Blast2Go Local Www-Blast Not Working

Question

[Adrian Pelin]

I followed the tutorial and setup local nr and nt databases and was able to get them working on the web interface, and was able to link them to my blast2go, and select the local server as a www-blast database.

A problem I am encounter however, is that no matter what I blast, i get no results returned. When I blast manually on the web server, I get a result, when I feed it to blast2go, and start the blast, everything gets no results returned.

This is somewhat odd. I even tried asking for my server for an Blast XML response, when I used the web server to search, and that worked just fine.

There is not much to go on, since there is no error anywhere... I was wondering if you had encountered this before? blast on NCBI right now works horrible for me, sometimes 5-10 minute per query... so I need to get the local one working asap.

My properties file for blast2go show: Blast.url=http://137.122.148.173/blast/blast.cgi Blast.urls=http://www.ncbi.nlm.nih.gov/blast/Blast.cgi,http://137.122.148.173/blast/blast.cgi Blast.blastdb=nt

Thank you for your time. Adrian

P.S. The URL is not accessible externally, only for people on intranet, but blast is run from a machine that has access to intranet. Hopefully that doesn't screw things up, there are no proxies setup.

EDIT1 Re-posted on: http://seqanswers.com/forums/showthread.php?p=123017 https://groups.google.com/forum/#!topic/blast2go/id6FnS3wVuU

[Istvan Albert]

find and read the access and error logs of your server, the answer will be there

[Adrian Pelin]

It's not that simple. I am blasting stuff right now, and getting no results returned, and yet the apache error log shows errors from November 19th:

[Mon Nov 18 20:40:43 2013] [error] [client 137.122.148.173] (70007)The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed
[Tue Nov 19 09:08:17 2013] [error] [client 137.122.207.33] File does not exist: /var/www/html/blast/images/E.gif, referer: http://137.122.148.173/blast/blast.cgi
[Tue Nov 19 09:08:17 2013] [error] [client 137.122.207.33] File does not exist: /var/www/html/blast/images/G.gif, referer: http://137.122.148.173/blast/blast.cgi
[Tue Nov 19 22:16:15 2013] [warn] [client 137.122.204.31] Timeout waiting for output from CGI script /var/www/html/blast/blast.cgi, referer: http://137.122.148.173/blast/blast.html
[Tue Nov 19 22:16:15 2013] [error] [client 137.122.204.31] (70007)The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed, referer: http://137.122.148.173/blast/blast.html
[Tue Nov 19 22:17:15 2013] [warn] [client 137.122.204.31] Timeout waiting for output from CGI script /var/www/html/blast/blast.cgi, referer: http://137.122.148.173/blast/blast.html
[Tue Nov 19 22:17:15 2013] [error] [client 137.122.204.31] (70007)The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed, referer: http://137.122.148.173/blast/blast.html
[Tue Nov 19 22:18:18 2013] [warn] [client 137.122.204.31] Timeout waiting for output from CGI script /var/www/html/blast/blast.cgi, referer: http://137.122.148.173/blast/blast.html
[Tue Nov 19 22:18:18 2013] [error] [client 137.122.204.31] (70007)The timeout specified has expired: ap_content_length_filter: apr_bucket_read() failed, referer: http://137.122.148.173/blast/blast.html
[Tue Nov 19 22:46:53 2013] [error] [client 137.122.204.31] File does not exist: /var/www/html/blast/images/G.gif, referer: http://137.122.148.173/blast/blast.cgi

So this does not show up at every single blast attempt.

[Istvan Albert]

troubleshooting a system that is not accessible to the outside world and one that you cannot post an error for is not particularly enticing - you need to formulate "answerable" questions

[Adrian Pelin]

You are right, troubleshooting without errors can be challenging. There is no sign of problems in the httpd access and error logs because there is no problem with httpd.

From the blast2go log i see:

Sun Nov 24 18:46:18 EST 2013    blast Seq1 against http://137.122.148.173/blast/blast.cgi with SEQUENCE=>Seq1%0D%0Agtgatggaaaagaaaagttttgttatcgtcgacgcatatgggtttctttttcgcgcgtattatgcgctgcctggattaagcacctcatacaattttcctgtaggaggtgtatatggttttataaacatacttttgaaacatctctctttccacgatgcagattatttagttgtggtatttgattcggggtcgaaaaattttcgtcacactatgtattccgaatacaaaactaatcgccctaaagcaccagaggatctgtcactacaatgtgctccgctacgtgaggctgttgaagcgtttaatattgtaagtgaagaagtgcttaactacgaagcagacgacgtaatagctacactctgtacaaaatatgcatctagtaatgttggagtgagaatactgtcagcagataaggatttactacaactcctaaatgataatgttcaagtttacgaccctataaaaagcagatacctcaccaatgaatacgttttagaaaaatttggtgtttcatcagataagttgcttgatgccatggctcttacaggagatgcatcggataatattcctggcgtgcctagcataggagtaaaaactgctgcaaagctgattaacgagtttggatcactagacaatgtgctgaattctgtagaacaggtggctcagaaaaagtgtcgcgacatgctaaccgagtacgctgatcgagcaattttatcacgtgacttgatatctctgtgtcatgatgtagaagtcgagggtgatttggagaagtatgctaaaagagtgccagatccggtaaagcttatggcctttttagaaaagtatgaactaacttctctagaaggcaaagtggcaaagtactgcaagatggttgctgcacccatccagagcagtgaagtagtcaagaaagaaaacgaaaaatgcatagacaagttggaggagttcctggagcaatgtcagcgcagtgggctattagggttatacatagaagtagagcaaggttttatcagtacaatatttgctgcgtgcgatgagactagatcttttactgtcagcagtcctgaaaaggtgcaaaagtttgtggcggcagtaacaccaattctgcattcagattcggtgctcaaagttgtttatgatgccaaatccatgatgcagttttttcctgagttgcgggcatttgacgatattatgattatgtcgtacagccttgatacaggtcatcacgatcacggctttgatagcatgtcgcagcgtcatcttggtcaaatatttggtattaccaatgggtgcatattgatacggttgcatcgagttataatgagaaaattattctcagctaagctgtacaccgtttattacacactcgaaaggccgttagtacctgtaatatacgaattggaaaaaacagggataaaaatagacactgagttattgaagcaattatctgatgagttttctctatccataagtaatttggaagaagaaatattcggccttgcaggatgtaaatttaacatagcttcctcacagcagttgggtaaagtcctctttgagcatatgcgtattgggggagctaaaaaaatgccttctggcagctactgcaccaatgcggaagttcttactgcactggcattagatggagttgaagttgctgataaaattctgaagtggcgtcactttactaaattaaagagcacgtacacagacgctttagtccggcaggttgatgctaatactggaagggtgcatacaaaatattccatgactgctacggcgacaggacggctcagttcaagtaacccaaatttgcagaatatacctatcaggagcaaagatggggaaaaaattcgcagtgcatttattgctgagaaaggccataaattgatagcagcagattattcacaaatggaactcaaaatcttggcacatattgctgatgtaaaagcttttagacaggcttttgctgagggattagacattcacgtcgttacagcacagcaaatttttggtgagtattatgaaattgattatgagctcagaagaagggcaaaatctatcaatttcgggataatctatggtatgggatcttatggattagcgagaaatataggcataagcagaagggaagcttctgagtacgtggaacagtattttcaatactatcctgaaatcaagcgttatatggaaacaacaaaggcatatgcaaaaaagcatggatatactattactgcttttgggaggaagtgctttattgaagggattaatagtccaaagcgagctttaagtagtgttgcagaacgagctgcaattaacgcaccaatccagggtactgcagctgatattgtaaaaaaggctatggtaaggttgcaagatcgactcacgcagggaacaatgcttctccaagtccatgacgaattattggtagaagtcccagaagagcacgtactctcagttgcacgtttgatgaaagaagtaatggagagtgctgtggtgttttctctacctttggatgttaatataagcgttggagataattggggagacatggttgaaatcgaggtataa&DATALIB=nt&DESCRIPTIONS=10&ALIGNMENTS=10&EXPECT=0.001&PROGRAM=blastn&FILTER=L&WORD_SIZE=28&CLIENT=web&SERVICE=plain&NCBI_GI=on&PAGE=Nucleotides&ALIGNMENT_VIEW=7&CMD=Put
Sun Nov 24 18:47:03 EST 2013    --------------no result returned

