So, running the toy dataset and in my own run, I had the same issue.
(sprayandpray) [mcallister@poseidon BmuCA187744_spades]$ spray-and-pray.py -g contigs.fasta -ref /data/blastdb/fasta/nr.gz -out sprayNpray_out -t 40 --makedb --spades --c
.
Reference database: /data/blastdb/fasta/nr.gz
Input genome: contigs.fasta
Running Prodigal: calling ORFs from provided contigs
Running Diamond: making DIAMOND BLAST database
Running Diamond BLAST
Calculating GC-content
Preparing summary: sprayNpray_out.csv
SprayNPray cannot find the following file: taxmap_slv_ssu_ref_nr_138.1.txt.
There is a good chance that it is present in its gzipped form in the SprayNPray
directory/folder on your system. Please unzip this file and try running the program
again. If you just waited for a length DIAMOND run to finish, you can provide the
DIAMOND BLAST output (contigs.fasta.blast) to the command when you re-run using the -blast argument
The taxmap_slv_ssu_ref_nr_138.1.txt file is definitely in the SprayNPray directory and is unzipped. Please let me know!
The only files created are: x.blast, x-cds.ffn, x-proteins.faa, and x-top100.csv. I think many files are missing. Also, can you please have the output files stored in the out directory from the start, so that when there is an interruption in the pipeline, all the files aren't scattered? The first three are in the in file directory and the last in the out directory. Thanks!
So, running the toy dataset and in my own run, I had the same issue.
The
taxmap_slv_ssu_ref_nr_138.1.txtfile is definitely in the SprayNPray directory and is unzipped. Please let me know!The only files created are: x.blast, x-cds.ffn, x-proteins.faa, and x-top100.csv. I think many files are missing. Also, can you please have the output files stored in the out directory from the start, so that when there is an interruption in the pipeline, all the files aren't scattered? The first three are in the in file directory and the last in the out directory. Thanks!