Issues

• Genomad end-to-end error: "Directory not empty: PosixPath(X)"

  apcamargo/genomad#186 · Filter by author miagrego opened on Sep 25, 2026
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• Recommendations for job resources

  apcamargo/genomad#182 · Filter by author nickp60 opened on May 18, 2026
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• plasmid identification in geNomad

  apcamargo/genomad#181 · Filter by author lungphage opened on Apr 26, 2026
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• Feature Request: Support iterative MMseqs2 sensitivity search for the Annotate module

  apcamargo/genomad#180 · Filter by author timghaly opened on Apr 22, 2026

• 33 hidden (binary) files mixed in with the profile HMMs in zenodo release

  apcamargo/genomad#177 · Filter by author traviswheeler opened on Mar 28, 2026
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• Feature request: DRAM-v compatibility

  apcamargo/genomad#175 · Filter by author Madhavbash opened on Feb 11, 2026
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• stopped at marker classification

  apcamargo/genomad#174 · Filter by author Caiyulu-818 opened on Feb 2, 2026
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• CalledProcessError - mmseqs align failed

  apcamargo/genomad#173 · Filter by author KailunZM opened on Dec 8, 2025

• output file names and summary directory name are truncated after a period in the prefix

  apcamargo/genomad#172 · Filter by author mflynn-lanl opened on Dec 1, 2025

• inquiry on attL/attR region

  apcamargo/genomad#171 · Filter by author LanSabb opened on Nov 26, 2025
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• tf version when using gctf to train seq_banch

  apcamargo/genomad#170 · Filter by author Persiapinkman opened on Nov 26, 2025
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• Bug when running end-to-end pipeline report and fix

  apcamargo/genomad#166 · Filter by author andreaniml opened on Sep 20, 2025
  9

• Issue: SIGILL error during mmseqs createdbin geNomad end-to-end execution​

  apcamargo/genomad#165 · Filter by author JustinRaoV opened on Aug 25, 2025

• free(): double free detected in tcache 2 Aborted (core dumped)

  apcamargo/genomad#162 · Filter by author TimoZhou1024 opened on Jul 4, 2025
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• genomad predict most of the contigs frrom sequencing as plasmids, while the majority should be chromosome.

  apcamargo/genomad#161 · Filter by author dzjxzyd opened on Jul 3, 2025
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• OSError: [Errno 12] Cannot allocate memory even with low --splits values

  apcamargo/genomad#158 · Filter by author jpinus opened on Jun 13, 2025
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• Low taxonomic resolution for prophages

  apcamargo/genomad#157 · Filter by author rpalcab opened on Jun 12, 2025
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• Is genomad applicable to both genome (DNA, Illumina) and transcriptome data (RNA, Illumina) obtained from plant sequencing?

  apcamargo/genomad#153 · Filter by author zhangwenda0518 opened on Apr 24, 2025
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• inquiry on result intepretation

  apcamargo/genomad#151 · Filter by author LanSabb opened on Mar 25, 2025
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• Unable to access database via zenodo weblink

  apcamargo/genomad#150 · Filter by author nkuyfq opened on Mar 24, 2025
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• geNomad Issue, no idea how to fix

  apcamargo/genomad#145 · Filter by author YuhanGiraffe opened on Feb 21, 2025
  11

• The question about calculation formula for SPM

  apcamargo/genomad#144 · Filter by author zzzfire opened on Jan 29, 2025
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• Question about geNomad’s marker dataset

  apcamargo/genomad#142 · Filter by author ZihengWu opened on Jan 14, 2025
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• plasmid/chromosome/virus Classification problem

  apcamargo/genomad#141 · Filter by author darwin4442 opened on Jan 8, 2025
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• Qinviridae classified as Paramyxoviridae

  apcamargo/genomad#137 · Filter by author LanderDC opened on Dec 16, 2024
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