search

legumeinfo / jira-issues

placeholder repo for issues migrating from JIRA system, to be moved to their appropriate places later
0 stars 0 forks source link

Peanutbase BLAST: possible malfunction reported via contact form #321

Closed adf-ncgr closed 8 years ago

adf-ncgr commented 9 years ago

Deepak: Could you please look into it in case there is any problem.

20150626 email:
Ye Chu (ye.chu.test@gmail.com) sent a message using the contact form at
http://www.peanutbase.org/contact.

I was trying to do a sequence alignment with blastn and the website suggested
an error was encountered. Could you please look into it?

[LEGUME-353] created by sdash-legume

adf-ncgr commented 9 years ago

After checking the Apache access & error logs on peanutbase.org, it seems likely the error the user encountered was the following:

[Fri Jun 26 12:16:04.944543 2015] [proxy_fcgi:error] [pid 5650:tid 34398521344] [client 168.18.68.65:27369] AH01071: Got error 'PHP message: [TRIPAL ERROR] NOTICE (TRIPAL_DEPRECATED): DEPRECATED: tripal_jobs_launch has been replaced with tripal_launch_job. Please update your code.\nPHP message: [TRIPAL ERROR] ERROR (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131602.blast.asn) to XML (sites/default/files/tripal/tripal_blast/2015Jun26_131602.blast.xml).\nPHP message: [TRIPAL ERROR] WARNING (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131602.blast.asn) to Tabular Output (sites/default/files/tripal/tripal_blast/2015Jun26_131602.blast.tsv).\nPHP message: [TRIPAL ERROR] WARNING (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131602.blast.asn) to HTML Output (sites/default/files/tripal/tripal_blast/2015Jun26_131602.blast.html).\n', referer: http://www.peanutbase.org/blast/nucleotide/nucleotide
[Fri Jun 26 12:17:09.807457 2015] [proxy_fcgi:error] [pid 5646:tid 34398512128] [client 168.18.68.65:26975] AH01071: Got error 'PHP message: [TRIPAL ERROR] NOTICE (TRIPAL_DEPRECATED): DEPRECATED: tripal_jobs_launch has been replaced with tripal_launch_job. Please update your code.\n', referer: http://www.peanutbase.org/blast/nucleotide/nucleotide?jid=ODMw
[Fri Jun 26 12:17:39.853064 2015] [proxy_fcgi:error] [pid 5648:tid 34398507008] [client 168.18.68.65:51570] AH01071: Got error 'PHP message: [TRIPAL ERROR] NOTICE (TRIPAL_DEPRECATED): DEPRECATED: tripal_jobs_launch has been replaced with tripal_launch_job. Please update your code.\nPHP message: [TRIPAL ERROR] ERROR (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131737.blast.asn) to XML (sites/default/files/tripal/tripal_blast/2015Jun26_131737.blast.xml).\nPHP message: [TRIPAL ERROR] WARNING (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131737.blast.asn) to Tabular Output (sites/default/files/tripal/tripal_blast/2015Jun26_131737.blast.tsv).\nPHP message: [TRIPAL ERROR] WARNING (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131737.blast.asn) to HTML Output (sites/default/files/tripal/tripal_blast/2015Jun26_131737.blast.html).\n', referer: http://www.peanutbase.org/blast/nucleotide/nucleotide?jid=ODMw
[Fri Jun 26 12:18:40.637370 2015] [proxy_fcgi:error] [pid 5646:tid 34398503936] [client 168.18.68.65:39037] AH01071: Got error 'PHP message: [TRIPAL ERROR] NOTICE (TRIPAL_DEPRECATED): DEPRECATED: tripal_jobs_launch has been replaced with tripal_launch_job. Please update your code.\nPHP message: [TRIPAL ERROR] ERROR (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131838.blast.asn) to XML (sites/default/files/tripal/tripal_blast/2015Jun26_131838.blast.xml).\nPHP message: [TRIPAL ERROR] WARNING (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131838.blast.asn) to Tabular Output (sites/default/files/tripal/tripal_blast/2015Jun26_131838.blast.tsv).\nPHP message: [TRIPAL ERROR] WARNING (BLAST_UI): Unable to convert BLAST ASN.1 archive (/tmp/2015Jun26_131838.blast.asn) to HTML Output (sites/default/files/tripal/tripal_blast/2015Jun26_131838.blast.html).\n', referer: http://www.peanutbase.org/blast/nucleotide/nucleotide

Shortly afterwards, this IP address (from Athens, Georgia) submitted a message via the contact form:

168.18.68.65 - - [26/Jun/2015:12:20:31 -0500] "POST /contact HTTP/1.0" 302 -

The ASN files in question are empty:

$ ls -l /tmp/2015Jun26_131602.blast.asn
-rw-r--r--  1 www  wheel  0 Jun 26 12:16 /tmp/2015Jun26_131602.blast.asn
$ ls -l /tmp/2015Jun26_131737.blast.asn
-rw-r--r--  1 www  wheel  0 Jun 26 12:17 /tmp/2015Jun26_131737.blast.asn
$ ls -l /tmp/2015Jun26_131838.blast.asn
-rw-r--r--  1 www  wheel  0 Jun 26 12:18 /tmp/2015Jun26_131838.blast.asn

Is it possible under normal circumstances for the ASN file to be empty? If so, can the blast_ui module handle this?

by nathanweeks

adf-ncgr commented 9 years ago

Response from reporter:

I got an error when I choose the match/mismatch score as 4/-5 instead of the 2/-3 default. I was try to see if I can find less homologous sequences from my query sequence. I was looking for potential off target site of the gRNA. I am not sure if the match/mismatch score 4/-5 allow more mismatch or not. What would you suggest?

Juliet

by ecannon

adf-ncgr commented 9 years ago

Response from Steven:

Ah – that helps me understand.

I am not sure how the match/mismatch scoring will affect the results.
You might instead try:

Or if your query sequence is genic (from CDS), try blastx (http://peanutbase.org/blast/nucleotide/protein). This should be more sensitive.

Let me know if any of these help you, or if you still run into problems.

Steven

by ecannon

adf-ncgr commented 8 years ago

Prateek, was this problem fixed with your change to word sizes?

by ecannon

adf-ncgr commented 8 years ago

Yes, I had made changes in word sizes which solve this problem.

by prateekg