Hi, I am trying to run my make.shared file following my phylotype command. However, when I run my make.shared I get the error:
[ERROR]: No definition for type shared output pattern.
Then each of my samples gets removed because all the sequences have been removed. I thought the shared output pattern would be defined by my label.
Here are the last few lines of code:
classify.seqs(classify.seqs(fasta=/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.fasta, count=/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80, relabund=T, processors=8)
It took 741 secs to classify 734453 sequences.
It took 45 secs to create the summary file for 734453 sequences.
Output File Names:
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.tax.summary
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.flip.accnos
remove.lineage(fasta=/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.fasta, count=/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, taxonomy=/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)
Output File Names:
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.accnos
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pick.fasta
phylotype(taxonomy=/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.taxonomy)
Output File Names:
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.sabund
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.rabund
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.list
make.shared(list=/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.list, count=/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.count_table, label=1)
[ERROR]: No definition for type shared output pattern.
Removing group: 10A_T_0 because all sequences have been removed.
Removing group: 10A_T_1 because all sequences have been removed.
Removing group: 10A_T_14 because all sequences have been removed.
Removing group: 10A_T_3 because all sequences have been removed.
Removing group: 10A_T_30 because all sequences have been removed.
Removing group: 10A_T_7 because all sequences have been removed.
Removing group: 10B_T_0 because all sequences have been removed.
Removing group: 10B_T_1 because all sequences have been removed.
Removing group: 10B_T_14 because all sequences have been removed.
Removing group: 10B_T_3 because all sequences have been removed.
Removing group: 10B_T_30 because all sequences have been removed.
Removing group: 10B_T_7 because all sequences have been removed.
Removing group: 10C_T_0 because all sequences have been removed.
Removing group: 10C_T_1 because all sequences have been removed.
Removing group: 10C_T_14 because all sequences have been removed.
Removing group: 10C_T_3 because all sequences have been removed.
Removing group: 10C_T_30 because all sequences have been removed.
Removing group: 10C_T_7 because all sequences have been removed.
Removing group: 11A_T_0 because all sequences have been removed.
Removing group: 11A_T_1 because all sequences have been removed.
Removing group: 11A_T_14 because all sequences have been removed.
Removing group: 11A_T_3 because all sequences have been removed.
Removing group: 11A_T_30 because all sequences have been removed.
Removing group: 11A_T_7 because all sequences have been removed.
Removing group: 11B_T_0 because all sequences have been removed.
Removing group: 11B_T_1 because all sequences have been removed.
Removing group: 11B_T_14 because all sequences have been removed.
Removing group: 11B_T_3 because all sequences have been removed.
Removing group: 11B_T_30 because all sequences have been removed.
Removing group: 11B_T_7 because all sequences have been removed.
Removing group: 12A_T_0 because all sequences have been removed.
Removing group: 12A_T_1 because all sequences have been removed.
Removing group: 12A_T_14 because all sequences have been removed.
Removing group: 12A_T_3 because all sequences have been removed.
Removing group: 12A_T_30 because all sequences have been removed.
Removing group: 12A_T_7 because all sequences have been removed.
Removing group: 12B_T_0 because all sequences have been removed.
Removing group: 12B_T_1 because all sequences have been removed.
Removing group: 12B_T_14 because all sequences have been removed.
Removing group: 12B_T_3 because all sequences have been removed.
Removing group: 12B_T_30 because all sequences have been removed.
Removing group: 12B_T_7 because all sequences have been removed.
Removing group: 1A_T_0 because all sequences have been removed.
Removing group: 1A_T_1 because all sequences have been removed.
Removing group: 1A_T_14 because all sequences have been removed.
Removing group: 1A_T_3 because all sequences have been removed.
Removing group: 1A_T_30 because all sequences have been removed.
Removing group: 1A_T_7 because all sequences have been removed.
Removing group: 1B_T_0 because all sequences have been removed.
Removing group: 1B_T_1 because all sequences have been removed.
Removing group: 1B_T_14 because all sequences have been removed.
Removing group: 1B_T_3 because all sequences have been removed.
Removing group: 1B_T_30 because all sequences have been removed.
Removing group: 1B_T_7 because all sequences have been removed.
Removing group: 2A_T_0 because all sequences have been removed.
Removing group: 2A_T_1 because all sequences have been removed.
Removing group: 2A_T_14 because all sequences have been removed.
Removing group: 2A_T_3 because all sequences have been removed.
Removing group: 2A_T_30 because all sequences have been removed.
Removing group: 2A_T_7 because all sequences have been removed.
Removing group: 2B_T_0 because all sequences have been removed.
Removing group: 2B_T_1 because all sequences have been removed.
Removing group: 2B_T_14 because all sequences have been removed.
Removing group: 2B_T_3 because all sequences have been removed.
Removing group: 2B_T_30 because all sequences have been removed.
Removing group: 2B_T_7 because all sequences have been removed.
Removing group: 4A_T_0 because all sequences have been removed.
Removing group: 4A_T_1 because all sequences have been removed.
Removing group: 4A_T_14 because all sequences have been removed.
