Issues

• orfm: command not found and hmmsearch: command not found

  wwood/singlem#321 · Filter by author SebasSaenz opened on Sep 4, 2026
  3

• Inquiry on interpretation of output results

  wwood/singlem#297 · Filter by author ZihengWu opened on Apr 15, 2026

• methodological niche & short or long reads

  wwood/singlem#296 · Filter by author xjhzjucas opened on Apr 9, 2026
  6

• SQLite "disk I/O error" when running under SLURM (works on login node)

  wwood/singlem#293 · Filter by author isidoramorel opened on Mar 31, 2026
  8

• trying to build a new eukaryotic species SingleM metapackage

  wwood/singlem#286 · Filter by author fanch1122 opened on Mar 10, 2026
  5

• ERROR: Process (DIAMOND?) failed

  wwood/singlem#282 · Filter by author LiZhihua1982 opened on Jan 19, 2026
  20

• OTU table

  wwood/singlem#268 · Filter by author Fatemeh-qasemnejad opened on Nov 28, 2025
  1

• How did you add off-target entries to metapackage?

  wwood/singlem#255 · Filter by author Andyargueasae opened on Sep 17, 2025
  13

• Downstream statisical tests

  wwood/singlem#224 · Filter by author lauramason326 opened on Jun 9, 2025
  4

• Species-wise EM within vs across samples

  wwood/singlem#222 · Filter by author lauramason326 opened on May 13, 2025
  12

• Output taxonomic-level-coverage has integer levels when 0% species

  wwood/singlem#214 · Filter by author AroneyS opened on Apr 7, 2025

• Applying singleM to single cell sequencing data

  wwood/singlem#206 · Filter by author lingrongjin opened on Jan 16, 2025
  10

• Comparing metagenome profiles with publicly available profiles from sandpiper

  wwood/singlem#192 · Filter by author adityabandla opened on Sep 11, 2024
  5

• Some potentially useful options to consider?

  wwood/singlem#164 · Filter by author adityabandla opened on Feb 26, 2024

• singlem incorrectly parse sample name with paired-end data

  wwood/singlem#151 · Filter by author fplazaonate opened on Nov 20, 2023
  5

• Question on alpha diveristy

  wwood/singlem#141 · Filter by author LanSabb opened on Sep 21, 2023

• Do singleM result be suitable for phylogenetic tree?

  wwood/singlem#137 · Filter by author LiZhihua1982 opened on Sep 2, 2023
  3

• Option to output site by species tables

  wwood/singlem#124 · Filter by author wwood opened on Mar 26, 2023

• singlem error with conda installation

  wwood/singlem#95 · Filter by author PuspenduSardar opened on Aug 4, 2022
  5

• Taxonomic assignment discrepancy

  wwood/singlem#81 · Filter by author ashwinssudarshan opened on May 28, 2021
  1

• using combined singlem pipe output

  wwood/singlem#77 · Filter by author slambrechts opened on Mar 21, 2021
  1

• Mismatching numbers of read names were observed

  wwood/singlem#76 · Filter by author kjvilardi opened on Mar 16, 2021
  4

• krona issue

  wwood/singlem#75 · Filter by author slambrechts opened on Mar 12, 2021
  2

• subprocess.CalledProcessError: while running GroopM2

  wwood/singlem#67 · Filter by author michaelwoodworth opened on Jan 19, 2021

• Targeting functional genes using SingleM

  wwood/singlem#62 · Filter by author daisyzhangsysu opened on Dec 18, 2020
  7