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GMOD / jblast-jbconnect-hook

JBrowse/Galaxy-Blast Plugin
http://jblast.readthedocs.io
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server crash issues #279

Closed ihh closed 4 years ago

ihh commented 4 years ago

Reviewer comment from demo:

I also appear to have crashed the instance when trying to perform a BLAST using the sequence underlying one of the primer pairs. Does this mean I hit a real limit which affects the stability of a site?

I've confirmed that (after logging in) clicking the first BLAST button in the PRIMER_PAIR_1 feature detail popup launches a BLAST job that then does not terminate.

enuggetry commented 4 years ago

Address issue where query or result set is very large. (reapply bpSizeLimit= setting). https://github.com/GMOD/jbconnect/issues/175

This will serve to:

enuggetry commented 4 years ago

http://graingenes.org:1337/jbrowse/?data=IWGSC&loc=chr1A%3A365715001..366846000&tracks=DNA%2Chiconf-1.1&highlight=chr1A%3A366275000..366282999

>>>>> workflowresults  {
    "type": "blastn",
    "outputDirectory": "/home/ericiam/jb1151/IWGSC/jblastdata",
    "rawOutput": false,
    "db": "/home/ericiam/jbconnect/blastdb/wheat/wheat",
    "outfmt": 5,
    "queryFile": "/home/ericiam/jb1151/IWGSC/jblastdata/blast_region1589559739997.fa",
    "outFileExt": "blastxml",
    "returnParams": true,
    "out": "/home/ericiam/jb1151/IWGSC/jblastdata/432c6530-96c8-11ea-8695-3ba48121fa95.blastxml"
}

debug: mv /home/ericiam/jb1151/IWGSC/jblastdata/432c6530-96c8-11ea-8695-3ba48121fa95.blastxml /home/ericiam/jb1151/IWGSC/jblastdata/67_1589560080324.blastxml
debug: converting blast to json
debug: blastxml2json /home/ericiam/jb1151/IWGSC/jblastdata/67_1589560080324.blastxml /home/ericiam/jb1151/IWGSC/jblastdata/67_1589560080324.json
buffer.js:645
    return this.utf8Slice(0, this.length);
                ^

Error: Cannot create a string longer than 0x3fffffe7 characters
    at Buffer.toString (buffer.js:645:17)
    at Parser.exports.Parser.Parser.parseString (/home/ericiam/jbconnect/node_modules/xml2js/lib/xml2js.js:269:15)
    at Parser.parseString (/home/ericiam/jbconnect/node_modules/xml2js/lib/xml2js.js:6:61)
    at exports.parseString (/home/ericiam/jbconnect/node_modules/xml2js/lib/xml2js.js:296:19)
    at module.exports (/home/ericiam/jbconnect/node_modules/xmljson/lib/to_json.js:17:9)
    at /home/ericiam/jbconnect/node_modules/jblast-jbconnect-hook/api/services/blastxml2json.js:51:13
    at FSReqWrap.readFileAfterClose [as oncomplete] (internal/fs/read_file_context.js:53:3)

test 1 (68) no parameters string crash

594102056

xml size 1176453742

test2 (69) max_target_seqs 100 max_hsps 3

594102056

66 hits xml size 481262

test3 (70) max_target_seqs: 100, max_hsps: 5

594102056

xml size 785319 110 hits

test 4 (71) max_target_seqs: 200, max_hsps: 5 xml size 785319 (same as 70) 110 hits (same as 70)

test (72) no parameters handle error from xmljson module

enuggetry commented 4 years ago

added max_hsps blast option to jbconnect.config.js (the local config file), which reduces the number of hit results.

        jblast: {
            blastProfiles: {
                'wheat': {
                    'db': 'wheat',
                    'max_hsps':10
                }
            }

        },
ihh commented 4 years ago

This bug is not yet fixed.

ihh commented 4 years ago

Correction - it is fixed, just took a long time to run.