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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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ST_KV_DATABASE_EXCEPTION uncaught exception #376

Open stlomo opened 3 years ago

stlomo commented 3 years ago

Hi I`m running progressive cactus on a small number of genomes in order to test it, running the provided examples with evolverMammals do not cause any issue, however when I try to run it on my own I got this error message 

    [2020-12-15T14:20:27+0100] [MainThread] [I] [toil.worker] ---TOIL WORKER OUTPUT LOG---
    [2020-12-15T14:20:27+0100] [MainThread] [I] [toil] Running Toil version 4.2.0-3aa1da130141039cb357efe36d7df9b9f6ae9b5b on host pcsy384.
    [2020-12-15T14:20:29+0100] [MainThread] [I] [cactus.shared.common] Work dirs: {'/tmp/node-697781c4-0552-4665-8fcf-6f9fedaa826d-696b7710-9209-4ccc-a9fc-16e7a595162b/tmpobf8a1pc/309661cb-e808-4c0f-a8de-4f6c8ce9702f'}
    [2020-12-15T14:20:29+0100] [MainThread] [I] [cactus.shared.common] Docker work dir: /tmp/node-697781c4-0552-4665-8fcf-6f9fedaa826d-696b7710-9209-4ccc-a9fc-16e7a595162b/tmpobf8a1pc/309661cb-e808-4c0f-a8de-4f6c8ce9702f
    [2020-12-15T14:20:29+0100] [MainThread] [I] [cactus.shared.common] Running the command ['docker', 'run', '--interactive', '--net=host', '--log-driver=none', '-u', '1000:1001', '-v', '/tmp/node-697781c4-0552-4665-8fcf-6f9fedaa826d-696b7710-9209-4ccc-a9fc-16e7a595162b/tmpobf8a1pc/309661cb-e808-4c0f-a8de-4f6c8ce9702f:/data', '--entrypoint', '/opt/cactus/wrapper.sh', '--name', '37ead286-3064-4c95-9bea-fc394a6d8fb0', '--rm', 'quay.io/comparative-genomics-toolkit/cactus:43bb27d2bd7016306940515e6b9ed08c0137dcc2', 'cactus_setup', 'Saccharomyces_mikatae', 'tmpm4czhfkv.tmp', 'N_castellii', 'tmps0jnrih0.tmp', 'Saccharomyces_paradoxus', 'tmp119m2n9g.tmp', 'Saccharomyces_cerevisiae', 'tmp0vgj8ud6.tmp', 'Saccharomyces_bayanus', 'tmpzr8aygjg.tmp', '--speciesTree', '(Saccharomyces_bayanus:1.00000050002909,((Saccharomyces_mikatae:1.00000050002909,N_castellii:0.539717490893829)Anc2:0.008288096774417985,(Saccharomyces_paradoxus:0.010896256351366871,Saccharomyces_cerevisiae:1.00000050002909)Anc3:0.00267580704204121)Anc1:0.0400104416578197)Anc0;', '--cactusDisk', '<st_kv_database_conf type="kyoto_tycoon">\n\t\t\t<kyoto_tycoon database_dir="fakepath" host="172.29.134.47" port="29613" />\n\t\t</st_kv_database_conf>\n\t', '--logLevel', 'INFO', '--outgroupEvents', 'Saccharomyces_paradoxus Saccharomyces_cerevisiae Saccharomyces_bayanus']
    [2020-12-15T14:20:29+0100] [MainThread] [I] [toil-rt] 2020-12-15 14:20:29.074687: Running the command: "docker run --interactive --net=host --log-driver=none -u 1000:1001 -v /tmp/node-697781c4-0552-4665-8fcf-6f9fedaa826d-696b7710-9209-4ccc-a9fc-16e7a595162b/tmpobf8a1pc/309661cb-e808-4c0f-a8de-4f6c8ce9702f:/data --entrypoint /opt/cactus/wrapper.sh --name 37ead286-3064-4c95-9bea-fc394a6d8fb0 --rm quay.io/comparative-genomics-toolkit/cactus:43bb27d2bd7016306940515e6b9ed08c0137dcc2 cactus_setup Saccharomyces_mikatae tmpm4czhfkv.tmp N_castellii tmps0jnrih0.tmp Saccharomyces_paradoxus tmp119m2n9g.tmp Saccharomyces_cerevisiae tmp0vgj8ud6.tmp Saccharomyces_bayanus tmpzr8aygjg.tmp --speciesTree (Saccharomyces_bayanus:1.00000050002909,((Saccharomyces_mikatae:1.00000050002909,N_castellii:0.539717490893829)Anc2:0.008288096774417985,(Saccharomyces_paradoxus:0.010896256351366871,Saccharomyces_cerevisiae:1.00000050002909)Anc3:0.00267580704204121)Anc1:0.0400104416578197)Anc0;  <...> gLevel INFO --outgroupEvents Saccharomyces_paradoxus Saccharomyces_cerevisiae Saccharomyces_bayanus"
    Running command catchsegv 'cactus_setup' 'Saccharomyces_mikatae' 'tmpm4czhfkv.tmp' 'N_castellii' 'tmps0jnrih0.tmp' 'Saccharomyces_paradoxus' 'tmp119m2n9g.tmp' 'Saccharomyces_cerevisiae' 'tmp0vgj8ud6.tmp' 'Saccharomyces_bayanus' 'tmpzr8aygjg.tmp' '--speciesTree' '(Saccharomyces_bayanus:1.00000050002909,((Saccharomyces_mikatae:1.00000050002909,N_castellii:0.539717490893829)Anc2:0.008288096774417985,(Saccharomyces_paradoxus:0.010896256351366871,Saccharomyces_cerevisiae:1.00000050002909)Anc3:0.00267580704204121)Anc1:0.0400104416578197)Anc0;' '--cactusDisk' '<st_kv_database_conf type="kyoto_tycoon">
                            <kyoto_tycoon database_dir="fakepath" host="172.29.134.47" port="29613" />
                    </st_kv_database_conf>
            ' '--logLevel' 'INFO' '--outgroupEvents' 'Saccharomyces_paradoxus Saccharomyces_cerevisiae Saccharomyces_bayanus'
    Flower disk name : <st_kv_database_conf type="kyoto_tycoon">
                            <kyoto_tycoon database_dir="fakepath" host="172.29.134.47" port="29613" />
                    </st_kv_database_conf>

    Sequence file/directory Saccharomyces_mikatae
    Sequence file/directory tmpm4czhfkv.tmp
    Sequence file/directory N_castellii
    Sequence file/directory tmps0jnrih0.tmp
    Sequence file/directory Saccharomyces_paradoxus
    Sequence file/directory tmp119m2n9g.tmp
    Sequence file/directory Saccharomyces_cerevisiae
    Sequence file/directory tmp0vgj8ud6.tmp
    Sequence file/directory Saccharomyces_bayanus
    Sequence file/directory tmpzr8aygjg.tmp
    Exception: ST_KV_DATABASE_EXCEPTION: Opening connection to host: 172.29.134.47 with error: network error
    Uncaught exception

I tried to run the pipeline stepwise using cactus-prepare but I encounter the same issue during round 0 I know it could be a firewall issue but I`m not able to identify the problem. Thank you for your help

glennhickey commented 3 years ago

Not too sure what too suggest beyond verifying your firewall. Perhaps you could try --database redis (which may only be available if you build the latest source) to use a different type of database, but I'm not confident that would help here.