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TheSEED / RASTtk-Distribution

KBase distribution module for RASTtk.
http://www.nature.com/articles/srep08365
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Error: Can't connect to walnut.mcs.anl.gov:7080 #8

Closed MostafaYA closed 5 years ago

MostafaYA commented 5 years ago

Hello, I have installed rasttk on ubuntu. While running the script rast-process-genome-batch , such an error appeared (Can't connect to walnut.mcs.anl.gov:7080). Below is the full eror. The question is: what is the outgoing port that needs to be unlocked form out IT department, or simply how can I fix this issue? thanks

Full error JSONRPC error: submit failed: Can't connect to walnut.mcs.anl.gov:7080

Connection refused at /disks/patric-common/runtime/lib/perl5/site_perl/5.20.2/LWP/Protocol/http.pm line 47.

{ "info" : { "name" : "rasttk", "clientgroups" : "", "project" : "rasttk", "pipeline" : "rasttk", "user" : "MostafaYA" }, "tasks" : [ { "skip" : 0, "taskid" : "0", "userattr" : { "genome_id" : "6666666.407234", "filename" : "10CS0073" }, "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "description" : "rast_run_pipeline_local", "name" : "rast_run_pipeline_local", "args" : "@pipeinput_0.json pipeoutput_0.json stdout_0.txt stderr_0.txt" }, "outputs" : { "pipeoutput_0.json" : { "node" : "-", "name" : "pipeoutput_0.json", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "stdout_0.txt" : { "name" : "stdout_0.txt", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" }, "stderr_0.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_0.txt", "node" : "-" } }, "inputs" : { "pipeinput_0.json" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_0.json", "node" : "58fcc5fa-e715-4b24-9877-268d99ce43d7" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1 }, { "skip" : 0, "taskid" : "1", "userattr" : { "genome_id" : "6666666.407232", "filename" : "10CS0048" }, "cmd" : { "description" : "rast_run_pipeline_local", "name" : "rast_run_pipeline_local", "args" : "@pipeinput_1.json pipeoutput_1.json stdout_1.txt stderr_1.txt", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "outputs" : { "stderr_1.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_1.txt" }, "pipeoutput_1.json" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeoutput_1.json" }, "stdout_1.txt" : { "name" : "stdout_1.txt", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" } }, "inputs" : { "pipeinput_1.json" : { "node" : "f489834e-97c3-46ad-a628-df4bd0176b6d", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_1.json" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1 }, { "skip" : 0, "outputs" : { "stderr_2.txt" : { "node" : "-", "name" : "stderr_2.txt", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "pipeoutput_2.json" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeoutput_2.json" }, "stdout_2.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_2.txt" } }, "userattr" : { "filename" : "10CS0082", "genome_id" : "6666666.407238" }, "cmd" : { "args" : "@pipeinput_2.json pipeoutput_2.json stdout_2.txt stderr_2.txt", "name" : "rast_run_pipeline_local", "description" : "rast_run_pipeline_local", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "taskid" : "2", "partinfo" : {}, "inputs" : { "pipeinput_2.json" : { "name" : "pipeinput_2.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "84daabd6-b34c-4ed6-9531-0c0546c0f149" } }, "totalwork" : 1, "dependsOn" : [] }, { "dependsOn" : [], "totalwork" : 1, "inputs" : { "pipeinput_3.json" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_3.json", "node" : "05c5af62-eb99-4f27-802f-8d9d104992af" } }, "partinfo" : {}, "taskid" : "3", "userattr" : { "genome_id" : "6666666.407237", "filename" : "10CS0081" }, "outputs" : { "stderr_3.txt" : { "node" : "-", "name" : "stderr_3.txt", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "stdout_3.