Hi, Prof. Priyam
The program ran very well yesterday, but today it became very slow, including the startup and query. The same sequence query took 30s yesterday, but today maybe 3 min. And the start time (seen in the figure) was much longer than yesterday (about 5s). My computer has not been made any changes.
Environment:
Ubuntu 18.04,
Sequenceserver 2.0
The debug log is following
[2021-01-31 17:55:27] DEBUG {“job_id”=>“1f193349-c16d-4bc4-b80e-4f684124eab7”}
... - - [31/Jan/2021:17:55:27 +09] “GET /?job_id=1f193349-c16d-4bc4-b80e-4f684124eab7 HTTP/1.1” 200 2819
[2021-01-31 17:55:28] DEBUG {}
... - - [31/Jan/2021:17:55:28 +09] “GET /favicon.ico HTTP/1.1” 200 2649
[2021-01-31 17:55:28] DEBUG {“job_id”=>“1f193349-c16d-4bc4-b80e-4f684124eab7”}
... - - [31/Jan/2021:17:55:28 +09] “GET /searchdata.json?job_id=1f193349-c16d-4bc4-b80e-4f684124eab7&job_id=1f193349-c16d-4bc4-b80e-4f684124eab7 HTTP/1.1” 200 352
[2021-01-31 17:55:30] DEBUG {“job_id”=>“1f193349-c16d-4bc4-b80e-4f684124eab7”, “sequence”=>">POLF1\r\nAKYACCTGCCATCTGTTTTCCAT\r\n>POLR1\r\nCAGAGAYCCAATTTGGAAAGGACC\r\n>POLP1\r\nCTCTGGAAAGGTGAAGGIGCAGTAGTAATACA", “databases”=>[“9a4b8d7aec86130340806e13778c0a8c”], “advanced”=>"-task blastn-short -evalue 1e-2", “method”=>“blastn”}
... - - [31/Jan/2021:17:55:30 +09] “POST /?job_id=1f193349-c16d-4bc4-b80e-4f684124eab7 HTTP/1.1” 303 0
[2021-01-31 17:55:30] DEBUG Executing: blastn -db ‘/home/fdd/hiv/HIV_database.fa’ -query ‘/home/fdd/.sequenceserver/33eaf442-37ab-454c-a66a-aefb7731be82/query.fa’ -task blastn-short -evalue 1e-2 -outfmt ‘11 qcovs qcovhsp’ -num_threads 4
[2021-01-31 17:55:30] DEBUG {}
... - - [31/Jan/2021:17:55:30 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82 HTTP/1.1” 200 2652
[2021-01-31 17:55:32] DEBUG {}
... - - [31/Jan/2021:17:55:32 +09] “GET /favicon.ico HTTP/1.1” 200 2655
[2021-01-31 17:55:33] DEBUG {}
... - - [31/Jan/2021:17:55:33 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:33] DEBUG {}
... - - [31/Jan/2021:17:55:33 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:33] DEBUG {}
... - - [31/Jan/2021:17:55:33 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:34] DEBUG {}
... - - [31/Jan/2021:17:55:34 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:35] DEBUG {}
... - - [31/Jan/2021:17:55:35 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:37] DEBUG {}
... - - [31/Jan/2021:17:55:37 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:40] DEBUG {}
... - - [31/Jan/2021:17:55:40 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:45] DEBUG {}
... - - [31/Jan/2021:17:55:45 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:50] DEBUG {}
... - - [31/Jan/2021:17:55:50 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:55:55] DEBUG {}
... - - [31/Jan/2021:17:55:55 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:00] DEBUG {}
... - - [31/Jan/2021:17:56:00 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:05] DEBUG {}
... - - [31/Jan/2021:17:56:05 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:10] DEBUG {}
... - - [31/Jan/2021:17:56:10 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:15] DEBUG {}
... - - [31/Jan/2021:17:56:15 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:20] DEBUG {}
... - - [31/Jan/2021:17:56:20 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:25] DEBUG {}
... - - [31/Jan/2021:17:56:25 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:30] DEBUG {}
... - - [31/Jan/2021:17:56:30 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:35] DEBUG {}
... - - [31/Jan/2021:17:56:35 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:40] DEBUG {}
... - - [31/Jan/2021:17:56:40 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:45] DEBUG {}
... - - [31/Jan/2021:17:56:45 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:50] DEBUG {}
... - - [31/Jan/2021:17:56:50 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:56:55] DEBUG {}
... - - [31/Jan/2021:17:56:55 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 202 0
[2021-01-31 17:57:00] DEBUG {}
[2021-01-31 17:57:00] DEBUG Executing: blast_formatter -archive ‘/home/fdd/.sequenceserver/33eaf442-37ab-454c-a66a-aefb7731be82/stdout’ -outfmt '5 ’
[2021-01-31 17:58:31] DEBUG Executing: blast_formatter -archive ‘/home/fdd/.sequenceserver/33eaf442-37ab-454c-a66a-aefb7731be82/stdout’ -outfmt ‘7 qseqid sseqid sscinames qcovs qcovhsp’
... - - [31/Jan/2021:17:57:00 +09] “GET /33eaf442-37ab-454c-a66a-aefb7731be82.json HTTP/1.1” 200 5047
[2021-01-31 18:02:52] DEBUG {}
... - - [31/Jan/2021:18:02:52 +09] “GET /favicon.ico HTTP/1.1” 200 2654
[2021-01-31 18:02:56] DEBUG {}
... - - [31/Jan/2021:18:02:56 +09] “GET /favicon.ico HTTP/1.1” 200 2643
[2021-01-31 18:02:59] DEBUG {}
... - - [31/Jan/2021:18:02:59 +09] “GET /favicon.ico HTTP/1.1” 200 2653
[2021-01-31 18:03:03] DEBUG {}
... - - [31/Jan/2021:18:03:03 +09] “GET /favicon.ico HTTP/1.1” 200 2652
[2021-01-31 18:03:16] DEBUG {}
... - - [31/Jan/2021:18:03:16 +09] “GET /favicon.ico HTTP/1.1” 200 2650
[2021-01-31 18:03:17] DEBUG {}
... - - [31/Jan/2021:18:03:17 +09] “GET /favicon.ico HTTP/1.1” 200 2650
Hello,
Do you know what changed between yesterday and today? I noticed in the log you sent, that you are using BLAST 2.11.0? Could it be that you updated BLAST and that caused things to slow down?
ps: I am not a professor
Priyam
Hi,
Thanks for your kind reply, and I am so sorry for the wrong title ‘Prof.".
I didn’t change anything and the only difference was that the program had run in the background with “nohup” command for a night. The day before yesterday I also use the Blast Version 2.11. As can be seen, the time took to ’ Executing: blast_formatter -archive’ was too long than before, so today I will try to reinstall the lower version blast and lower version sequenceserver to figure out whether the time will be short. I would like to express my heartful gratitude to you.
Regards,
Feb.1, 2021
Hi,
I solved the problems!
I replaced Blast 2.11.0 with 2.10.1, but unfortunately, version 2.10.1 reported errors, the same message as “https://github.com/wurmlab/sequenceserver/issues/458”. Then I replaced the blast_formatter with version 2.9.0, and no error was reported again, and the time took to handle a query was about 1s. Now, everything works well. Thanks a lot for your work and help.
Devin