adam-submit: Not able to transform fasta file to adam format.

[shashwatwork]

I tried running adam-submit on AWS EMR in order to convert fasta genomic sequence file to adam but no transformation has been applied. Following commands have been used -

adam-submit --fasta2adam s3://gendata/cov2.fasta s3://gendata/cov2.adam
adam-submit --fasta2adam cov2.fasta cov2.adam
adam-submit --transformAlignments s3://gendata/cov2.fasta s3://gendata/cov2.adam

Please let me know if I am making any errors in running the above commands or any additional args required.

[heuermh]

Hello @shashwatwork, thanks for submitting this issue!

First, based on the list of ADAM commands in the screenshot, you are running a very old version of ADAM. You may wish to update to a more recent version, see https://github.com/bigdatagenomics/adam/releases

Second, the format of your command line is a bit off, it should be

adam-submit fasta2adam s3://gendata/cov2.fasta s3://gendata/cov2.adam
adam-submit fasta2adam cov2.fasta cov2.adam
adam-submit transformAlignments s3://gendata/cov2.fasta s3://gendata/cov2.adam

instead of what you have above.

Hope this helps!

[shashwatwork]

Thnx, a bunch @heuermh updated adam to a recent version and modified cmd line args based on your suggestions that worked.

[heuermh]

Good to hear!