I ran the make.shared command: make.shared(list=V4_515F_New_V4_806R_New_designfile.trim.contigs.good.pick.pick.pick.chop.unique.an.list, group=V4_515F_New_V4_806R_New_designfile.contigs.good.pick.pick.pick.groups, label=0.03)
And received this message:
Your group file contains 1073527 sequences and list file contains 875594 sequences. Please correct.
Output File Names:
I can’t find the shared file anywhere in my files and I’m guessing because there’s a difference in sequence number between the list and group files. I was wondering if anyone has had a similar problem or if someone knows how to go about producing a shared file?
If I had to guess it’s because you chopped your sequences and that there were sequences shorter than what you chopped them to that were tossed, but weren’t also removed from your groups file. Why are you chopping them instead of using the SOP approach?
This was also happening before I chopped them. I had a majority of my reads between 291 - 293 (~880,000), some 465 (~20,000). Cluster.split wants all reads at the same length, so I was trying to keep as much as possible and chopped those reads from 293 and 292 to 291. I ended up losing quite a bit of sequences which I’m not sure how. But was able to make a shared file eventually after using the list file to create an accnos file, then used that to create an updated group file so that the # of sequences matched in the group and list file for the make.shared command.
Could you recommend another way of going about it?
Mismatches in between files most often occur when a file is omitted from a command or a typo in a filename causes an older version of a file to be used. Since you had the mismatch at the chop.seqs command, can you post the commands in the log file you ran before that?