Argument is of length zero
Closed this issue · 9 comments
Hello!
I've managed to run some hg19 exomes through ClinCNV, but not that I'm attempting some b37 exomes, it crashes like so:
[1] "We run script located in folder /home/joel/Programs/ClinCNV . All the paths will be calculated realtive to this one. If everything crashes, please, check the correctness of this path first."
[1] "START cluster allocation."
[1] "Cluster allocated."
[1] "END cluster allocation."
[1] "We are started with reading the coverage files and bed files 2022-08-19 14:32:58"
[1] "Started basic quality filtering. 2022-08-19 14:33:00"
[1] "Amount of regions after filtering of 0-covered regions 94.373"
Error in if (ends_of_chroms[[chrom]] < max(bedFile[bedFile[, 1] == chrom, :
argument is of length zero
Execution halted
My input files are here:
https://file.io/rr1fFFpq8PzH
Thanks in advance!
Hi, there are chromosomes such as GL000228, but they are not by default included into the cytobands file https://github.com/imgag/ClinCNV/blob/master/cytobands.txt so ClinCNV does not know where to place them =)
Hello German, and thanks for such a speedy reply.
I have tried removing those non-standard contigs from my bams but the bam files become corrupted in the process no matter how I go about it. Is there instead a way to make ClinCNV ignore them? I've been dumping so many hours into this, I can't give up now!
Hi Jolleboll, ClinCNV does not know about your BAMs, so you don't need to do anything with them. Simply remove non-standard contigs from your BED file (before you count coverages, or remove from both BED and COV files).
Hello again German, I did what you suggested but still get the same error:
[1] "We run script located in folder /home/joel/Programs/ClinCNV . All the paths will be calculated realtive to this one. If everything crashes, please, check the correctness of this path first."
[1] "START cluster allocation."
[1] "Cluster allocated."
[1] "END cluster allocation."
[1] "We are started with reading the coverage files and bed files 2022-08-30 14:54:29"
[1] "Started basic quality filtering. 2022-08-30 14:54:31"
[1] "Amount of regions after filtering of 0-covered regions 94.373"
Error in if (ends_of_chroms[[chrom]] < max(bedFile[bedFile[, 1] == chrom, :
argument is of length zero
Execution halted
My inputs are here:
https://file.io/4SWgIx6LuRIE
Hi Jolleboll,
either remove chrM from your files or add chrM start/end in https://github.com/imgag/ClinCNV/blob/master/cytobands.txt =)
There is no chrM in cytobands
Right you are! I should have noticed. Anyway, new error now:
[1] "We run script located in folder /home/joel/Programs/ClinCNV . All the paths will be calculated realtive to this one. If everything crashes, please, check the correctness of this path first."
[1] "START cluster allocation."
[1] "Cluster allocated."
[1] "END cluster allocation."
[1] "We are started with reading the coverage files and bed files 2022-08-30 15:28:41"
[1] "Started basic quality filtering. 2022-08-30 15:28:43"
[1] "Amount of regions after filtering of 0-covered regions 94.372"
[1] "Normalization with GC and length starts. 2022-08-30 15:29:07"
[1] "Percentage of regions remained after GC correction: 0.998206912049738"
[1] "Amount of regions after GC-extreme filtering 94.203"
[1] "Amount of regions after Systematically Low Covered regions filtering 94.203"
[1] "We start to cluster your data (you will find a plot if clustering is possible in your output directory) /home/joel/Projects/Miscellaneous/Effie/ClinCNV/output/ctg_and_blueprint 2022-08-30 15:29:51"
Error: umap: number of neighbors must be smaller than number of items
Execution halted
Any idea what's going on? Thank you for your patience :)
That means you number of samples is really low. How many samples is in your cohort? ClinCNV works best with 15+ samples... With just several samples it can't efficiently normalize the data.
Right you are! I forgot I was running my test set of just eight samples. I now ran ~50 and it works fine. Thank you so much for all your help, German.
yeeeey! good luck with the analysis!