SaelinB
commented
1 year ago I realized that the problem were the missing columns, and I fixed it by removing "Missing" columns from the busco file. However now I get this issue:
[Sun Jul 16 14:57:09 2023] #BLOCK Generated 10946 synteny blocks.
[Sun Jul 16 14:57:10 2023] #BLOCK Reduced to 156 synteny blocks based on minregion=INT filtering.
`summarise()` has grouped output by 'Genome', 'HitGenome', 'SeqName', 'Hit'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'Genome', 'HitGenome', 'SeqName'. You can override using the `.groups` argument.
[Sun Jul 16 14:57:10 2023] #FOCUS Focal genome for orientation: scaffold16_size3654323
[Sun Jul 16 14:57:11 2023] Warning: problem with missing seqname for scaffold28_size2676831
Error in if (is.na(seqname)) { : argTument is of length zero
Calls: seqRev
Execution haltedI removed scaffold28_size2676831.fa from my analysis just to check, which worked further but then I get different errors about seq names:
[Sun Jul 16 15:00:54 2023] #SAVE All chromsyn data output to chromsyn.xlsx
1 plot(s)...Generating plot...(1) 10%
[Sun Jul 16 15:00:54 2023] Warning: problem with missing seqname for NA
[Sun Jul 16 15:00:54 2023] Warning: problem with missing seqname for NA
<simpleError in if (fwd) { pD <- data.frame(x = c(xa1, xa2, xb2, xb1), y = c(ya, ya, yb, yb)) if (settings$ypad) { pD <- data.frame(x = c(xa1, xa1, xa2, xa2, xb2, xb2, xb1, xb1), y = c(ya2, ya, ya, ya2, yb2, yb, yb, yb2))
} plt <- plt + geom_polygon(data = pD, mapping = aes(x = x, y = y), fill = "steelblue", color = NA, alpha = settings$opacity)} else { pD <- data.frame(x = c(xa1, xa2, xb1, xb2), y = c(ya, ya, yb, yb)) if (settings$ypad) {
pD <- data.frame(x = c(xa1, xa1, xa2, xa2, xb1, xb1, xb2, xb2), y = c(ya2, ya, ya, ya2, yb2, yb, yb, yb2)) } plt <- plt + geom_polygon(data = pD, mapping = aes(x = x, y = y), fill = "indianred", color = NA, alpha = settings$opa
city)}: missing value where TRUE/FALSE needed>
[Sun Jul 16 15:00:54 2023] #ERROR Error in if (fwd) {: missing value where TRUE/FALSE needed
=> splitting plot into 2
2 plot(s)...Generating plot...(1) 16.7%
[Sun Jul 16 15:00:54 2023] Warning: problem with missing seqname for NA
[Sun Jul 16 15:00:54 2023] Warning: problem with missing seqname for NA
<simpleError in if (fwd) { pD <- data.frame(x = c(xa1, xa2, xb2, xb1), y = c(ya, ya, yb, yb)) if (settings$ypad) { pD <- data.frame(x = c(xa1, xa1, xa2, xa2, xb2, xb2, xb1, xb1), y = c(ya2, ya, ya, ya2, yb2, yb, yb, yb2))
} plt <- plt + geom_polygon(data = pD, mapping = aes(x = x, y = y), fill = "steelblue", color = NA, alpha = settings$opacity)} else { pD <- data.frame(x = c(xa1, xa2, xb1, xb2), y = c(ya, ya, yb, yb)) if (settings$ypad) {
pD <- data.frame(x = c(xa1, xa1, xa2, xa2, xb1, xb1, xb2, xb2), y = c(ya2, ya, ya, ya2, yb2, yb, yb, yb2)) } plt <- plt + geom_polygon(data = pD, mapping = aes(x = x, y = y), fill = "indianred", color = NA, alpha = settings$opa
city)}: missing value where TRUE/FALSE needed> this error keeps going. I am analyzing a single chromosome from different assemblies, so each fasta file has a single sequence
cabbagesofdoom
Hello, thanks for making this tool! I'm trying to run chromsyn but I get this error:
Rscript chromsyn.R busco=busco.fofn seqeuneces=sequences.fofn focus=scaffold16_size3654323
It seems to think the format is v3, but this is what my scaffold13_size4067469.busco5.tsv looks like:
Any ideas on how to fix this?