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_3.txt", "node" : "-" }, "pipeoutput_3.json" : { "node" : "-", "name" : "pipeoutput_3.json", "host" : "http://tutorial.theseed.org/services/shock_api2" } }, "cmd" : { "args" : "@pipeinput_3.json pipeoutput_3.json stdout_3.txt stderr_3.txt", "name" : "rast_run_pipeline_local", "description" : "rast_run_pipeline_local", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "skip" : 0 }, { "inputs" : { "pipeinput_4.json" : { "name" : "pipeinput_4.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "942c0fcd-fe3c-458c-9b9b-bfa6fe1b654e" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1, "skip" : 0, "taskid" : "4", "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "name" : "rast_run_pipeline_local", "args" : "@pipeinput_4.json pipeoutput_4.json stdout_4.txt stderr_4.txt", "description" : "rast_run_pipeline_local" }, "userattr" : { "genome_id" : "6666666.407233", "filename" : "10CS0052" }, "outputs" : { "stderr_4.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_4.txt" }, "stdout_4.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_4.txt", "node" : "-" }, "pipeoutput_4.json" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeoutput_4.json" } } }, { "outputs" : { "stderr_5.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_5.txt", "node" : "-" }, "pipeoutput_5.json" : { "node" : "-", "name" : "pipeoutput_5.json", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "stdout_5.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_5.txt", "node" : "-" } }, "userattr" : { "genome_id" : "6666666.407236", "filename" : "10CS0077" }, "cmd" : { "args" : "@pipeinput_5.json pipeoutput_5.json stdout_5.txt stderr_5.txt", "name" : "rast_run_pipeline_local", "description" : "rast_run_pipeline_local", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "taskid" : "5", "skip" : 0, "totalwork" : 1, "dependsOn" : [], "partinfo" : {}, "inputs" : { "pipeinput_5.json" : { "node" : "97bdc8bd-3679-426f-8fb5-4c453d5f9663", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_5.json" } } }, { "partinfo" : {}, "inputs" : { "pipeinput_6.json" : { "name" : "pipeinput_6.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "997af0d5-bcfd-4883-8aac-9eb22046817c" } }, "totalwork" : 1, "dependsOn" : [], "skip" : 0, "outputs" : { "stderr_6.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_6.txt" }, "stdout_6.txt" : { "node" : "-", "name" : "stdout_6.txt", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "pipeoutput_6.json" : { "name" : "pipeoutput_6.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" } }, "userattr" : { "filename" : "10CS0083", "genome_id" : "6666666.407239" }, "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "description" : "rast_run_pipeline_local", "args" : "@pipeinput_6.json pipeoutput_6.json stdout_6.txt stderr_6.txt", "name" : "rast_run_pipeline_local" }, "taskid" : "6" }, { "taskid" : "7", "outputs" : { "stdout_7.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_7.txt" }, "stderr_7.txt" : { "name" : "stderr_7.txt", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" }, "pipeoutput_7.json" : { "name" : "pipeoutput_7.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" } }, "userattr" : { "filename" : "10CS0074", "genome_id" : "6666666.407235" }, "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "description" : "rast_run_pipeline_local", "name" : "rast_run_pipeline_local", "args" : "@pipeinput_7.json pipeoutput_7.json stdout_7.txt stderr_7.txt" }, "skip" : 0, "dependsOn" : [], "totalwork" : 1, "inputs" : { "pipeinput_7.json" : { "name" : "pipeinput_7.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "a7b380df-782e-49b7-90a7-376535df2ce2" } }, "partinfo" : {} } ] }

