align.seqs removes sequences

Commands in mothur
1

Hi,

I am not sure if it has been discussed before but it seems like align.seqs removes sequences such that summary.seqs cannot be performed after.

mothur > align.seqs(fasta=A.good.unique.fasta, reference=silva.nr_v128.align, flip=t, processors=16)
which completes but gives errors below.

[ERROR]: Could not open A.good.unique.align28866.num.temp
[ERROR]: Could not open A.good.unique.align28869.num.temp
[ERROR]: Could not open A.good.unique.align28870.num.temp
[WARNING]: Some of your sequences generated alignments that eliminated too many bases, a list is provided in A.good.unique.flip.accnos. If the reverse compliment proved to be better it was reported.
It took 2607 secs to align 26567 sequences.

mothur > summary.seqs(fasta=current, count=current)
Using A.count_table as input file for the count parameter.
Using A.good.unique.align as input file for the fasta parameter.

Using 8 processors.
[ERROR]: Your count file contains 53773 unique sequences, but your fasta file contains 42272. File mismatch detected, quitting command.

Running summary.seqs on the pre-aligned fasta file and count file gives 53773 sequences.
Note that this is a MinIon data so each reads are significantly longer than Illumina reads.
Thanks in advance!

2

Try reducing the number of processors from 16 to a smaller number. This is a known bug that we are working on for 1.40. You’re basically crashing your computer because of the RAM requirements of keeping 16 copies of the reference datbase.

Pat

3

Thanks Pat, will try that and wait for the next update!

Sou