{"action":"created","issue":{"url":"https://api.github.com/repos/RWilton/Arioc/issues/4","repository_url":"https://api.github.com/repos/RWilton/Arioc","labels_url":"https://api.github.com/repos/RWilton/Arioc/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/RWilton/Arioc/issues/4/comments","events_url":"https://api.github.com/repos/RWilton/Arioc/issues/4/events","html_url":"https://github.com/RWilton/Arioc/issues/4","id":359054662,"node_id":"MDU6SXNzdWUzNTkwNTQ2NjI=","number":4,"title":"Error with encoding reference genome","user":{"login":"standage","id":566823,"node_id":"MDQ6VXNlcjU2NjgyMw==","avatar_url":"https://avatars2.githubusercontent.com/u/566823?v=4","gravatar_id":"","url":"https://api.github.com/users/standage","html_url":"https://github.com/standage","followers_url":"https://api.github.com/users/standage/followers","following_url":"https://api.github.com/users/standage/following{/other_user}","gists_url":"https://api.github.com/users/standage/gists{/gist_id}","starred_url":"https://api.github.com/users/standage/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/standage/subscriptions","organizations_url":"https://api.github.com/users/standage/orgs","repos_url":"https://api.github.com/users/standage/repos","events_url":"https://api.github.com/users/standage/events{/privacy}","received_events_url":"https://api.github.com/users/standage/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-11T13:45:00Z","updated_at":"2018-09-13T04:28:04Z","closed_at":null,"author_association":"NONE","body":"I'm trying out Arioc for the first time and I'm having trouble with the reference genome encoding. Running AriocE version v1.25.2401.18201 I get the following output while doing the nongapped encoding.\r\n\r\n```\r\n165230676 [000076b9] AriocE v1.25.2401.18201 (release)\r\n165230677 [000076b9] Copyright (c) 2015-2018 Johns Hopkins University.  All rights reserved.\r\n165230677 [000076b9]  data type sizes      : int=4 long=8 *=8\r\n165230677 [000076b9]  executable file      : \r\n165230679 [000076b9]  configuration file : /path/to/my/projdir/config/encode-refr-nongapped.xml\r\n165230691 [000076b9] encodeR: encoding 43 files (86 sequences) (8 CPU threads available)...\r\n170714855 [000076b9] encodeR: encoded 43 files (86 sequences)\r\n172715421 [000076b9] computeJlistSizes:  log2(nJ)  # J-lists\r\n172715422 [000076b9] computeJlistSizes:         0      10713\r\n172715422 [000076b9] computeJlistSizes:         1     341060\r\n172715422 [000076b9] computeJlistSizes:         2   17427473\r\n172715422 [000076b9] computeJlistSizes:         3  365417880\r\n172715422 [000076b9] computeJlistSizes:         4  560730395\r\n172715422 [000076b9] computeJlistSizes:         5   93906187\r\n172715422 [000076b9] computeJlistSizes:         6   22111708\r\n172715422 [000076b9] computeJlistSizes:         7    7880260\r\n172715422 [000076b9] computeJlistSizes:         8    3306299\r\n172715422 [000076b9] computeJlistSizes:         9    1535308\r\n172715422 [000076b9] computeJlistSizes:        10     705079\r\n172715422 [000076b9] computeJlistSizes:        11     246196\r\n172715422 [000076b9] computeJlistSizes:        12      87600\r\n172715422 [000076b9] computeJlistSizes:        13      28644\r\n172715422 [000076b9] computeJlistSizes:        14       5676\r\n172715422 [000076b9] computeJlistSizes:        15        511\r\n172715422 [000076b9] computeJlistSizes:        16          9\r\n172723704 [000076b9] ApplicationException ([0x30393] AriocE/AriocE.R.cpp 408): computeJlistSizes: too many J values (28464018949) for J table (maximum = 8589934591)\r\n```\r\n\r\nThe manual discusses the performance benefits of higher vs lower choices of the J parameter, but it is unclear whether the issue is due to parameter selection or an issue with the software. Please advise.\r\n\r\nThis is the configuration file I used.\r\n\r\n```xml\r\n<?xml version=\"1.0\" encoding=\"utf-8\"?