AAError in get.oturep

I’m trying to run get.oturep and keep getting this error

get.oturep(column=bac_final.sm.dist, list=bac_final.an.list, name=bac_final.names)

Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||AAError: Sequence ‘HVP’ was not found in the names file, please correct

I've searched the dist, list, and names files. I have lots of sequences the begin with HVP but didn't find any that were just HVP. I'm running 1.31

I uploaded the files onto the wiki

When I run your files with set.dir(debug=t), I see:


Did you run dist.seqs with processors > 1? We had a recent report, .dist file with more than 3 columns of merging issues when the user ran out of disk space.

Thanks Sarah, I’ll try again. so weird that grep 'HPV ’ didn’t catch that. I think I did use multiple processors creating this dist file (using cluster.split) but it was a few months ago so will take some digging to find the correct logfile

hum, so I found that error when I ran debug=t. it seems like that sequence pair was duplicated because the line above it is

HVPQ45002I7MT7 GM0HNNG02B3VLN 0.1858

But I’m not able to find it through grep. went ahead and opened the whole thing in vim. the actual last 2 lines of the dist file are

HVPQ45002I7MT7 GM0HNNG02B3VLN 0.1858

I deleted the last line and am trying get.oturep again. HVPQ45002 is the last plate for that batch of sequences but I’m not certain that the file truncated properly