Comments (3)
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 halted
I 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
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Another update.. I've found by testing one-by-one that it is 4 out of the 12 sequences that throw this error when they are included, although I see no differences in the files .. when this error occurs it also creates chromsyn-[1-3].pdf and .png files multiple times
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Sorry, I am at a conference and did not see the issue when you raised it. Yes, if the first row of the BUSCO file is Missing then it fails to recognise the right BUSCO version. I will get this bug fixed.
The other error is more intriguing. Would you be OK sharing your input data with me? You can email me at [email protected].
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