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I got this error when rendering the report locally:
processing file: index.qmd |....................... | 52% [ani_heatmap] Quitting from lines 268-269 [ani_heatmap] (index.qmd) Error in `.rowNamesDF<-`: ! missing values in 'row.names' are not allowed Backtrace: 1. psminer::make_ani_heatmap(ani_matrix * 100, ref_data, sample_data) 2. base::`rownames<-`(`*tmp*`, value = name_key[rownames(ani_matrix)]) 4. base::`row.names<-.data.frame`(`*tmp*`, value = value) 5. base::`.rowNamesDF<-`(x, value = value)
Here is how ref_data looks like for one of the samples:
reference_id Id LastMajorReleaseAccession AssemblyName Taxid Organism SpeciesTaxid SpeciesName AssemblyType AssemblyStatus Coverage PartialGenomeRepresentation ReleaseLevel ReleaseType RefSeq_category SubmissionDate LastUpdateDate ContigN50 ScaffoldN50 genus GCF_025961545_1 14287871 GCF_025961545.1 ASM2596154v1 375 Bradyrhizobium japonicum (a-proteobacteria) 375 Bradyrhizobium japonicum haploid Contig 164 false Major Major na 2022/11/02 00:00 2022/11/04 00:00 10943673 10943673 Bradyrhizobium GCF_024808455_1 13565421 GCF_024808455.1 ASM2480845v1 1079467 Bradyrhizobium japonicum USDA 38 (a-proteobacteria) 375 Bradyrhizobium japonicum haploid Contig 188 false Major Major na 2022/08/31 00:00 2022/09/02 00:00 9740125 9740125 Bradyrhizobium GCF_000284375_1 408298 GCF_000284375.1 ASM28437v1 1037409 Bradyrhizobium japonicum USDA 6 (a-proteobacteria) 375 Bradyrhizobium japonicum haploid Complete Genome 30 false Major Major na 2011/10/31 00:00 2012/08/07 00:00 9207384 9207384 Bradyrhizobium GCF_005157565_1 2758391 GCF_005157565.1 ASM515756v1 108015 Bradyrhizobium yuanmingense (a-proteobacteria) 108015 Bradyrhizobium yuanmingense haploid Chromosome 30 false Major Major na 2019/05/06 00:00 2022/11/14 00:00 8288891 8288991 Bradyrhizobium GCF_900324035_1 1723271 GCF_900324035.1 BRAD3257 1549949 Bradyrhizobium vignae (a-proteobacteria) 1549949 Bradyrhizobium vignae haploid Complete Genome 85 false Major Major representative genome 2018/05/23 00:00 2018/11/01 00:00 8156021 8156021 Bradyrhizobium GCF_011516625_4 12611291 GCF_011516625.4 ASM1151662v4 1404429 Bradyrhizobium sp. 2S1 (a-proteobacteria) 1404429 Bradyrhizobium sp. 2S1 haploid Contig 809 false Major Major na 2022/04/27 00:00 2022/04/29 00:00 10825806 10825806 Bradyrhizobium GCF_017565645_3 11411811 GCF_017565645.3 ASM1756564v3 2823807 Bradyrhizobium barranii subsp. barranii (a-proteobacteria) 2992140 Bradyrhizobium barranii haploid Complete Genome 149 false Major Major na 2021/11/09 00:00 2021/11/11 00:00 10692809 10692809 Bradyrhizobium GCF_036924615_1 21576551 GCF_036924615.1 ASM3692461v1 3117026 Bradyrhizobium sp. AZCC 2289 (a-proteobacteria) 3117026 Bradyrhizobium sp. AZCC 2289 haploid Contig 54 false Major Major na 2024/02/29 00:00 2024/03/02 00:00 10450701 10450701 Bradyrhizobium GCF_023101685_1 12588371 GCF_023101685.1 ASM2310168v1 2782654 Bradyrhizobium sp. 186 (a-proteobacteria) 2782654 Bradyrhizobium sp. 186 haploid Complete Genome 114 false Major Major na 2022/04/25 00:00 2022/04/27 00:00 10413025 10413025 Bradyrhizobium GCF_024199885_1 13241671 GCF_024199885.1 ASM2419988v1 2949630 Bradyrhizobium sp. CCGUVB23 (a-proteobacteria) 2949630 Bradyrhizobium sp. CCGUVB23 haploid Scaffold 439 false Major Major na 2022/07/10 00:00 2022/07/13 00:00 10227124 10227124 Bradyrhizobium
Here is the ani_matrix first row:
13A3_4_S76,11A5_5_S73,18A4_3_S86,12A2_2_S75,17A3_1_S83,14A2_2_S78,15K7_7_S221,14A3_1_S79,1A2_1_S60,12A1_1_S74,10K2_8_S213,10A2_2_S72,15A3_2_S80,18A2_2_S85,13A4_3_S77,2A6_8_S61,12F2_2_S108,16A1_2_S81,19A1_4_S87,5A2_2_S63,20A1_6_S88,8A1_2_S69,5A4_2_S64,9A4_8_S71,9A2_1_S70,17A6_3_S84,6K1_1_S207,20K3_10_S229,7A8_3_S68,7A4_7_S67,20A3_10_S89,16A2_2_S82,6A5_9_S66,GCF_000284375_1,GCF_036924615_1,GCF_007830635_1,GCF_023101685_1,GCF_024808455_1,GCF_011516625_4,GCF_900324035_1,GCF_017565645_3,GCF_025961545_1,GCF_002776695_1,GCF_018130685_1,GCF_004346455_1,GCF_900094605_1,GCF_000617845_2,GCF_024199885_1,GCF_000261785_1__CCBAU05623_By
The reference provided by the user was GCF_000261785_1__CCBAU05623_By but the ref_data for the samples does not contain the ref provided by the user.
GCF_000261785_1__CCBAU05623_By
The text was updated successfully, but these errors were encountered:
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I got this error when rendering the report locally:
Here is how ref_data looks like for one of the samples:
Here is the ani_matrix first row:
The reference provided by the user was
GCF_000261785_1__CCBAU05623_By
but the ref_data for the samples does not contain the ref provided by the user.The text was updated successfully, but these errors were encountered: