Hello Dr. Schloss,
I was trying to slign my sequences with the silva bacteria database using blast option for search and align. I used the command:
align.seqs(fasta=…/demultiplexed.unique.fna, reference=…/silva.bacteria/silva.bacteria.fasta, flip=T, search=blast, align=blast, processors=8)
I am getting this error.
Using 8 processors.
Reading in the …/silva.bacteria/silva.bacteria.fasta template sequences… DONE.
It took 24 to read 14956 sequences.
Aligning sequences from …/demultiplexed.unique.fna …
[ERROR]: 20595068.pairwise is blank. Please correct.
[ERROR]: 20595068.pairwise is blank. Please correct.
[ERROR]: 20595068.pairwise is blank. Please correct.
[ERROR]: 20595068.pairwise is blank. Please correct.
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[ERROR]: std::bad_alloc has occurred in the Nast class function getSimilarityScore. Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to inclu
de the mothur.logFile with your inquiry.
966
The above is my logfile.
I used the needleman and kmer method also, it ran fine with it. I was not able to understand the output of the alignment so I tried blast.
Thanks!!!