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

#662 - Error in Step4

Issue - State: closed - Opened by liuyinan19922 over 1 year ago - 2 comments

#661 - SqueezeMeta Step 1 Error: Failing in Megahit Assembly

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

#660 - Abundance plots

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

#659 - Error occurs when reading inputs

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

#658 - External database

Issue - State: closed - Opened by lisiruisusan over 1 year ago - 26 comments

#657 - Error: plotFunctions with metadata_groups parameter

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

#656 - A binning issue

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

#655 - Remove outliers when plotting nMDS

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

#654 - Illegal division by zero

Issue - State: closed - Opened by blaizereal over 1 year ago - 22 comments

#653 - Query regarding TPM calculation of KO

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

#652 - SQMlite coding error

Issue - State: closed - Opened by phlienhart over 1 year ago - 13 comments

#651 - How to specify memory and core parameter in command line?

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

#650 - 1.6.2

Pull Request - State: closed - Opened by fpusan over 1 year ago

#649 - SQM Tools 1.6.0 compatability with sqm_longreads.pl?

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

#648 - SqueezeMeta Takes almost One day at STEP 4

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

#647 - SQMtools version and numpy

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

#646 - combining tables of bins from unique folders

Issue - State: closed - Opened by croth204 over 1 year ago - 5 comments

#645 - Stuck at "solving enviroment"

Issue - State: closed - Opened by msanchezr99 over 1 year ago - 5 comments

#644 - SQMtools: loadSQM Error

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

#643 - Error at step 04.rundiamond.pl

Issue - State: closed - Opened by jahid10 over 1 year ago - 7 comments

#642 - Two -miniden cut-off for same Run

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

#641 - Error in subsetORFs

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

#640 - TPM and RPKM calculation inconsistent

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

#639 - Bin TPM

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

#638 - Conda recipe conflict - Perl version and dependency conflicts

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

#637 - Stopping in STEP10: Error: No input read files were valid

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

#636 - error at step 4 rundiamond.pl

Issue - State: closed - Opened by jahid10 over 1 year ago - 2 comments

#635 - GTDB with SqueezeMeta

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

#634 - Unknown option 'restart' when restarting a step

Issue - State: closed - Opened by jahid10 over 1 year ago - 2 comments

#633 - re-start with added options

Issue - State: closed - Opened by spongebob22 over 1 year ago - 7 comments

#632 - Stats on reads

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

#631 - doublepass post completion

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

#630 - Can I resume a sqm_longreads.pl run?

Issue - State: closed - Opened by jllavin77 over 1 year ago - 2 comments

#629 - Issue at Diamond FIle splitting and LCA

Issue - State: closed - Opened by vmevada102 over 1 year ago - 5 comments

#628 - Getting error in running Squeezemeta

Issue - State: closed - Opened by vmevada102 over 1 year ago - 4 comments

#627 - error in loadSQM

Issue - State: closed - Opened by Nykolazzo72 over 1 year ago - 6 comments

#626 - Running flye on fasta.gz

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

#625 - Having zero variances in the metabat2 depth file leads to less bins

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

#624 - Argument checking in SqueezeMeta.pl would prevent the use of custom assemblers?

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

#623 - How to run run sqm_hmm_reads.pl for fastq?

Issue - State: closed - Opened by luozhy88 over 1 year ago - 2 comments

#622 - mamba install not working

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

#621 - KEGG databse version

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

#620 - anvi-load-sqm.py : process stops midway and does not create the PROFILES.db

Issue - State: closed - Opened by Sneha-bioinfo over 1 year ago - 5 comments
Labels: sqm2anvio

#619 - run sqm_hmm_reads.pl error!

Issue - State: closed - Opened by luozhy88 over 1 year ago - 10 comments

#618 - minimum contig length can affect memory requirements?

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

#617 - Problem with loadSQM in local machine

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

#616 - pip install?

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

#615 - CD-HIT taking too long when running in merged mode. Is it as expected?

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

#614 - Analysing multiple metagenomes individually made into contigs

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

#613 - ways to reduce contamination from a particular taxon

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

#612 - Error at assembly with canu

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

#611 - Advice on rarefying data

Issue - State: closed - Opened by mradz19 over 1 year ago - 2 comments

#610 - Problem with database download

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

#609 - option parser issue

Issue - State: open - Opened by moritzbuck over 1 year ago - 1 comment
Labels: enhancement

#608 - what is the meaning of percentage in case of subsetting.

Issue - State: closed - Opened by jahid10 over 1 year ago - 2 comments

#607 - Changing gradient color and font size in plotFunction SQMtools

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

#606 - Bins refinement in anvio

Issue - State: closed - Opened by azam17 over 1 year ago - 1 comment

#604 - large percentage of unclassified taxon from family level.

Issue - State: closed - Opened by jahid10 over 1 year ago - 9 comments

#603 - Issues at step-10

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

#601 - Problem with external database

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

#598 - Is it possible running SQM in Merged mode with MinION long reads?

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

#593 - minimus2,spend 5 days!

Issue - State: closed - Opened by luozhy88 over 1 year ago - 2 comments

#592 - 01.run_assembly.pl. Program finished abnormally

Issue - State: closed - Opened by jahid10 over 1 year ago - 2 comments

#591 - Restart resumes from step 3 even if step 2 failed

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

#590 - Unclassified terminology

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

#587 - Error in aggregate.data.frame...

Issue - State: closed - Opened by SMOKO2022 over 1 year ago - 6 comments

#586 - sqm_reads.pl fails if -p is set to an absolute path instead of a relative one

Issue - State: open - Opened by fpusan over 1 year ago
Labels: bug, SQM_reads, sqm_longreads

#585 - MetaCyc pathways

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

#584 - can't find nr.db there, or it is corrupted

Issue - State: closed - Opened by Yaooo999 over 1 year ago - 3 comments

#578 - The database download seems to be stuck in the LCA_tax step

Issue - State: closed - Opened by Yaooo999 over 1 year ago - 5 comments

#576 - Large amount of unmapped reads

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

#571 - Restart keeps adding sample names at the end of contigs in merged mode?

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

#559 - Run stops at diamond process

Issue - State: closed - Opened by sakcham over 1 year ago - 21 comments

#553 - Trimmomatic option

Issue - State: closed - Opened by luozhy88 almost 2 years ago - 11 comments

#547 - Error in STEP 14

Issue - State: closed - Opened by EorgeKit almost 2 years ago - 12 comments

#506 - Support for EggNOG version 5.0.2

Issue - State: open - Opened by mdehollander about 2 years ago - 2 comments
Labels: enhancement, databases

#474 - Installing SQMtools in Windows or Mac (including RStudio)

Issue - State: closed - Opened by fpusan about 2 years ago - 3 comments
Labels: good first issue, SQMtools

#458 - Step 1.5 seqmerge crash

Issue - State: closed - Opened by phagelab over 2 years ago - 23 comments

#456 - Update SQMtools (and R recommendation) to >4.0

Issue - State: closed - Opened by fpusan over 2 years ago - 2 comments
Labels: enhancement

#416 - sqm2tables.py - All fixes in one place :-)

Issue - State: open - Opened by biobrad over 2 years ago - 8 comments
Labels: SQMtools

#367 - release dates of databases downloaded

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

#297 - sqm_counter

Issue - State: closed - Opened by chandnisidhu about 3 years ago - 14 comments

#258 - Stopping in STEP1 -> 01.run_assembly.pl issue

Issue - State: closed - Opened by leehwmj over 3 years ago - 20 comments