>\r\n\r\n<AriocE seed=\"ssi84_2_30\" maxDOP=\"8\" maxJ=\"*\">\r\n    <dataIn sequenceType=\"R\" srcId=\"0\" filePath=\"/path/to/my/projdir/refr\" uriPath=\"https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Assemblies/v1.0/iwgsc_refseqv1.0_all_chromosomes.zip\">\r\n        <file subId=\"1\">Taes_chr1A_part1.fasta</file>\r\n        <file subId=\"2\">Taes_chr1A_part2.fasta</file>\r\n        <file subId=\"3\">Taes_chr1B_part1.fasta</file>\r\n        <file subId=\"4\">Taes_chr1B_part2.fasta</file>\r\n        <file subId=\"5\">Taes_chr1D_part1.fasta</file>\r\n        <file subId=\"6\">Taes_chr1D_part2.fasta</file>\r\n        <file subId=\"7\">Taes_chr2A_part1.fasta</file>\r\n        <file subId=\"8\">Taes_chr2A_part2.fasta</file>\r\n        <file subId=\"9\">Taes_chr2B_part1.fasta</file>\r\n        <file subId=\"10\">Taes_chr2B_part2.fasta</file>\r\n        <file subId=\"11\">Taes_chr2D_part1.fasta</file>\r\n        <file subId=\"12\">Taes_chr2D_part2.fasta</file>\r\n        <file subId=\"13\">Taes_chr3A_part1.fasta</file>\r\n        <file subId=\"14\">Taes_chr3A_part2.fasta</file>\r\n        <file subId=\"15\">Taes_chr3B_part1.fasta</file>\r\n        <file subId=\"16\">Taes_chr3B_part2.fasta</file>\r\n        <file subId=\"17\">Taes_chr3D_part1.fasta</file>\r\n        <file subId=\"18\">Taes_chr3D_part2.fasta</file>\r\n        <file subId=\"19\">Taes_chr4A_part1.fasta</file>\r\n        <file subId=\"20\">Taes_chr4A_part2.fasta</file>\r\n        <file subId=\"21\">Taes_chr4B_part1.fasta</file>\r\n        <file subId=\"22\">Taes_chr4B_part2.fasta</file>\r\n        <file subId=\"23\">Taes_chr4D_part1.fasta</file>\r\n        <file subId=\"24\">Taes_chr4D_part2.fasta</file>\r\n        <file subId=\"25\">Taes_chr5A_part1.fasta</file>\r\n        <file subId=\"26\">Taes_chr5A_part2.fasta</file>\r\n        <file subId=\"27\">Taes_chr5B_part1.fasta</file>\r\n        <file subId=\"28\">Taes_chr5B_part2.fasta</file>\r\n        <file subId=\"29\">Taes_chr5D_part1.fasta</file>\r\n        <file subId=\"30\">Taes_chr5D_part2.fasta</file>\r\n        <file subId=\"31\">Taes_chr6A_part1.fasta</file>\r\n        <file subId=\"32\">Taes_chr6A_part2.fasta</file>\r\n        <file subId=\"33\">Taes_chr6B_part1.fasta</file>\r\n        <file subId=\"34\">Taes_chr6B_part2.fasta</file>\r\n        <file subId=\"35\">Taes_chr6D_part1.fasta</file>\r\n        <file subId=\"36\">Taes_chr6D_part2.fasta</file>\r\n        <file subId=\"37\">Taes_chr7A_part1.fasta</file>\r\n        <file subId=\"38\">Taes_chr7A_part2.fasta</file>\r\n        <file subId=\"39\">Taes_chr7B_part1.fasta</file>\r\n        <file subId=\"40\">Taes_chr7B_part2.fasta</file>\r\n        <file subId=\"41\">Taes_chr7D_part1.fasta</file>\r\n        <file subId=\"42\">Taes_chr7D_part2.fasta</file>\r\n        <file subId=\"43\">Taes_chrUn.fasta</file>\r\n    </dataIn>\r\n    <dataOut>\r\n        <path>/path/to/my/projdir/refr-encoded</path>\r\n    </dataOut>\r\n</AriocE>\r\n```"},"comment":{"url":"https://api.github.com/repos/RWilton/Arioc/issues/comments/420879513","html_url":"https://github.com/RWilton/Arioc/issues/4#issuecomment-420879513","issue_url":"https://api.github.com/repos/RWilton/Arioc/issues/4","id":420879513,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMDg3OTUxMw==","user":{"login":"RWilton","id":8249753,"node_id":"MDQ6VXNlcjgyNDk3NTM=","avatar_url":"https://avatars1.githubusercontent.com/u/8249753?v=4","gravatar_id":"","url":"https://api.github.com/users/RWilton","html_url":"https://github.com/RWilton","followers_url":"https://api.github.com/users/RWilton/followers","following_url":"https://api.github.com/users/RWilton/following{/other_user}","gists_url":"https://api.github.com/users/RWilton/gists{/gist_id}","starred_url":"https://api.github.com/users/RWilton/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RWilton/subscriptions","organizations_url":"https://api.github.com/users/RWilton/orgs","repos_url":"https://api.github.com/users/RWilton/repos","events_url":"https://api.github.com/users/RWilton/events{/privacy}","received_events_url":"https://api.github.com/users/RWilton/received_events","type":"User","site_admin":false},"created_at":"2018-09-13T04:28:04Z","updated_at":"2018-09-13T04:28:04Z","author_association":"OWNER","body":"Thank you for letting us know about this problem.  We will try to reproduce it and let you know what we see."}}
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