Missing format options in standalone BLAST

[kmcarr]

I never installed 2.2.27+ at all. The first time I installed is BLAST 2.2.28+.

Well the output from "blastn -version" sort of disputes that statement doesn't it? Could someone else have installed 2.2.27?

[vpi]

I never installed 2.2.27+ at all. The first time I installed is BLAST 2.2.28+.

[kmcarr]

-outfmt '6 std stitle' gives the same output as -outfmt 6

I downloaded this latest version for linux ncbi-blast-2.2.28+-x64-linux.tar.gz. But when I run the command blastn -version, it says BLAST 2.2.27+. This might be the problem. What might be wrong?

Did you install 2.2.28+ properly after downloading? Did you remove 2.2.27+? Or are both versions installed and is 2.2.27+ taking precedence based on their order in your $PATH environment variable?

[vpi]

-outfmt '6 std stitle' gives the same output as -outfmt 6

I downloaded this latest version for linux ncbi-blast-2.2.28+-x64-linux.tar.gz. But when I run the command blastn -version, it says BLAST 2.2.27+. This might be the problem. What might be wrong?

[kmcarr]

Hi,

I tried to look at the available -outfmt options using blastn -help and I cant find stitle or salltitle options.

Please help!

This bit of information ties directly to maubp's question. Which version are you using? Run this command to find out.

# blastn -version

The stitle & salltitle outfmt options were only added in the latest version, 2.2.28 (released April 2013). If you don't see them listed in the help message then it is a good guess that you don't really have the latest version.

[maubp]

You said 'latest', but which version of BLAST+ exactly are you using?

[rhinoceros]

What about -outfmt '6 std stitle' or -outfmt '6 std salltitles'. Perhaps refseq entries simply don't have subject titles? How did you create your refseq? Did you download it from ftp://ftp.ncbi.nlm.nih.gov/blast/db/ and simply tar zxvf?

[vpi]

Even without -num_alignments I get the same results. But earlier I tried num_alignments 1 -outfmt 6 and it worked.

NODE_1_length_10131_cov_55.7043_ID_695104 gi|296556485|gb|M19921.2|HIVNL43 100.00 822 0 0 6686 7507 12281 11460 0.0 1519
NODE_2_length_3299_cov_8.97446_ID_698840 gi|109255272|ref|NC_008168.1| 92.63 95 2 3 957 1051 25902 25991 2e-27 132
NODE_3_length_2648_cov_1.88378_ID_694314 gi|237784637|ref|NC_012704.1| 82.29 2688 371 89 1 2648 114906 117528 0.0 2230
NODE_4_length_1757_cov_30.9221_ID_695832 gi|154149549|ref|NC_009712.1| 78.86 175 33 4 490 663 2250989 2251160 1e-22 115
NODE_6_length_1496_cov_25.8736_ID_702132 gi|304313778|ref|NC_014408.1| 76.42 246 45 9 666 903 324067 324307 2e-24 121
NODE_7_length_1489_cov_0.428047_ID_692868 gi|170745058|ref|NC_010510.1| 95.06 1337 47 14 1 1325 547100 545771 0.0 2085

If the path for refseq was not correct then the blast wouldn't run. Isnt it like that? Anyways I get the same result with full path as well (just query).

[rhinoceros]

Hi,

Here are the commands I used and the first five lines of the output,

blastn -query /home/viraja/Desktop/samples_with_no_flags/sample_01/contigs_01_without_flag.fasta -db refseq -num_alignments 1 -outfmt '6 qseqid stitle'

NODE_1_length_10131_cov_55.7043_ID_695104
NODE_2_length_3299_cov_8.97446_ID_698840
NODE_3_length_2648_cov_1.88378_ID_694314
NODE_4_length_1757_cov_30.9221_ID_695832
NODE_6_length_1496_cov_25.8736_ID_702132

-num_alignments is not a valid flag for outfmt 6

Also, are you sure you have setup refseq properly? Try with using full path to it..

[vpi]

Hi,

Here are the commands I used and the first five lines of the output,

blastn -query /home/viraja/Desktop/samples_with_no_flags/sample_01/contigs_01_without_flag.fasta -db refseq -num_alignments 1 -outfmt '6 qseqid stitle'

NODE_1_length_10131_cov_55.7043_ID_695104
NODE_2_length_3299_cov_8.97446_ID_698840
NODE_3_length_2648_cov_1.88378_ID_694314
NODE_4_length_1757_cov_30.9221_ID_695832
NODE_6_length_1496_cov_25.8736_ID_702132

[Dario1984]

I used -outfmt "6 qacc sacc stitle score length mismatch gaps evalue qlen slen qstart qend sstart send" and in the third column I got the subject title. stitle is the correct option. Can you show the first five lines of the output file ?

[vpi]

Hi,

I am using latest version of standalone BLAST on linux. I tried to use custom output format and few options are missing. For example, I want to print the title of the subject along with the query, so I say

-outfmt '6 qseqid stitle'

With the above command I just get a list of queries. I tried to look at the available -outfmt options using blastn -help and I cant find stitle or salltitle options.

Please help!