running BLAST on Raven -- invalid syntax error

[grace-ac]

will keep working to figure out- posting issue in case anyone has quick answer

link to Rmd that I am running on raven: https://github.com/grace-ac/project-pycno-sizeclass-2022/blob/main/code/10-BLAST-summ22-phelgenome_raven.Rmd

error:

Error: Too many positional arguments (1), the offending value: \
Error:  (CArgException::eSynopsis) Too many positional arguments (1), the offending value: \
  File "<string>", line 1
    -query augustus.hints.codingseq \
                  ^
SyntaxError: invalid syntax
  File "<string>", line 1
    -db ../analyses/10-BLAST/blast/uniprot_sprot_r2021_03 \
         ^
SyntaxError: invalid syntax
  File "<string>", line 1
    -out ../analyses/10-BLAST/summer2022-uniprot_blastx.tab \
          ^
SyntaxError: invalid syntax
  File "<string>", line 1
    -evalue 1E-20 \
                ^
SyntaxError: invalid syntax
  File "<string>", line 1
    -num_threads 8 \
                 ^
SyntaxError: invalid syntax
  File "<string>", line 1
    -max_target_seqs 1 \
                     ^
SyntaxError: invalid syntax
  File "<string>", line 1
    -outfmt 6
            ^
SyntaxError: invalid syntax

Code chunk that's the problem:

!/home/shared/ncbi-blast-2.15.0+/bin/blastx \
-query augustus.hints.codingseq \
-db ../analyses/10-BLAST/blast/uniprot_sprot_r2021_03 \
-out ../analyses/10-BLAST/summer2022-uniprot_blastx.tab \
-evalue 1E-20 \
-num_threads 8 \
-max_target_seqs 1 \
-outfmt 6

[sr320]

Remove "!" That is leftover from Jupyter notebooks.

[grace-ac]

oh i should be running a bash chunk rather than jupyter?

[kubu4]

Yes.

Jupyter Notebooks are the "equivalent" of RStudio, except Jupyter Notebooks run cells (i.e. chunks) in Python by default.

Rstudio runs chunks in R by default.

Jupyter allows you to run Bash by using the ! shortcut. It's the same as starting the Jupyter cell with %bash - it's just a shortcut.

[sr320]

See also updated example using R.. https://robertslab.github.io/tusk/modules/04-blast.html

[grace-ac]

thanks! yes i fixed it on Saturday and it ran! code (i'm cleaning up rmd now): https://github.com/grace-ac/project-pycno-sizeclass-2022/blob/main/code/10-BLAST-summ22-phelgenome_raven.Rmd

thank you both!