{"action":"created","issue":{"url":"https://api.github.com/repos/ohlerlab/PARpipe/issues/3","repository_url":"https://api.github.com/repos/ohlerlab/PARpipe","labels_url":"https://api.github.com/repos/ohlerlab/PARpipe/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/ohlerlab/PARpipe/issues/3/comments","events_url":"https://api.github.com/repos/ohlerlab/PARpipe/issues/3/events","html_url":"https://github.com/ohlerlab/PARpipe/issues/3","id":309164708,"node_id":"MDU6SXNzdWUzMDkxNjQ3MDg=","number":3,"title":"Not sure how to troubleshoot this error message:","user":{"login":"jsolvason","id":29126182,"node_id":"MDQ6VXNlcjI5MTI2MTgy","avatar_url":"https://avatars0.githubusercontent.com/u/29126182?v=4","gravatar_id":"","url":"https://api.github.com/users/jsolvason","html_url":"https://github.com/jsolvason","followers_url":"https://api.github.com/users/jsolvason/followers","following_url":"https://api.github.com/users/jsolvason/following{/other_user}","gists_url":"https://api.github.com/users/jsolvason/gists{/gist_id}","starred_url":"https://api.github.com/users/jsolvason/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jsolvason/subscriptions","organizations_url":"https://api.github.com/users/jsolvason/orgs","repos_url":"https://api.github.com/users/jsolvason/repos","events_url":"https://api.github.com/users/jsolvason/events{/privacy}","received_events_url":"https://api.github.com/users/jsolvason/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2018-03-27T23:06:48Z","updated_at":"2018-07-24T15:02:52Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI would greatly appreciate some help.\r\n\r\nI have split up the pre-processing (up to and including alignment) and post-processing of parpipe to enable me to do my own processing before moving onto parpipes post-processing. Our library produces reads that are too long for bowtie to align. \r\n\r\nI am using hisat2 to align reads to hg19 index file. I built the index file myself from hg19.fa (concatenated chromosome.fa files from ucsc), and also converted it to 2bit. I used the gtf file you provided.\r\n\r\nTo do this, I wrote a shell script that runs `cutadapt`, `hisat2` (aligned against hg19) and `samtools view -F 4` to prepare the aligned.sam file. After running bpipe with this sam file (below), the test.aligned.sam file successfully ran through the post-processing pipeline. I created the post-processing pipeline simply by removing the preprocessing and align steps.\r\n\r\n`bpipe run ../parclip_pipe_post-processing.sh test.aligned.sam`\r\n\r\nError:\r\n\r\n```\r\nubuntu@ip-172-31-35-208:~/parpipe2/parclip2-hiseq-downsample-pe$ bpipe run ../parclip2-post-processing-analysis.sh S-glu-0_S2_L005.aligned.sam \r\n====================================================================================================\r\n|                              Starting Pipeline at 2018-03-27 22:47                               |\r\n====================================================================================================\r\n\r\n========================================= Stage PARparams ==========================================\r\n\r\n========================================== Stage PARalyze ==========================================\r\nRunning PARalyzer v1.5\r\nParsing SAM file(s)...\r\nException in thread \"main\" java.lang.ArrayIndexOutOfBoundsException: 1\r\n\tat PARCLIPsamParser.parseFile(PARCLIPsamParser.java:42)\r\n\tat PARalyze.main(PARalyze.java:118)\r\nERROR: stage PARalyze failed: Command in stage PARalyze failed with exit status = 1 : \r\n\r\n/home/ubuntu/parpipe2/scripts/PARalyzer 8G S-glu-0_S2_L005.ini \r\n\r\n\r\n========================================= Pipeline Failed ==========================================\r\n\r\nCommand in stage PARalyze failed with exit status = 1 : \r\n\r\n/home/ubuntu/parpipe2/scripts/PARalyzer 8G S-glu-0_S2_L005.ini\r\n\r\nUse 'bpipe errors' to see output from failed commands.