{"action":"created","issue":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18","labels_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18/comments","events_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18/events","html_url":"https://github.com/loeblab/Duplex-Sequencing/issues/18","id":118489111,"number":18,"title":"Error with PE_BASH_MAKER.py","user":{"login":"KonstantinosC","id":15989335,"avatar_url":"https://avatars.githubusercontent.com/u/15989335?v=3","gravatar_id":"","url":"https://api.github.com/users/KonstantinosC","html_url":"https://github.com/KonstantinosC","followers_url":"https://api.github.com/users/KonstantinosC/followers","following_url":"https://api.github.com/users/KonstantinosC/following{/other_user}","gists_url":"https://api.github.com/users/KonstantinosC/gists{/gist_id}","starred_url":"https://api.github.com/users/KonstantinosC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KonstantinosC/subscriptions","organizations_url":"https://api.github.com/users/KonstantinosC/orgs","repos_url":"https://api.github.com/users/KonstantinosC/repos","events_url":"https://api.github.com/users/KonstantinosC/events{/privacy}","received_events_url":"https://api.github.com/users/KonstantinosC/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-11-23T22:36:24Z","updated_at":"2015-11-24T14:23:09Z","closed_at":null,"body":"I was getting this error when running the PE_BASH_MAKER.py\r\n\r\nTraceback (most recent call last):\r\n  File \"PE_BASH_MAKER.py\", line 183, in <module>\r\n    main()\r\n  File \"PE_BASH_MAKER.py\", line 131, in main\r\n    inBash = open(spath + \"/bash_template.sh\", \"r\")\r\nIOError: [Errno 20] Not a directory: 'PE_BASH_MAKER.py/bash_template.sh'\r\n\r\nI changed the line 131 by erasing the \"spath +\" and it run fine. Let me know if by doing that I messed anything up.\r\n\r\nThank you "},"comment":{"url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/comments/159281510","html_url":"https://github.com/loeblab/Duplex-Sequencing/issues/18#issuecomment-159281510","issue_url":"https://api.github.com/repos/loeblab/Duplex-Sequencing/issues/18","id":159281510,"user":{"login":"bkohrn","id":5421924,"avatar_url":"https://avatars.githubusercontent.com/u/5421924?v=3","gravatar_id":"","url":"https://api.github.com/users/bkohrn","html_url":"https://github.com/bkohrn","followers_url":"https://api.github.com/users/bkohrn/followers","following_url":"https://api.github.com/users/bkohrn/following{/other_user}","gists_url":"https://api.github.com/users/bkohrn/gists{/gist_id}","starred_url":"https://api.github.com/users/bkohrn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bkohrn/subscriptions","organizations_url":"https://api.github.com/users/bkohrn/orgs","repos_url":"https://api.github.com/users/bkohrn/repos","events_url":"https://api.github.com/users/bkohrn/events{/privacy}","received_events_url":"https://api.github.com/users/bkohrn/received_events","type":"User","site_admin":false},"created_at":"2015-11-24T14:23:09Z","updated_at":"2015-11-24T14:23:09Z","body":"If I recall correctly, spath is designed to point to the default template\n(which should be in the same directory as PE_BASH_MAKER.py, and which I\nassumed when writing the script would be a different directory than the one\nyou were running the script in).  Spath is created by taking the path to\nthe script and removing the string \"/PE_BASH_MAKER.py\".  The error is\nhappening because the path you give doesn't include the pattern the script\nis looking for.\n\nBrendan\n\nOn Tue, Nov 24, 2015 at 5:53 AM, KonstantinosC <notifications@github.com>\nwrote:\n\n> python PE_BASH_MAKER.py --ref /media/kostas/OS/indexes/hg19.fa --r1src\n> /media/kostas/OS/NGS_Data/YB8R1.fastq --r2src\n> /media/kostas/OS/NGS_Data/YB8R2.fastq --rlength 75 --blength 6 --slength\n> 11 --runIdentifier 001\n>\n> Also I have another comment.\n> When I run the ./001.script.sh 3>&1 1>&2 2>&3 | tee -a 001.se.log.txt\" it\n> gave me a similar error\n> python: can't open file 'PE_BASH_MAKER.py/tag_to_header.py': [Errno 20] Not\n> a directory\n> and I had to do the same, go and erase the PE_BASH_MAKER.py/ in front of\n> the tag_to_header.py.\n>\n> I'm running ubuntu 14.04 but that should not have any impact on the script.\n> Also, Even though I told the script barcode lenght (blength) 6 and stem\n> length 11, it did the oposite. it grabbed the first 11 and append them on\n> the header per read and then erased 6 as stem hahah. easy fix for me but I\n> just had to let you know just in case a)I'm doing something wrong b)you\n> accidentally swapped something in your script.\n> I didn't have time to go dig :)\n>\n> Thanks for you super prompt response!\n>\n> Kostas\n>\n> On Mon, Nov 23, 2015 at 11:34 PM, S. Kennedy <notifications@github.com>\n> wrote:\n>\n> > What was the precise command you used to invoke PE_BASH_MAKER.py?\n> >\n> > On 11/23/15 2:36 PM, KonstantinosC wrote:\n> > >\n> > > I was getting this error when running the PE_BASH_MAKER.py\n> > >\n> > > Traceback (most recent call last):\n> > > File \"PE_BASH_MAKER.py\", line 183, in\n> > > main()\n> > > File \"PE_BASH_MAKER.py\", line 131, in main\n> > > inBash = open(spath + \"/bash_template.sh\", \"r\")\n> > > IOError: [Errno 20] Not a directory:\n> 'PE_BASH_MAKER.py/bash_template.sh'\n> > >\n> > > I changed the line 131 by erasing the \"spath +\" and it run fine. Let\n> > > me know if by doing that I messed anything up.\n> > >\n> > > Thank you\n> > >\n> > > —\n> > > Reply to this email directly or view it on GitHub\n> > > <https://github.com/loeblab/Duplex-Sequencing/issues/18>.\n> > >\n> >\n> > —\n> > Reply to this email directly or view it on GitHub\n> > <\n> https://github.com/loeblab/Duplex-Sequencing/issues/18#issuecomment-159147365\n> >\n> > .\n>\n> >\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/loeblab/Duplex-Sequencing/issues/18#issuecomment-159274232>\n> .\n>\n"}}