Removing group: 4A_T_3 because all sequences have been removed.
Removing group: 4A_T_30 because all sequences have been removed.
Removing group: 4A_T_7 because all sequences have been removed.
Removing group: 4B_T_0 because all sequences have been removed.
Removing group: 4B_T_1 because all sequences have been removed.
Removing group: 4B_T_14 because all sequences have been removed.
Removing group: 4B_T_3 because all sequences have been removed.
Removing group: 4B_T_30 because all sequences have been removed.
Removing group: 4B_T_7 because all sequences have been removed.
Removing group: 4C_T_0 because all sequences have been removed.
Removing group: 4C_T_1 because all sequences have been removed.
Removing group: 4C_T_14 because all sequences have been removed.
Removing group: 4C_T_3 because all sequences have been removed.
Removing group: 4C_T_30 because all sequences have been removed.
Removing group: 4C_T_7 because all sequences have been removed.
Removing group: 5A_T_0 because all sequences have been removed.
Removing group: 5A_T_1 because all sequences have been removed.
Removing group: 5A_T_14 because all sequences have been removed.
Removing group: 5A_T_3 because all sequences have been removed.
Removing group: 5A_T_30 because all sequences have been removed.
Removing group: 5A_T_7 because all sequences have been removed.
Removing group: 5B_T_0 because all sequences have been removed.
Removing group: 5B_T_1 because all sequences have been removed.
Removing group: 5B_T_14 because all sequences have been removed.
Removing group: 5B_T_3 because all sequences have been removed.
Removing group: 5B_T_30 because all sequences have been removed.
Removing group: 5B_T_7 because all sequences have been removed.
Removing group: 6A_T_0 because all sequences have been removed.
Removing group: 6A_T_1 because all sequences have been removed.
Removing group: 6A_T_14 because all sequences have been removed.
Removing group: 6A_T_3 because all sequences have been removed.
Removing group: 6A_T_30 because all sequences have been removed.
Removing group: 6A_T_7 because all sequences have been removed.
Removing group: 6B_T_0 because all sequences have been removed.
Removing group: 6B_T_1 because all sequences have been removed.
Removing group: 6B_T_14 because all sequences have been removed.
Removing group: 6B_T_3 because all sequences have been removed.
Removing group: 6B_T_30 because all sequences have been removed.
Removing group: 6B_T_7 because all sequences have been removed.
Removing group: 7A_T_0 because all sequences have been removed.
Removing group: 7A_T_1 because all sequences have been removed.
Removing group: 7A_T_14 because all sequences have been removed.
Removing group: 7A_T_3 because all sequences have been removed.
Removing group: 7A_T_30 because all sequences have been removed.
Removing group: 7A_T_7 because all sequences have been removed.
Removing group: 7B_T_0 because all sequences have been removed.
Removing group: 7B_T_1 because all sequences have been removed.
Removing group: 7B_T_14 because all sequences have been removed.
Removing group: 7B_T_3 because all sequences have been removed.
Removing group: 7B_T_30 because all sequences have been removed.
Removing group: 7B_T_7 because all sequences have been removed.
Removing group: 8A_T_0 because all sequences have been removed.
Removing group: 8A_T_1 because all sequences have been removed.
Removing group: 8A_T_14 because all sequences have been removed.
Removing group: 8A_T_3 because all sequences have been removed.
Removing group: 8A_T_30 because all sequences have been removed.
Removing group: 8A_T_7 because all sequences have been removed.
Removing group: 8B_T_0 because all sequences have been removed.
Removing group: 8B_T_1 because all sequences have been removed.
Removing group: 8B_T_14 because all sequences have been removed.
Removing group: 8B_T_3 because all sequences have been removed.
Removing group: 8B_T_30 because all sequences have been removed.
Removing group: 8B_T_7 because all sequences have been removed.
Removing group: 9A_T_0 because all sequences have been removed.
Removing group: 9A_T_1 because all sequences have been removed.
Removing group: 9A_T_14 because all sequences have been removed.
Removing group: 9A_T_3 because all sequences have been removed.
Removing group: 9A_T_30 because all sequences have been removed.
Removing group: 9A_T_7 because all sequences have been removed.
Removing group: 9B_T_0 because all sequences have been removed.
Removing group: 9B_T_1 because all sequences have been removed.
Removing group: 9B_T_14 because all sequences have been removed.
Removing group: 9B_T_3 because all sequences have been removed.
Removing group: 9B_T_30 because all sequences have been removed.
Removing group: 9B_T_7 because all sequences have been removed.
Removing group: 9C_T_0 because all sequences have been removed.
Removing group: 9C_T_14 because all sequences have been removed.
Removing group: 9C_T_3 because all sequences have been removed.
Removing group: 9C_T_30 because all sequences have been removed.
Removing group: 9C_T_7 because all sequences have been removed.
Removing group: E_T_14 because all sequences have been removed.
Removing group: E_T_30 because all sequences have been removed.
Removing group: E_T_7 because all sequences have been removed.
[ERROR]: requesting groups not present in files, aborting.
Output File Names:
/Desktop/bact_optho/combined.trim.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.shared