align.seqs removes sequences


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!

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.


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