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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length #144

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago 
Tissues to be included: leaf, flower, root, photosynthetic_leaf
Both counts and effective length files found: Melastoma_candidum
Starting Rscript to obtain curated log2p1-fpkm values.
Warning messages:
1: package ‘pcaMethods’ was built under R version 4.1.3 
2: package ‘Biobase’ was built under R version 4.1.3 
Warning message:
package ‘colorspace’ was built under R version 4.1.3 
Warning message:
package ‘RColorBrewer’ was built under R version 4.1.3 
Warning message:
package ‘MASS’ was built under R version 4.1.3 
Warning messages:
1: package ‘NMF’ was built under R version 4.1.3 
2: package ‘pkgmaker’ was built under R version 4.1.3 
3: package ‘registry’ was built under R version 4.1.3 
4: package ‘rngtools’ was built under R version 4.1.3 
5: package ‘cluster’ was built under R version 4.1.3 
Warning message:
package ‘dendextend’ was built under R version 4.1.3 
Warning message:
package ‘amap’ was built under R version 4.1.3 
Warning message:
package ‘pvclust’ was built under R version 4.1.3 
Warning message:
package ‘Rtsne’ was built under R version 4.1.3 
transcriptome_curation.r: mode = batch 
est_counts_path: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data/cstmm/Melastoma_candidum/Melastoma_candidum_cstmm_counts.tsv 
metadata_path: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data/cstmm/metadata.tsv 
out_dir: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data 
eff_length_path: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data/cstmm/Melastoma_candidum/Melastoma_candidum_eff_length.tsv 
dist_method: pearson 
mapping_rate_cutoff: 0.2 
min_dif: 0 
plot_intermediate: FALSE 
selected_curate_groups: leaf flower root photosynthetic_leaf 
transform_method: log2p1-fpkm 
one_outlier_per_iteration: 0 
correlation_threshold: 0.3 
batch_effect_alg: sva 
clip_negative: TRUE 
Warning messages:
1: package ‘sva’ was built under R version 4.1.3 
2: package ‘mgcv’ was built under R version 4.1.3 
3: package ‘nlme’ was built under R version 4.1.3 
4: package ‘genefilter’ was built under R version 4.1.3 
5: package ‘BiocParallel’ was built under R version 4.1.3 
transcriptome_curation.r: Working at: /Volumes/kfT7/Dropbox/data/evolutionary_transcriptomics/20230527_gfe_pipeline/gfe_data/curate 
Number of SRA runs for this species: 6 
Number of SRA runs for selected curate groups: 4493 
Number of non-excluded SRA runs (exclusion=="no"): 5 
Applying FPKM transformation.
Applying log_2(x+1) normalization.
Removing samples with mapping rate of 0.
Mapping rate cutoff: 0%
No entry removed due to low mapping rate.
initial  value 0.041213 
final  value 0.000000 
converged
No significant surrogate variables
SVA correction was correctly performed.
Number of negative values clipped to zero: 0/231,980 (46,396 x 5 matrix)
initial  value 0.041213 
final  value 0.000000 
converged
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
Calls: save_plot ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
Execution halted