Closed enriquepola1996 closed 1 month ago
Hi, it looks like there might have been a parsing error with the fasta, as there is a space in the filenames between fungal
and _T9
. I think this is within the divergence_calc.py script. @jamesdgalbraith might have a better insight into this. We are also about to push some updates that I am testing at the moment which might solve this...
Hello, I repeated the run and this time it finished and generated the graphs, I'm just worried that at the end of the process warnings and an error appeared:
log file:
[9] "/home/enriquepola/earlgrey_ascomycota/earlGreyOutputs_Ascomycota/fungal_T9_kmer_EarlGrey/fungal_T9_kmer_summaryFiles/fungal_T9_kmer.summaryPie.pdf"
[10] "/home/enriquepola/earlgrey_ascomycota/earlGreyOutputs_Ascomycota/fungal_T9_kmer_EarlGrey/fungal_T9_kmer_summaryFiles/fungal_T9_kmer.highLevelCount.txt"
Splitting repeat library
Reading in gff
Starting calculations
Finished calculations
Total run time for 11605 rows was 333.69530034065247 seconds
Warning message:
Removed 2 rows containing missing values or values outside the scale range
(`geom_col()`).
Warning message:
Removed 2 rows containing missing values or values outside the scale range
(`geom_col()`).
Error in combine_vars(data, params$plot_env, rows, drop = params$drop) :
At least one layer must contain all faceting variables: `subclass`
✖ Plot is missing `subclass`
✖ Layer 1 is missing `subclass`
Warning messages:
1: Removed 1 row containing missing values or values outside the scale range
(`geom_col()`).
2: Graphs cannot be vertically aligned unless the axis parameter is set. Placing graphs unaligned.
........
<<< TE library, Summary Figures, and TE Quantifications in Standard Formats Can Be Found in /home/enriquepola/earlgrey_ascomycota/earlGreyOutputs_Ascomycota/fungal_T9_kmer_EarlGrey/fungal_T9_kmer_summaryFiles/ >>>
The process ended with these results:
(base) enriquepola@DESKTOP-62E8R2K:~/earlgrey_ascomycota/earlGreyOutputs_Ascomycota/fungal_T9_kmer_EarlGrey/fungal_T9_kmer_summaryFiles$ ls
fungal_T9_kmer-families.fa.strained fungal_T9_kmer.summaryPie.pdf
fungal_T9_kmer.familyLevelCount.txt fungal_T9_kmer_classification_landscape.pdf
fungal_T9_kmer.filteredRepeats.bed fungal_T9_kmer_combined_library.fasta
fungal_T9_kmer.filteredRepeats.gff fungal_T9_kmer_split_class_landscape.pdf
fungal_T9_kmer.highLevelCount.txt fungal_T9_kmer_superfamily_div_plot.pdf
fungal_T9_kmer.softmasked.fasta
Hi, this is okay. The R warnings are because the Rscript has to be generic enough to account for all TE families, some of which will not be found in your species of interest. I haven't silenced the warnings as they are sometimes useful for debugging, but you have the expected files!
I can double-check for you to be sure - could you attachfungal_T9_kmer.filteredRepeats.gff
and fungal_T9_kmer.highLevelCount.txt
here if that is okay? I can double check you get the required results
Yes @TobyBaril . fungal_T9_kmer.filteredRepeats.gff.txt fungal_T9_kmer.highLevelCount.txt
In the end my command was:
earlGrey -g fungal_T9_kmer.fasta -s fungal_T9_kmer -t 8 -r Ascomycota -d yes -o ./earlGreyOutputs_Ascomycota
Thank so much for your support.
Hi @enriquepola1996, I've had a look at the outputs and the summaries look correct. Feel free to reach out if you have any other questions!
Thanks so much.
Hello, thank you very much for this nice tool, I am running a fungal genome for the first time but it seems that there was a problem at the end, "Could not understand FASTA index", how could I solve this? At the exit, only a pdf returned to me.
I will greatly appreciate the help.
My installation:
My commands:
My output fyles:
My log file: