SINA not processing fasta files that have been filtered using vsearch

epruesse / SINA

SINA - Reference based multiple sequence alignment

https://sina.readthedocs.io

GNU General Public License v3.0

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SINA not processing fasta files that have been filtered using vsearch #89

Closed dpar21 closed 4 years ago

dpar21 commented 4 years ago

I am trying to use SINA to align and classify 96 fastq files obtained from here: https://www.ebi.ac.uk/ena/data/view/PRJEB11512. I am really confused on how to use SINA to process these files, as whenever I process them it states that 0 sequences have been processed, kills the job, and my output files are all empty:

Screen Shot 2020-04-15 at 2 01 38 PM

I am also using 20 GB of memory, not sure if that is an issue. I believe it is with the fasta file itself (see below for first 2 sequences):

Screen Shot 2020-04-15 at 2 04 19 PM

dpar21 commented 4 years ago

Nevermind, I believe I may have figured out the issue: my fasta file was not in the correct order in terms of sequences (i.e. it should start from sequence 1 and then ascend)

epruesse commented 4 years ago

Sorry - I was too busy the last weeks :(

Happy to see that you worked it out youself! :)