When I actually go an issue that command:

http://137.122.148.173/blast/blast.cgi?SEQUENCE=%3ESeq1%0D%0Agtgatggaaaagaaaagttttgttatcgtcgacgcatatgggtttctttttcgcgcgtattatgcgctgcctggattaagcacctcatacaattttcctgtaggaggtgtatatggttttataaacatacttttgaaacatctctctttccacgatgcagattatttagttgtggtatttgattcggggtcgaaaaattttcgtcacactatgtattccgaatacaaaactaatcgccctaaagcaccagaggatctgtcactacaatgtgctccgctacgtgaggctgttgaagcgtttaatattgtaagtgaagaagtgcttaactacgaagcagacgacgtaatagctacactctgtacaaaatatgcatctagtaatgttggagtgagaatactgtcagcagataaggatttactacaactcctaaatgataatgttcaagtttacgaccctataaaaagcagatacctcaccaatgaatacgttttagaaaaatttggtgtttcatcagataagttgcttgatgccatggctcttacaggagatgcatcggataatattcctggcgtgcctagcataggagtaaaaactgctgcaaagctgattaacgagtttggatcactagacaatgtgctgaattctgtagaacaggtggctcagaaaaagtgtcgcgacatgctaaccgagtacgctgatcgagcaattttatcacgtgacttgatatctctgtgtcatgatgtagaagtcgagggtgatttggagaagtatgctaaaagagtgccagatccggtaaagcttatggcctttttagaaaagtatgaactaacttctctagaaggcaaagtggcaaagtactgcaagatggttgctgcacccatccagagcagtgaagtagtcaagaaagaaaacgaaaaatgcatagacaagttggaggagttcctggagcaatgtcagcgcagtgggctattagggttatacatagaagtagagcaaggttttatcagtacaatatttgctgcgtgcgatgagactagatcttttactgtcagcagtcctgaaaaggtgcaaaagtttgtggcggcagtaacaccaattctgcattcagattcggtgctcaaagttgtttatgatgccaaatccatgatgcagttttttcctgagttgcgggcatttgacgatattatgattatgtcgtacagccttgatacaggtcatcacgatcacggctttgatagcatgtcgcagcgtcatcttggtcaaatatttggtattaccaatgggtgcatattgatacggttgcatcgagttataatgagaaaattattctcagctaagctgtacaccgtttattacacactcgaaaggccgttagtacctgtaatatacgaattggaaaaaacagggataaaaatagacactgagttattgaagcaattatctgatgagttttctctatccataagtaatttggaagaagaaatattcggccttgcaggatgtaaatttaacatagcttcctcacagcagttgggtaaagtcctctttgagcatatgcgtattgggggagctaaaaaaatgccttctggcagctactgcaccaatgcggaagttcttactgcactggcattagatggagttgaagttgctgataaaattctgaagtggcgtcactttactaaattaaagagcacgtacacagacgctttagtccggcaggttgatgctaatactggaagggtgcatacaaaatattccatgactgctacggcgacaggacggctcagttcaagtaacccaaatttgcagaatatacctatcaggagcaaagatggggaaaaaattcgcagtgcatttattgctgagaaaggccataaattgatagcagcagattattcacaaatggaactcaaaatcttggcacatattgctgatgtaaaagcttttagacaggcttttgctgagggattagacattcacgtcgttacagcacagcaaatttttggtgagtattatgaaattgattatgagctcagaagaagggcaaaatctatcaatttcgggataatctatggtatgggatcttatggattagcgagaaatataggcataagcagaagggaagcttctgagtacgtggaacagtattttcaatactatcctgaaatcaagcgttatatggaaacaacaaaggcatatgcaaaaaagcatggatatactattactgcttttgggaggaagtgctttattgaagggattaatagtccaaagcgagctttaagtagtgttgcagaacgagctgcaattaacgcaccaatccagggtactgcagctgatattgtaaaaaaggctatggtaaggttgcaagatcgactcacgcagggaacaatgcttctccaagtccatgacgaattattggtagaagtcccagaagagcacgtactctcagttgcacgtttgatgaaagaagtaatggagagtgctgtggtgttttctctacctttggatgttaatataagcgttggagataattggggagacatggttgaaatcgaggtataa&DATALIB=nt&DESCRIPTIONS=10&ALIGNMENTS=10&EXPECT=0.001&PROGRAM=blastn&FILTER=L&WORD_SIZE=28&CLIENT=web&SERVICE=plain&NCBI_GI=on&PAGE=Nucleotides&ALIGNMENT_VIEW=7&CMD=Put

I get the result in xml format:

2 gi|526276138|gb|CP006616.1| Anaplasma phagocytophilum str. HZ2, complete genome CP006616 1477581 1 5037.65 2541 0 1 2562 122 2683 1 1 2555 2555 2562

So the problem is in blast2go reading the output. It doesn't seem to be a timeout issue based on how long it takes blast2go to decide there is no results and how long it takes me to get the results. The time is identical.

I was wondering if someone who linked blast2go with local www-Blast perhaps ran into something similar and found a solution.

[Shyam]

If you want to run the analysis faster why can't you run the blast on command line and generate a XML output and import the blast xml output into blast2go.

[Adrian Pelin]

Brilliant. outfmt 5.