Long time lurker first time poster.
I’m running into a similar issue. I’m analyzing some PacBio full-length data and the .count_table does not seem to be populating with group information. I do have group information until the initial formation of the count_table, then it seems to go sideways. So, considering I’m able to form a group table, I’m presuming the information is there, right? We’re also interested in holding onto group information throughout so we can determine where reads are being lost.
I tried Sarah’s suggestion above with this to try to resolve it early in the process:
mothur fastq.info(file=fixrun.files, checkorient=T, pacbio=T, qfile=F)
mothur count.groups(group=fixrun.group) - have group file populated
mothur screen.seqs(fasta=fixrun.fasta, group=fixrun.group, maxambig=0, minlength=1478, maxlength=1559, maxhomop=8) - still looks good
mothur count.groups(group=fixrun.good.group) -have groups populated
mothur unique.seqs(fasta=fixrun.good.fasta, name=fixrun.good.group, output=count)
[ERROR]: Your count file does not have any group information, aborting.
[ERROR]: did not complete count.groups.
Any insight would be welcome. Everything else seems to work well, but I just can’t seem to find where the issue lies where group info is being disconnected from the rest of the data.
I ended up figuring out a workaround using v1.46.1 using the following. Wouldn’t work in 1.47 due to the lack of a name file being produced. I’d still be interested in suggestions moving forward if the names and groups files are going to be removed from new versions.
fastq.info(file=fixrun.files, checkorient=T, pacbio=T, qfile=F)
screen.seqs(fasta=current, maxambig=0, maxhomop=6, bdiffs=0, pdiffs=0, minlength=1478, maxlength=1559, maxhomop=8)