\r\n\r\nubuntu@ip-172-31-35-208:~/parpipe2/parclip2-hiseq-downsample-pe$ bpipe errors\r\n\r\n============================== Found 1 failed commands from run 6478 ===============================\r\n\r\n====================================== Command PARalyze (15) =======================================\r\n\r\nCommand    : /home/ubuntu/parpipe2/scripts/PARalyzer 8G S-glu-0_S2_L005.ini\r\nStarted    : Tue Mar 27 22:47:20 UTC 2018\r\nStopped    : Tue Mar 27 22:47:21 UTC 2018\r\nExit Code  : 1\r\nConfig: \r\n                   Name           |                  Value                 \r\n          -----------------------------------------------------------------\r\n          max_per_command_threads | 16                                     \r\n          executor                | local                                  \r\n          maxFileNameLength       | 2048                                   \r\n          name                    | /home/ubuntu/parpipe2/scripts/PARalyzer\r\n          procs                   | 1                                      \r\n\r\nOutput    : \r\n\r\n\tRunning PARalyzer v1.5\r\n\tParsing SAM file(s)...\r\n\tException in thread \"main\" java.lang.ArrayIndexOutOfBoundsException: 1\r\n\t\tat PARCLIPsamParser.parseFile(PARCLIPsamParser.java:42)\r\n\t\tat PARalyze.main(PARalyze.java:118)\r\n\r\nubuntu@ip-172-31-35-208:~/parpipe2/parclip2-hiseq-downsample-pe$ lsj\r\n\r\n```\r\n\r\nAny ideas?\r\n\r\nJoe"},"comment":{"url":"https://api.github.com/repos/ohlerlab/PARpipe/issues/comments/407439415","html_url":"https://github.com/ohlerlab/PARpipe/issues/3#issuecomment-407439415","issue_url":"https://api.github.com/repos/ohlerlab/PARpipe/issues/3","id":407439415,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNzQzOTQxNQ==","user":{"login":"saidiwang","id":31391403,"node_id":"MDQ6VXNlcjMxMzkxNDAz","avatar_url":"https://avatars1.githubusercontent.com/u/31391403?v=4","gravatar_id":"","url":"https://api.github.com/users/saidiwang","html_url":"https://github.com/saidiwang","followers_url":"https://api.github.com/users/saidiwang/followers","following_url":"https://api.github.com/users/saidiwang/following{/other_user}","gists_url":"https://api.github.com/users/saidiwang/gists{/gist_id}","starred_url":"https://api.github.com/users/saidiwang/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/saidiwang/subscriptions","organizations_url":"https://api.github.com/users/saidiwang/orgs","repos_url":"https://api.github.com/users/saidiwang/repos","events_url":"https://api.github.com/users/saidiwang/events{/privacy}","received_events_url":"https://api.github.com/users/saidiwang/received_events","type":"User","site_admin":false},"created_at":"2018-07-24T15:02:51Z","updated_at":"2018-07-24T15:02:51Z","author_association":"NONE","body":"Thanks for your reply and sorry to bother you.When you using the PARpipe,\nhow did you get the bindings? which one is the right file?Thanks agian\n\n2018-07-24 10:46 GMT-04:00 jsolvason <notifications@github.com>:\n\n> I have never used PARalyzer by itself. Only PARpipe. I also have not used\n> it for miRNA targets. Sorry!\n>\n>\n> On Tue, Jul 24, 2018 at 7:32 AM saidiwang <notifications@github.com>\n> wrote:\n>\n> > hi,sorry to bother you.Could you give me some help about the PARalyzer?\n> > hi,sorry to bother you.When I just try to use the PARalyzer to get the\n> > miRNA targets.I got this in its read-me file.\n> > FIND_MIRNA_SEEDMATCHES=#filepath/filename#\n> > #filepath/filename# = Location of the file that contains mature miRNA\n> name\n> > and sequences\n> > Does this file have a format?\n> > Best Regards\n> >\n> >\n> > 2018-07-23 17:05 GMT-04:00 wang saidi <tjwangsaidi@gmail.com>:\n> >\n> > > hi,sorry to bother you.When I just try to use the PARalyzer to get the\n> > > miRNA targets.I got this in its read-me file.