JSONRPC error code: -32603 JSONRPC error data:submit failed: Can't connect to walnut.mcs.anl.gov:7080

Connection refused at /disks/patric-common/runtime/lib/perl5/site_perl/5.20.2/LWP/Protocol/http.pm line 47.

{ "info" : { "name" : "rasttk", "clientgroups" : "", "project" : "rasttk", "pipeline" : "rasttk", "user" : "MostafaYA" }, "tasks" : [ { "skip" : 0, "taskid" : "0", "userattr" : { "genome_id" : "6666666.407234", "filename" : "10CS0073" }, "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "description" : "rast_run_pipeline_local", "name" : "rast_run_pipeline_local", "args" : "@pipeinput_0.json pipeoutput_0.json stdout_0.txt stderr_0.txt" }, "outputs" : { "pipeoutput_0.json" : { "node" : "-", "name" : "pipeoutput_0.json", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "stdout_0.txt" : { "name" : "stdout_0.txt", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" }, "stderr_0.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_0.txt", "node" : "-" } }, "inputs" : { "pipeinput_0.json" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_0.json", "node" : "58fcc5fa-e715-4b24-9877-268d99ce43d7" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1 }, { "skip" : 0, "taskid" : "1", "userattr" : { "genome_id" : "6666666.407232", "filename" : "10CS0048" }, "cmd" : { "description" : "rast_run_pipeline_local", "name" : "rast_run_pipeline_local", "args" : "@pipeinput_1.json pipeoutput_1.json stdout_1.txt stderr_1.txt", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "outputs" : { "stderr_1.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_1.txt" }, "pipeoutput_1.json" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeoutput_1.json" }, "stdout_1.txt" : { "name" : "stdout_1.txt", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" } }, "inputs" : { "pipeinput_1.json" : { "node" : "f489834e-97c3-46ad-a628-df4bd0176b6d", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_1.json" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1 }, { "skip" : 0, "outputs" : { "stderr_2.txt" : { "node" : "-", "name" : "stderr_2.txt", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "pipeoutput_2.json" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeoutput_2.json" }, "stdout_2.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_2.txt" } }, "userattr" : { "filename" : "10CS0082", "genome_id" : "6666666.407238" }, "cmd" : { "args" : "@pipeinput_2.json pipeoutput_2.json stdout_2.txt stderr_2.txt", "name" : "rast_run_pipeline_local", "description" : "rast_run_pipeline_local", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "taskid" : "2", "partinfo" : {}, "inputs" : { "pipeinput_2.json" : { "name" : "pipeinput_2.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "84daabd6-b34c-4ed6-9531-0c0546c0f149" } }, "totalwork" : 1, "dependsOn" : [] }, { "dependsOn" : [], "totalwork" : 1, "inputs" : { "pipeinput_3.json" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_3.json", "node" : "05c5af62-eb99-4f27-802f-8d9d104992af" } }, "partinfo" : {}, "taskid" : "3", "userattr" : { "genome_id" : "6666666.407237", "filename" : "10CS0081" }, "outputs" : { "stderr_3.txt" : { "node" : "-", "name" : "stderr_3.txt", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "stdout_3.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_3.txt", "node" : "-" }, "pipeoutput_3.json" : { "node" : "-", "name" : "pipeoutput_3.json", "host" : "http://tutorial.theseed.org/services/shock_api2" } }, "cmd" : { "args" : "@pipeinput_3.json pipeoutput_3.json stdout_3.txt stderr_3.txt", "name" : "rast_run_pipeline_local", "description" : "rast_run_pipeline_local", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "skip" : 0 }, { "inputs" : { "pipeinput_4.json" : { "name" : "pipeinput_4.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "942c0fcd-fe3c-458c-9b9b-bfa6fe1b654e" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1, "skip" : 0, "taskid" : "4", "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "name" : "rast_run_pipeline_local", "args" : "@pipeinput_4.json pipeoutput_4.json stdout_4.txt stderr_4.txt", "description" : "rast_run_pipeline_local" }, "userattr" : { "genome_id" : "6666666.407233", "filename" : "10CS0052" }, "outputs" : { "stderr_4.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_4.txt" }, "stdout_4.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_4.txt", "node" : "-" }, "pipeoutput_4.json" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeoutput_4.json" } } }, { "outputs" : { "stderr_5.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_5.txt", "node" : "-" }, "pipeoutput_5.json" : { "node" : "-", "name" : "pipeoutput_5.json", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "stdout_5.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_5.txt", "node" : "-" } }, "userattr" : { "genome_id" : "6666666.407236", "filename" : "10CS0077" }, "cmd" : { "args" : "@pipeinput_5.json pipeoutput_5.json stdout_5.txt stderr_5.txt", "name" : "rast_run_pipeline_local", "description" : "rast_run_pipeline_local", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "taskid" : "5", "skip" : 0, "totalwork" : 1, "dependsOn" : [], "partinfo" : {}, "inputs" : { "pipeinput_5.json" : { "node" : "97bdc8bd-3679-426f-8fb5-4c453d5f9663", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_5.json" } } }, { "partinfo" : {}, "inputs" : { "pipeinput_6.json" : { "name" : "pipeinput_6.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "997af0d5-bcfd-4883-8aac-9eb22046817c" } }, "totalwork" : 1, "dependsOn" : [], "skip" : 0, "outputs" : { "stderr_6.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_6.txt" }, "stdout_6.txt" : { "node" : "-", "name" : "stdout_6.txt", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "pipeoutput_6.json" : { "name" : "pipeoutput_6.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" } }, "userattr" : { "filename" : "10CS0083", "genome_id" : "6666666.407239" }, "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "description" : "rast_run_pipeline_local", "args" : "@pipeinput_6.json pipeoutput_6.json stdout_6.txt stderr_6.txt", "name" : "rast_run_pipeline_local" }, "taskid" : "6" }, { "taskid" : "7", "outputs" : { "stdout_7.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_7.txt" }, "stderr_7.txt" : { "name" : "stderr_7.txt", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" }, "pipeoutput_7.json" : { "name" : "pipeoutput_7.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" } }, "userattr" : { "filename" : "10CS0074", "genome_id" : "6666666.407235" }, "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "description" : "rast_run_pipeline_local", "name" : "rast_run_pipeline_local", "args" : "@pipeinput_7.json pipeoutput_7.json stdout_7.txt stderr_7.txt" }, "skip" : 0, "dependsOn" : [], "totalwork" : 1, "inputs" : { "pipeinput_7.json" : { "name" : "pipeinput_7.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "a7b380df-782e-49b7-90a7-376535df2ce2" } }, "partinfo" : {} } ] }

