I am running a blastp search:
time ~/bin/ncbi-blast-2.14.0+-src/c++/ReleaseMT/bin/blastp -db nr -query X.fasta -out nr.X -num_descriptions 4000 -remote
but I have 2 problems with the output:
Sequences producing significant alignments:,
the output is truncated, and I can't read the exact species name:
XP_002906761.1 elongation factor 3, putative [Phytophthora infest... 848 0.0 KAG3108573.1 Elongation factor 3 [Phytophthora idaei] >gb|KAG3151... 845 0.0 KAG2772535.1 Elongation factor 3 [Phytophthora cactorum] >gb|KAG2... 845 0.0 KAG6976665.1 hypothetical protein JG688_00001147 [Phytophthora al... 844 0.0
The above sequences do not show up on the detailed sequence alignments below.
I have tried numerous variations of "outfmt" variations, but now am getting warnings that I'm using the system too much. So far, output format
0 is the best.
How can I get the full names and not the truncations?
Why aren't the above species showing up later on, and how can I get the full alignment to show?