Hi There,
I’m running mothur ‘classify.seqs’ command with mpi and am getting some very unusual output. Many entries are truncated by the start of others and it is very inconsistent. Some lines begin with what appears to the be end of a line. I’ve included the command issued below. Any advice would be greatly appreciated.
Thanks!
Roli
DRR068868.718 k__Bacteria(100);p__Bacteroidetes(97);c__Saprospirae;o__Saprospirales;f__ChitinophagDRR068860.2DRR068871.2508 k__Bacteria(100);p__Actinobacteria(100);c__Actinobacteria(100);o__Actinomycetales(100);f__ADRR068862.3DRR068885.498 k__Bacteria(100);p__Firmicutes(40);c__Clostridia(37);o__Clostridiales(37);f__Ruminococcaceae(28);
DRR068877.711 k__Bacteria(100);p__Bacteroidetes(79);c__Bacteroidia(51);o__Bacteroidales(51);
eriales(100);
DRR068868.719 k__Bacteria(99);p__Proteobacteria(54);c__Gammaproteobacteria(49);o__Enterobacteriales(48);f__Enterobacteriaceae(48);g__Enterobacter(44);s__nimipressuralis(4DRR0DRR068871.2509 k__Bacteria(100);p__Actinobacteria(97);c__Actinobacteria(97);o__Actinomycetales(97);f__ACK-M1(65);
DRR068861.4211 k__Bacteria(100);p__Bacteroidetes(100);c__Cytophagia(99);o__Cytophagales(99);f__Cytophagaceae(99);
DRR068878.3193 k__Bacteria(100);p__Actinobacteria(100);c__Acidimicrobiia(100);o__Acidimicrobiales(100);f__C111(100DRRDRR068868.720 k__Bacteria(100);p__Bacteroidetes(98);c__Saprospirae;o__Saprospirales;f__Chitinophagaceae(85);
DRR068871.2511 k__Bacteria(100);p__Actinobacteria(99);c__Actinobacteria(99);o__Actinomycetales(99);f__ACK-M1(85);
DRR068861.4213 k__Bacteria(100);p__Proteobacteria(100);c__Betaproteobacteria(100);o__Burkholderiales(100);f__Comamonadaceae(100);g__Limnohabitans(99);
DRR068867.9 k__Bacteria(95);p__Proteobacteria(79);c__Gammaproteobacteria(36);o__Enterobacteriales(34);f__Enterobacteriaceae(34);g__Enterobacter(34);s__nimipressDRR068877.713 k__Bacteria(100);p__Firmicutes(37);c__Clostridia(37);o__Clostridiales(37);f__Clostridiaceae(19);g__Clostridium(19);
aceae(40);g__Synechococcus(40);
DRR068868.721 k__Bacteria(97);p__Planctomycetes(41);c__Planctomycetia(36);o__Pirellulales(36);f__Pirellulaceae(36);
DRR068871.2512 k__Bacteria(100);p__Bacteroidetes(100);c__Sphingobacteriia(100);o__Sphingobacteriales(100);
DRR068861.4214 k__Bacteria(100);p__Bacteroidetes(100);c__Saprospirae;o__Saprospirales;f__Chitinophagaceae(100);
DRR068885.502 k__Bacteria(94);p__Planctomycetes(44);c__Planctomycetia(28);o__Pirellulales(28);f__Pirellulaceae(28);
72);c__Gammaproteobacteria(26);o__Enterobacteriales(24);f__Enterobacteriaceae(24);g__EnterobacteDRR068878.3195 k__Bacteria(100);p__Actinobacteria(98);c__Acidimicrobiia(95);o__Acidimicrobiales(95);
DRR068860.2603 k__Bacteria(100);p__Actinobacteria(97);c__Actinobacteria(96);o__Actinomycetales(96);f__ACK-M1(84);
Type 'quit()' to exit program Using MPI version 2.1 Script Mode
mothur > classify.seqs(taxonomy=~/db/gg_13_8_99.gg.tax, template=~/db/gg_13_8_99.fasta, fasta=/global/scratch/rwilhelm/mothur_output/PRJDB5151.groups, processors=16)
Using 16 processors.
Reading template taxonomy… DONE.
Reading template probabilities… DONE.
It took 19 seconds get probabilities.
Classifying sequences from /global/scratch/rwilhelm/mothur_output/PRJDB5151.trim.unique.fasta …