Trace begun at /usr/share/rasttk/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm line 21037 Bio::KBase::GenomeAnnotation::Client::pipeline_batch_start('Bio::KBase::GenomeAnnotation::Client=HASH(0x561b134e8908)', 'ARRAY(0x561b13204348)', 'HASH(0x561b134d2398)') called at /usr/share/rasttk/deployment/plbin/rast-process-genome-batch.pl line 105

olsonanl commented 5 years ago

Good morning - we had a crash of the workflow server yesterday that would have caused that error. Please try your job again and let us know if you see any additional problems.

—bob

On Jan 10, 2019, at 2:52 AM, MostafaYA notifications@github.com<mailto:notifications@github.com> wrote:

Hello, I have installed rasttk on ubuntu. While running the script rast-process-genome-batch , such an error appeared (Can't connect to walnut.mcs.anl.gov:7080http://walnut.mcs.anl.gov:7080). Below is the full eror. The question is: what is the outgoing port that needs to be unlocked form out IT department, or simply how can I fix this issue? thanks

Full error JSONRPC error: submit failed: Can't connect to walnut.mcs.anl.gov:7080http://walnut.mcs.anl.gov:7080

Connection refused at /disks/patric-common/runtime/lib/perl5/site_perl/5.20.2/LWP/Protocol/http.pm line 47.

