I ran the following commands :
remove.rare(list=fichier.ITS1.trim.precluster.phylip.an.list, nseqs=0, label=0.03)"
but in make.shared, i got the following error :
[ERROR]: HWUYNKI01A is in your listfile and not in your groupfile. Please correct.
Your group file contains 67399 sequences and list file contains 67400 sequences. Please correct.
I’ve checked the listfile and the groupfiles and there is no HWUYNKI01A
all my sequences names have more letter then that (some begin with HWUYNKI01A, but there supposed to be more letter after that)
I can’t find the bug, could you help me please ?
Hmm… seems odd. Why are you trying to remove OTUs with 0 sequences in them? There shouldn’t be any. Did you manually modify the files? If you send your files to email@example.com I can take a look?
I just send the files to the bugs mail
I seem to have similar kind of trouble after.
remove.groups(list=stomaP.final.fn.0.05.abund.list, taxonomy=stomaP.final.0.05.abund.HOMD.wang.taxonomy, name=stomaP.final.names, group=stomaP.final.0.05.abund.groups,fasta=stomaP.final.0.05.abund.fasta, groups=10-20-30-40-50-60-70-80-90-100-110-120-MOCK)
Previously with all the groups still in them they made shares file without complaints.
if I remove some groups and try it now, then new list and group file wont match anymore.
make.shared(list=stomaP.final.fn.0.05.abund.pick.list, group=stomaP.final.0.05.abund.pick.groups, label=0.05)
will produce two kinds of errors/notifications.
[ERROR]: DBNW5DQ1_135_C092BACXX_8_1102_2523_32850_1_N_0_CGATGT_3B029 is in your listfile and not in your groupfile. Please correct.
DBNW5DQ1_135_C092BACXX_8_1204_15783_34226_1_N_0_CGATGT_1B060 is in your list file more than once. Sequence names must be unique. please correct.
Patg13 error was due to an outside program he used to create the files. Could you send your log file and input files to firstname.lastname@example.org so I can track down the issue?