Closed adf-ncgr closed 8 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
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
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
Prateek, was this problem fixed with your change to word sizes?
by ecannon
Yes, I had made changes in word sizes which solve this problem.
by prateekg
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