Error in { : task 3 failed - "object 'contig' not found"
Calls: %dopar% ->
Execution halted
Done!
Calculating fixation index FST starting at: 26/09/2023 00:11:14...Done!
Calculating and visualizing Macrodiversity starting at: 26/09/2023 00:11:32...Error in uniroot(d1fun, c(1, 50), extendInt = "upX", S = S, N = N, ...) :
did not succeed extending the interval endpoints for f(lower) * f(upper) <= 0
Calls: fisher.alpha -> apply -> FUN -> uniroot
In addition: Warning message:
In log(1 + N/x) : NaNs produced
Execution halted
Done!
Visualizing preprocessing starting at: 26/09/2023 00:11:36...Warning message:
In overall_summaries$finish_counts[match(c_d_names, overall_summaries$sample)] <- finish_read_counts :
number of items to replace is not a multiple of replacement length
There were 50 or more warnings (use warnings() to see the first 50)
null device
1
Done!
Visualizing Microdiversity starting at: 26/09/2023 00:16:26...[1] "MetaPop/01.Genomes_and_Genes/base_corrected_genomes.fa"
[1] "MetaPop/01.Genomes_and_Genes/base_corrected_genes.fa"
null device
1
null device
1
[1] "Creating local scale SNP plots..."
Error in fread("MetaPop/10.Microdiversity/local_gene_microdiversity.tsv", :
File 'MetaPop/10.Microdiversity/local_gene_microdiversity.tsv' does not exist or is non-readable. getwd()=='/data/lcp/viru_result/diversity'
Execution halted
Here are some specific points:
While calculating microdiversity, there was an error indicating that the object 'contig' was not found.
There was another error regarding the file 'MetaPop/10.Microdiversity/local_gene_microdiversity.tsv', which seems to be missing or not readable.
In addition to these, there were some warnings and errors in other steps as well, such as during the calculation of the fixation index FST and the visualization of macrodiversity.
Can you please guide me on how to fix these issues? I appreciate any help you can provide.
Hi,
I encountered some errors and warnings while trying to calculate and visualize microdiversity using MetaPop. Here are the logs:
[[20]] [1] "data.table" "stats" "graphics" "grDevices" "utils"
[6] "datasets" "methods" "base"
Error in { : task 3 failed - "object 'contig' not found" Calls: %dopar% ->
Execution halted
Done!
Calculating fixation index FST starting at: 26/09/2023 00:11:14...Done!
Calculating and visualizing Macrodiversity starting at: 26/09/2023 00:11:32...Error in uniroot(d1fun, c(1, 50), extendInt = "upX", S = S, N = N, ...) :
did not succeed extending the interval endpoints for f(lower) * f(upper) <= 0
Calls: fisher.alpha -> apply -> FUN -> uniroot
In addition: Warning message:
In log(1 + N/x) : NaNs produced
Execution halted
Done!
Visualizing preprocessing starting at: 26/09/2023 00:11:36...Warning message:
In overall_summaries$finish_counts[match(c_d_names, overall_summaries$sample)] <- finish_read_counts :
number of items to replace is not a multiple of replacement length
There were 50 or more warnings (use warnings() to see the first 50)
null device
1
Done!
Visualizing Microdiversity starting at: 26/09/2023 00:16:26...[1] "MetaPop/01.Genomes_and_Genes/base_corrected_genomes.fa"
[1] "MetaPop/01.Genomes_and_Genes/base_corrected_genes.fa"
null device
1
null device
1
[1] "Creating local scale SNP plots..."
Error in fread("MetaPop/10.Microdiversity/local_gene_microdiversity.tsv", :
File 'MetaPop/10.Microdiversity/local_gene_microdiversity.tsv' does not exist or is non-readable. getwd()=='/data/lcp/viru_result/diversity'
Execution halted
Here are some specific points:
In addition to these, there were some warnings and errors in other steps as well, such as during the calculation of the fixation index FST and the visualization of macrodiversity.
Can you please guide me on how to fix these issues? I appreciate any help you can provide.
Thank you!