

Issue - State: closed - Opened by DrJoshVandenbrink about 1 year ago - 28 comments

#732 - SQM to Phyloseq

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

#730 - Problem with step 10, and step 14

Issue - State: closed - Opened by jonaskohh about 1 year ago - 13 comments

#729 - SQMtools version

Issue - State: closed - Opened by HannahBenisty about 1 year ago - 12 comments

#728 - Test Data Failure

Issue - State: closed - Opened by NLZT about 1 year ago - 6 comments

#727 - Can't find sample file

Issue - State: closed - Opened by zhenzhao123 about 1 year ago - 9 comments

#726 - Calculating the RPKM value for species and phylum?

Issue - State: closed - Opened by lisiruisusan about 1 year ago - 2 comments

#725 - SQMTOOLS PLOTTAXONOMY 45º labels

Issue - State: closed - Opened by H1889 about 1 year ago - 3 comments

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

Issue - State: closed - Opened by Michaelijesse about 1 year ago - 26 comments

#723 - SPECIFICATION ENQUIRY FOR SQUEEZEMETA

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

#722 - Can you remove outdated flags for metabat2?

Issue - State: closed - Opened by mkbwang about 1 year ago - 3 comments

#721 - Can we analyze the fungal function?

Issue - State: closed - Opened by yjiakang about 1 year ago - 2 comments

#720 - download_database.pl failed

Issue - State: closed - Opened by yjiakang about 1 year ago - 2 comments

#719 - SQMtools subsetTax error

Issue - State: closed - Opened by mradz19 about 1 year ago - 4 comments

#718 - assembly error

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

#717 - Formatting external database

Issue - State: closed - Opened by mradz19 about 1 year ago - 1 comment

#716 - ERROR: STEP14 -> BINNING & STEP 18 checkM_batch.pl

Issue - State: closed - Opened by sogada about 1 year ago - 7 comments

#715 - Problem with $installpath in SqueezeMeta

Issue - State: closed - Opened by lichen-fungus about 1 year ago - 8 comments

#714 - Can't open samples file (-s) in /data/00..samples.

Issue - State: closed - Opened by lichen-fungus about 1 year ago - 2 comments

#713 - restart

Issue - State: closed - Opened by HannahBenisty about 1 year ago - 14 comments

#712 - Are the rRNA gene sequences removed?

Issue - State: closed - Opened by yjiakang about 1 year ago - 8 comments

#711 - KEGG database

Issue - State: closed - Opened by alicegrih about 1 year ago - 3 comments

#710 - How to extract sequences for a specific KEGG ID

Issue - State: closed - Opened by mradz19 about 1 year ago - 8 comments

#709 - Error in Spades assembly (ver1.6.2 post3)

Issue - State: closed - Opened by RIJP-SU about 1 year ago - 10 comments

#708 - Exit code -9

Issue - State: closed - Opened by AntonioPuriel about 1 year ago - 2 comments

#707 - Stopping in STEP4

Issue - State: closed - Opened by RIJP-SU about 1 year ago - 13 comments

#706 - Faillure : Stopping in STEP18 -> 17.checkM_batch.pl

Issue - State: closed - Opened by bbalog87 about 1 year ago - 5 comments

#705 - Checking all installs

Issue - State: closed - Opened by bioforkgithub over 1 year ago - 11 comments

#703 - restart at step 10 question

Issue - State: closed - Opened by bresyd over 1 year ago - 8 comments

#702 - Run stopped during step 10 due to missing files

Issue - State: closed - Opened by mradz19 over 1 year ago

#701 - Using dedupe.sh to identify and remove contigs contained in others (merged mode)

Issue - State: open - Opened by eperezv over 1 year ago - 2 comments
Labels: enhancement, merged mode, Assembly, seqmerge mode

#698 - Determining the abundance of bins

Issue - State: closed - Opened by mradz19 over 1 year ago - 1 comment

#697 - Species Abundance with different higher levels of Taxa names

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

#695 - STEP10 - frozen at sqm_counter

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

#694 - STEP10 -> 10.mapsamples.pl.

Issue - State: closed - Opened by kostovci over 1 year ago - 25 comments

#693 - Squeezemeta warning for STEP15

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