Hello!
I wondered if you would be willing to help me, my screen.seqs is removing 1528936 of 1529102 sequences, whats happening here? See below:
mothur > summary.seqs(fasta=/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/align/bps.trim.contigs.good.unique.align, count=/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/bps.trim.contigs.good.count_table)
Using 28 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1044 1044 1 0 1 1
2.5%-tile: 13862 23444 252 0 3 302545
25%-tile: 13862 23444 253 0 4 3025444
Median: 13862 23444 253 0 4 6050888
75%-tile: 13862 23444 253 0 5 9076332
97.5%-tile: 13862 23444 253 0 6 11799231
Maximum: 43113 43116 254 0 8 12101775
Mean: **13861** **23442** 252 0 4
No. of unique seqs: 1529102
total # of seqs: 12101775
It took 251 secs to summarize 12101775 sequences.
Output File Names:
/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/summary/bps.trim.contigs.good.unique.summary
mothur > screen.seqs(fasta=/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/align/bps.trim.contigs.good.unique.align, count=/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/bps.trim.contigs.good.count_table, summary=home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/summary/bps.trim.contigs.good.unique.summary, start=**13861**, end=**23442**)
Using 28 processors.
It took 265 secs to screen 1529102 sequences, removed 1528936.
/******************************************/
Running command: remove.seqs(accnos=/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/new/new/bps.trim.contigs.good.unique.bad.accnos.temp, count=/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/bps.trim.contigs.good.count_table)
Removing group: B.10.raw because all sequences have been removed.
Removing group: B.2.raw because all sequences have been removed.
Removing group: B.3.raw because all sequences have been removed.
Removing group: B.5.raw because all sequences have been removed.
Removing group: B.6.raw because all sequences have been removed.
Removing group: B.7.raw because all sequences have been removed.
Removing group: B.8.raw because all sequences have been removed.
Removing group: C.13.1.raw because all sequences have been removed.
Removing group: C.13.2.raw because all sequences have been removed.
Removing group: C.2.2.raw because all sequences have been removed.
Removing group: C.2.3.raw because all sequences have been removed.
Removing group: C.3.2.raw because all sequences have been removed.
Removing group: C.4.2.raw because all sequences have been removed.
Removing group: C.4.3.raw because all sequences have been removed.
Removing group: C.5.3.raw because all sequences have been removed.
Removing group: C.6.1.raw because all sequences have been removed.
Removing group: C.6.2.raw because all sequences have been removed.
Removing group: C.6.3.raw because all sequences have been removed.
Removing group: C.7.1.raw because all sequences have been removed.
Removing group: C.7.3.raw because all sequences have been removed.
Removing group: C.8.3.raw because all sequences have been removed.
Removing group: C.9.3.raw because all sequences have been removed.
Removing group: F.10.1.raw because all sequences have been removed.
Removing group: F.13.2.raw because all sequences have been removed.
Removing group: F.13.3.raw because all sequences have been removed.
Removing group: F.2.3.raw because all sequences have been removed.
Removing group: F.3.1.raw because all sequences have been removed.
Removing group: F.3.2.raw because all sequences have been removed.
Removing group: F.3.3.raw because all sequences have been removed.
Removing group: F.5.1.raw because all sequences have been removed.
Removing group: F.6.3.raw because all sequences have been removed.
Removing group: F.7.3.raw because all sequences have been removed.
Removed 12101186 sequences from your count file.
Output File Names:
/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/new/new/bps.trim.contigs.good.pick.count_table
/******************************************/
Output File Names:
/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/new/new/bps.trim.contigs.good.unique.good.summary
/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/new/new/bps.trim.contigs.good.unique.good.align
/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/new/new/bps.trim.contigs.good.unique.bad.accnos
/home/n/nb326/miniconda3/envs/bpsenv/03_preprocess/new/new/bps.trim.contigs.good.good.count_table
It took 546 secs to screen 1529102 sequences.