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ani heatmap rendering fails #15

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cahuparo opened this issue May 1, 2024 · 0 comments
Open

ani heatmap rendering fails #15

cahuparo opened this issue May 1, 2024 · 0 comments

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@cahuparo
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cahuparo commented May 1, 2024

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.

@cahuparo cahuparo changed the title ani matrix rendering fails ani heatmap rendering fails May 1, 2024
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