\n> > > FIND_MIRNA_SEEDMATCHES=#filepath/filename#\n> > > #filepath/filename# = Location of the file that contains mature miRNA\n> > name\n> > > and sequences\n> > > Does this file have a format?\n> > > Best Regards\n> > > Saidi Wang\n> > >\n> > > 2018-07-23 15:18 GMT-04:00 wang saidi <tjwangsaidi@gmail.com>:\n> > >\n> > >> Hi, sorry to bother you,but I have to.I just running the PARpine\n> > >> example.And I want to know the binding site information between the\n> mRAN\n> > >> and the miRNA.How could I read the output? I just see the result,but\n> the\n> > >> result seems not easy for me to understand.Or there are any guidelines\n> > to\n> > >> get the output of the binding site information between the mRNA and\n> the\n> > >> miRNA.\n> > >> Best Regards\n> > >> Saidi Wang\n> > >>\n> > >> 2018-07-11 19:12 GMT-04:00 wang saidi <tjwangsaidi@gmail.com>:\n> > >>\n> > >>> Ok,thanks.I have solved that problem and now I am just working on the\n> > >>> output to get the bindings.I need to know which files is the\n> > >>> bindings.Thanks\n> > >>>\n> > >>> On Wed, Jul 11, 2018 at 19:10 jsolvason <notifications@github.com>\n> > >>> wrote:\n> > >>>\n> > >>>> Did you download the reference files?\n> > >>>>\n> > >>>>\n> > >>>> Joseph Solvason\n> > >>>> Chimera Bioengineering\n> > >>>>\n> > >>>>\n> > >>>> On Wed, Jul 11, 2018 at 7:55 AM saidiwang <notifications@github.com\n> >\n> > >>>> wrote:\n> > >>>>\n> > >>>> > hi,sorry to bother you.But I have run the parpipe like the read-me\n> > >>>> file.And\n> > >>>> > I get this questions.\n> > >>>> > Could not open index file ../files/hg19.rev.1.ebwt\n> > >>>> > Could not open index file ../files/hg19.rev.2.ebwt\n> > >>>> > Does I need any other tools/\n> > >>>> > Best Regards\n> > >>>> > Saidi Wang\n> > >>>> >\n> > >>>> >\n> > >>>> > 2018-07-09 17:19 GMT-04:00 jsolvason <notifications@github.com>:\n> > >>>> >\n> > >>>> > > Definitely! I'll try to help best I can.\n> > >>>> > >\n> > >>>> > > Joe\n> > >>>> > >\n> > >>>> > > —\n> > >>>> > > You are receiving this because you commented.\n> > >>>> > > Reply to this email directly, view it on GitHub\n> > >>>> > > <https://github.com/ohlerlab/PARpipe/issues/3#issuecomment-4\n> > >>>> 03624028>,\n> > >>>> > or mute\n> > >>>> > > the thread\n> > >>>> > > <\n> > >>>> > https://github.com/notifications/unsubscribe-auth/Ad7-qyV3mp\n> > >>>> t_AIZXDbWnzpyql0kzoDZrks5uE8j3gaJpZM4S9xa-\n> > >>>> > >\n> > >>>> > > .\n> > >>>> > >\n> > >>>> >\n> > >>>> > —\n> > >>>> > You are receiving this because you authored the thread.\n> > >>>> > Reply to this email directly, view it on GitHub\n> > >>>> > <\n> > https://github.com/ohlerlab/PARpipe/issues/3#issuecomment-404199584>,\n> > >>>> or mute\n> > >>>> > the thread\n> > >>>> > <https://github.com/notifications/unsubscribe-auth/AbxuJiNXA\n> > >>>> xKf8JTiMgeUnXZZONQq6vWsks5uFhHPgaJpZM4S9xa->\n> > >>>> > .\n> > >>>> >\n> > >>>>\n> > >>>> —\n> > >>>> You are receiving this because you commented.\n> > >>>> Reply to this email directly, view it on GitHub\n> > >>>> <https://github.com/ohlerlab/PARpipe/issues/3#issuecomment-\n> 404338560\n> > >,\n> > >>>> or mute the thread\n> > >>>> <\n> > https://github.com/notifications/unsubscribe-\n> auth/Ad7-q7EGmuQKaUg7I7YnqB_VRoP4t_IVks5uFoXugaJpZM4S9xa-\n> > >\n> > >>>> .\n> > >>>>\n> > >>>\n> > >>\n> > >\n> >\n> > —\n> > You are receiving this because you authored the thread.\n> > Reply to this email directly, view it on GitHub\n> > <https://github.com/ohlerlab/PARpipe/issues/3#issuecomment-407428315>,\n> or mute\n> > the thread\n> > <https://github.com/notifications/unsubscribe-auth/\n> AbxuJvbIbNtjRAMHvpKnyhboJDzum4Jrks5uJzAQgaJpZM4S9xa->\n> > .\n> >\n> --\n>\n> Joseph Solvason\n> Chimera Bioengineering\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/ohlerlab/PARpipe/issues/3#issuecomment-407433225>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe-auth/Ad7-q1MWsrPe2Gox52ym8Edhs2zrqbTlks5uJzMugaJpZM4S9xa->\n> .\n>\n"}}
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