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Originally posted by GenoMax View PostYou need to enclose the outfmt options in single quotes (') and not double quotes like you have in your script. Give this a try.
Code:-outfmt '6 qseqid sgi sseqid pident length mismatch qstart qend sstart send evalue bitscore staxids'
Code:$ head lab8output_tabular.txt gi|645685058:1370684-1379063 0 CL3111Contig1 97.78 45 1 5808 5852 1 45 2e-13 78.7 N/A gi|645685058:1370684-1379063 0 CL3747Contig1 89.66 58 5 7069 7126 859 803 1e-11 73.1 N/A gi|645685058:1370684-1379063 0 gi|75720587|gb|DT788599.1|DT788599 94.29 35 2 7069 7103 47 81 4e-06 54.7 N/A
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Originally posted by dschika View PostI understood that it produces output. But I would like to know if you have any hits at all. If you don't have hits, you won't get any output in the second case.
How often can you find the phrase "producing significant alignments" in first, default output file?
I'm sorry I misunderstood your question earlier. Thank you for the elaboration. Since I used an extremely small fasta file, then it follows that I would also not expect many alignments. In other words, the results were also small. I only had 1 producing significant alignments.
Now that being said, I would at least expect to see that output for tabular. I'm still not clear why the second script fails. I hope however, that I helped answer questions you had about my approach. If not, please feel free to ask followup questions.
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Hi GenoMax, are you sure about the quote? Because, I'm using the double quote and it works... My blast version is quite old (2.2.25+) but it works with double quotes...
Actually, do you get an output if you remove the staxids? Because, I do not have this option in my blast version (don't know if it exist in blast 2.2.29)...Last edited by SylvainL; 06-15-2015, 02:20 AM.
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You need to enclose the outfmt options in single quotes (') and not double quotes like you have in your script. Give this a try.
Code:-outfmt '6 qseqid sgi sseqid pident length mismatch qstart qend sstart send evalue bitscore staxids'
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Originally posted by hlyates View PostHere are the answer to your questions:- The first script works with no errors. It produces output.
How often can you find the phrase "producing significant alignments" in first, default output file?
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Originally posted by GenoMax View PostWere there any errors reported when you made the database (DB files are non-zero bytes)? Are query/db composed of nucleotides?
The output is given below:
Code:Building a new DB, current time: 06/12/2015 22:10:13 New DB name: tbd New DB title: /databases/tribolium-est-transcripts.fasta Sequence type: Nucleotide Deleted existing BLAST database with identical name. Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 46% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 44% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 48% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 48% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 44% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 48% ambiguous nucleotides (shouldn't be over 40%)
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Here are the answer to your questions:- The first script works with no errors. It produces output.
- The makedb did produce some errors, but I don't believe this is causing the problem. I have tried this problem on a protein database I made as well and experience the exact same behaviour. The first script gives me output, then the tabular output is blank.
Code:Building a new DB, current time: 06/12/2015 13:25:46 New DB name: tbd New DB title: /databases/tribolium-est-transcripts.fasta Sequence type: Nucleotide Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 46% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 44% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 48% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 48% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 44% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 48% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 44% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 44% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 54% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 44% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 48% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 46% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 42% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 48% ambiguous nucleotides (shouldn't be over 40%) Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is a bout 46% ambiguous nucleotides (shouldn't be over 40%) Adding sequences from FASTA; added 18611 sequences in 2.75514 seconds.
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Were there any errors reported when you made the database (DB files are non-zero bytes)? Are query/db composed of nucleotides?
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Were there any hits reported in the output of the first command? If there were no hits at all, I guess the tabular output format will not produce a file.
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Why is this blast script giving me empty tabular output?
Instead of using an ncbi database, I ran the makeblastdb command on a fasta file I downloaded from ncbi.
The following script will produce output for me:
Code:#!/bin/bash /homes/bioinfo/ncbi-blast-2.2.29+/bin/blastn -db ~/databases/tbd -query ~/databases/even_tribolium.fasta -out output.txt
However, when I modify the script as follows, I get absolutely no output.
Code:#!/bin/bash /homes/bioinfo/ncbi-blast-2.2.29+/bin/blastn -db ~/databases/tbd -query ~/databases/even_tribolium.fasta -out output.txt -evalue 10E-30 -outfmt "6 qseqid sgi sseqid pident length mismatch qstart qend sstart send evalue bitscore staxids"
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