{ "info" : { "name" : "rasttk", "clientgroups" : "", "project" : "rasttk", "pipeline" : "rasttk", "user" : "MostafaYA" }, "tasks" : [ { "skip" : 0, "taskid" : "0", "userattr" : { "genome_id" : "6666666.407234", "filename" : "10CS0073" }, "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "description" : "rast_run_pipeline_local", "name" : "rast_run_pipeline_local", "args" : "@pipeinput_0.json pipeoutput_0.json stdout_0.txt stderr_0.txt" }, "outputs" : { "pipeoutput_0.json" : { "node" : "-", "name" : "pipeoutput_0.json", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "stdout_0.txt" : { "name" : "stdout_0.txt", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" }, "stderr_0.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_0.txt", "node" : "-" } }, "inputs" : { "pipeinput_0.json" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_0.json", "node" : "58fcc5fa-e715-4b24-9877-268d99ce43d7" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1 }, { "skip" : 0, "taskid" : "1", "userattr" : { "genome_id" : "6666666.407232", "filename" : "10CS0048" }, "cmd" : { "description" : "rast_run_pipeline_local", "name" : "rast_run_pipeline_local", "args" : "@pipeinput_1.json pipeoutput_1.json stdout_1.txt stderr_1.txt", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "outputs" : { "stderr_1.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_1.txt" }, "pipeoutput_1.json" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeoutput_1.json" }, "stdout_1.txt" : { "name" : "stdout_1.txt", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "-" } }, "inputs" : { "pipeinput_1.json" : { "node" : "f489834e-97c3-46ad-a628-df4bd0176b6d", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_1.json" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1 }, { "skip" : 0, "outputs" : { "stderr_2.txt" : { "node" : "-", "name" : "stderr_2.txt", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "pipeoutput_2.json" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeoutput_2.json" }, "stdout_2.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_2.txt" } }, "userattr" : { "filename" : "10CS0082", "genome_id" : "6666666.407238" }, "cmd" : { "args" : "@pipeinput_2.json pipeoutput_2.json stdout_2.txt stderr_2.txt", "name" : "rast_run_pipeline_local", "description" : "rast_run_pipeline_local", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "taskid" : "2", "partinfo" : {}, "inputs" : { "pipeinput_2.json" : { "name" : "pipeinput_2.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "84daabd6-b34c-4ed6-9531-0c0546c0f149" } }, "totalwork" : 1, "dependsOn" : [] }, { "dependsOn" : [], "totalwork" : 1, "inputs" : { "pipeinput_3.json" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "pipeinput_3.json", "node" : "05c5af62-eb99-4f27-802f-8d9d104992af" } }, "partinfo" : {}, "taskid" : "3", "userattr" : { "genome_id" : "6666666.407237", "filename" : "10CS0081" }, "outputs" : { "stderr_3.txt" : { "node" : "-", "name" : "stderr_3.txt", "host" : "http://tutorial.theseed.org/services/shock_api2" }, "stdout_3.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_3.txt", "node" : "-" }, "pipeoutput_3.json" : { "node" : "-", "name" : "pipeoutput_3.json", "host" : "http://tutorial.theseed.org/services/shock_api2" } }, "cmd" : { "args" : "@pipeinput_3.json pipeoutput_3.json stdout_3.txt stderr_3.txt", "name" : "rast_run_pipeline_local", "description" : "rast_run_pipeline_local", "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } } }, "skip" : 0 }, { "inputs" : { "pipeinput_4.json" : { "name" : "pipeinput_4.json", "host" : "http://tutorial.theseed.org/services/shock_api2", "node" : "942c0fcd-fe3c-458c-9b9b-bfa6fe1b654e" } }, "partinfo" : {}, "dependsOn" : [], "totalwork" : 1, "skip" : 0, "taskid" : "4", "cmd" : { "environ" : { "private" : { "KB_AUTH_TOKEN" : "un=MostafaYA|tokenid=CFD78E24-141F-11E9-B082-159D682E0674|expiry=1578582247|client_id=MostafaYA|token_type=Bearer|SigningSubject=http://rast.nmpdr.org/goauth/keys/E087E220-F8B1-11E3-9175-BD9D42A49C03|this_is_globus=globus_style_token|sig=b337da49f8eb51b35350728d84253ef5d2ae978914cb741e0fad8a2eee673314a200cd7be0cf37a8dc92db3cf5484251b590fc0109df1f0e5ac8880e5d2c0ef2ff3e81fd22422331dd34b2770d6849b58c21143aa223af1d688efe41ec2a45fca45df545871f6972ca4361117bc456522f437b6c9a1be0de7f5ef4c65f3a95ec" } }, "name" : "rast_run_pipeline_local", "args" : "@pipeinput_4.json pipeoutput_4.json stdout_4.txt stderr_4.txt", "description" : "rast_run_pipeline_local" }, "userattr" : { "genome_id" : "6666666.407233", "filename" : "10CS0052" }, "outputs" : { "stderr_4.txt" : { "node" : "-", "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stderr_4.txt" }, "stdout_4.txt" : { "host" : "http://tutorial.theseed.org/services/shock_api2", "name" : "stdout_4.txt", "node" : "-" }, 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JSONRPC error code: -32603 JSONRPC error data:submit failed: Can't connect to walnut.mcs.anl.gov:7080http://walnut.mcs.anl.gov:7080

Connection refused at /disks/patric-common/runtime/lib/perl5/site_perl/5.20.2/LWP/Protocol/http.pm line 47.

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Trace begun at /usr/share/rasttk/deployment/lib/Bio/KBase/GenomeAnnotation/Client.pm line 21037 Bio::KBase::GenomeAnnotation::Client::pipeline_batch_start('Bio::KBase::GenomeAnnotation::Client=HASH(0x561b134e8908)', 'ARRAY(0x561b13204348)', 'HASH(0x561b134d2398)') called at /usr/share/rasttk/deployment/plbin/rast-process-genome-batch.pl line 105

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MostafaYA commented 5 years ago

Thanks a lot for your answer. The error regarding connection to walnut.mcs.anl.gov is no longer there. What I am experiencing now is that all jobs are queued even I have submitted 5 days ago id: e45bd108-185b-4014-bca6-6bdc6f03eb80 id: 6492a556-2999-457c-af14-f9b8d7749612 I am not sure what is the reason for that. Another question: how can I abort such jobs that are taking too long so I can start new ones

olsonanl commented 5 years ago

Hi - the workflow engine workers were stuck. I've restarted them and jobs are processing.

In current RASTtk we don't expose a job kill function; definitely something we should add. I'll be doing a revamp of the RASTtk processing stuff sometime this spring as we are changing the backend scheduler we're using to handle RASTtk and the other PATRIC backend work.