remove.lineage removing all seaquences from FASTA file

mothur bugs
1

Hi,
My output FASTA file is empty after this step. Please suggest me what should I do. My script is,

classify.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, cutoff=80)

Using 8 processors.
Reading template taxonomy...     DONE.
Reading template probabilities...     DONE.
It took 22 seconds get probabilities. 
Classifying sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta ...
Reading template taxonomy...     Reading template taxonomy...     Reading template taxonomy...     Reading template taxonomy...     Reading template taxonomy...     DONE.
DONE.Reading template probabilities...     
Reading template taxonomy...     Reading template probabilities...     DONE.DONE.
DONE.Reading template probabilities...     Reading template taxonomy...     DONE.

Reading template probabilities...     [WARNING]: M02127_231_000000000-AYDY1_1_1105_12621_25851 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.Reading template probabilities...     
Reading template probabilities...     
[WARNING]: M02127_231_000000000-AYDY1_1_1104_9653_10259 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
DONE.
Reading template probabilities...     [WARNING]: M02127_231_000000000-AYDY1_1_1104_8741_8376 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M02127_231_000000000-AYDY1_1_1104_7509_18696 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M02127_231_000000000-AYDY1_1_1104_6091_15351 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: M02127_231_000000000-AYDY1_1_1104_3958_17847 could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.....
................................................

mothur > 
remove.lineage(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table, taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.taxonomy, taxon=Chloroplast-Mitochondria-unknown-Archaea-Eukaryota)

[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.

Your taxonomy file contains only sequences from Chloroplast-Mitochondria-unknown-Archaea-Eukaryota.
Your fasta file contains only sequences from Chloroplast-Mitochondria-unknown-Archaea-Eukaryota.

Removing group: 153B because all sequences have been removed.

Removing group: 154B because all sequences have been removed.

Removing group: 156SO because all sequences have been removed.

and so on........

Removing group: mockD121416 because all sequences have been removed.
Your group file contains only sequences from Chloroplast-Mitochondria-unknown-Archaea-Eukaryota.
2

It looks like the sequences are not getting classified. Could you delete the trainset files, redownload, and try again? If this doesn’t solve the problem, could you post one of the sequences?

Thanks,
Pat

3

Thanks, it did work when I used latest trainset files and the latest version of mothur.