{"action":"created","issue":{"url":"https://api.github.com/repos/mahulchak/quickmerge/issues/27","repository_url":"https://api.github.com/repos/mahulchak/quickmerge","labels_url":"https://api.github.com/repos/mahulchak/quickmerge/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/mahulchak/quickmerge/issues/27/comments","events_url":"https://api.github.com/repos/mahulchak/quickmerge/issues/27/events","html_url":"https://github.com/mahulchak/quickmerge/issues/27","id":312545285,"node_id":"MDU6SXNzdWUzMTI1NDUyODU=","number":27,"title":"'std::out_of_range' error","user":{"login":"zfuller5280","id":6641995,"node_id":"MDQ6VXNlcjY2NDE5OTU=","avatar_url":"https://avatars2.githubusercontent.com/u/6641995?v=4","gravatar_id":"","url":"https://api.github.com/users/zfuller5280","html_url":"https://github.com/zfuller5280","followers_url":"https://api.github.com/users/zfuller5280/followers","following_url":"https://api.github.com/users/zfuller5280/following{/other_user}","gists_url":"https://api.github.com/users/zfuller5280/gists{/gist_id}","starred_url":"https://api.github.com/users/zfuller5280/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zfuller5280/subscriptions","organizations_url":"https://api.github.com/users/zfuller5280/orgs","repos_url":"https://api.github.com/users/zfuller5280/repos","events_url":"https://api.github.com/users/zfuller5280/events{/privacy}","received_events_url":"https://api.github.com/users/zfuller5280/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2018-04-09T14:06:48Z","updated_at":"2018-11-01T22:29:53Z","closed_at":null,"author_association":"NONE","body":"Hi Mahul,\r\nI am trying to use quickmerge but am receiving the following error:\r\n```\r\nterminate called after throwing an instance of 'std::out_of_range'\r\n  what():  basic_string::substr: __pos (which is 18446744073709536653) > this->size() (which is 342465)\r\n```\r\nLooking at some of the other issues, I've seen this error come up a few other times. However, it looked the culprit was fasta files with whitespaces in the header names, or sequences not on one line. I do not believe this to be the issue in this case, as I first started with the merge_wrapper.py script. I run the command as follows:\r\n```\r\nmerge_wrapper.py ../scaff10x_rounds2/renamed.sspace_scaff10x.2.fasta ../canu_assembly/asm/AM.contigs.fasta\r\n```\r\nI can see that it correctly creates the files hybrid_oneline.fa and self_oneline.fa in my current working directory. If I look at the first few headers in each file:\r\n```\r\ncat hybrid_oneline.fa|grep \">\"|head -n 5\r\n>1\r\n>2\r\n>3\r\n>4\r\n>5\r\n```\r\n```\r\ncat self_oneline.fa|grep \">\"|head -n 5\r\n>tig00000004_len=34946_reads=29_covStat=35.85_gappedBases=no_class=contig_suggestRepeat=no_suggestCircular=no\r\n>tig00000005_len=26830_reads=11_covStat=22.77_gappedBases=no_class=contig_suggestRepeat=no_suggestCircular=no\r\n>tig00000007_len=146883_reads=146_covStat=247.16_gappedBases=no_class=contig_suggestRepeat=no_suggestCircular=no\r\n>tig00000009_len=142320_reads=139_covStat=238.60_gappedBases=no_class=contig_suggestRepeat=no_suggestCircular=no\r\n>tig00000013_len=39096_reads=25_covStat=60.84_gappedBases=no_class=contig_suggestRepeat=no_suggestCircular=no\r\n```\r\nEverything looks correct. I have also tried cutting a lot of the unnecessary text in the headers for self_oneline.fa, leaving the headers as \">tigXXXX\" in a file called renamed_self.fa. If I try running the quickmerge command, following the order of arguments as on the wiki\r\n```\r\nquickmerge -d out.rq.delta -q hybrid_oneline.fa -r renamed_self.fa -hco 5 -c 1.5 -l 200000 -ml 5000\r\n```\r\nI still get the same error. What else, if anything, besides wrongly formatted fasta files could be throwing this error? Thanks for any information/insight and I hope to get this working!\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/mahulchak/quickmerge/issues/comments/435208759","html_url":"https://github.com/mahulchak/quickmerge/issues/27#issuecomment-435208759","issue_url":"https://api.github.com/repos/mahulchak/quickmerge/issues/27","id":435208759,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNTIwODc1OQ==","user":{"login":"esolares","id":4340414,"node_id":"MDQ6VXNlcjQzNDA0MTQ=","avatar_url":"https://avatars0.githubusercontent.com/u/4340414?v=4","gravatar_id":"","url":"https://api.github.com/users/esolares","html_url":"https://github.com/esolares","followers_url":"https://api.github.com/users/esolares/followers","following_url":"https://api.github.com/users/esolares/following{/other_user}","gists_url":"https://api.github.com/users/esolares/gists{/gist_id}","starred_url":"https://api.github.com/users/esolares/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/esolares/subscriptions","organizations_url":"https://api.github.com/users/esolares/orgs","repos_url":"https://api.github.com/users/esolares/repos","events_url":"https://api.github.com/users/esolares/events{/privacy}","received_events_url":"https://api.github.com/users/esolares/received_events","type":"User","site_admin":false},"created_at":"2018-11-01T22:29:53Z","updated_at":"2018-11-01T22:29:53Z","author_association":"COLLABORATOR","body":"Interesting. Could you send over some example headers along with their next\nline, it can just be 20-50nts. I would like to do some tests with them.\n\nThank you,\n\nEdwin\n\nOn Thu, Nov 1, 2018, 3:08 PM Nick Carleson <notifications@github.com wrote:\n\n> Hi, I actually ran each step individually rather than running the wrapper\n> so that I could pin the issue down. nucmer and delta-filter both ran fine,\n> it was quickmerge that had the issue.\n>\n> I used the --clean-only flag hidden within the merge-wrapper script to get\n> the FASTA files to put into the pipeline first. This is where I noticed my\n> issue: when I had long tags with commas, my fasta was not being converted\n> properly; the spaces were removed, but it was still on multiple lines. The\n> multiple lines didn't cause any issues with MUMmer steps but, again,\n> quickmerge errord out. The exact error message was:\n>\n> terminate called after throwing an instance of 'std::out_of_range'\n>   what():  basic_string::substr: __pos (which is 495327) > this->size() (which is 0)\n>\n> It created all the output files, including param_summary, anchor_summary,\n> etc. But the merged_.fasta was empty.\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/mahulchak/quickmerge/issues/27#issuecomment-435203356>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AEI6vokUBVNiwylVXPnzHGlH4HL4iRbFks5uq3BfgaJpZM4TMmm2>\n> .\n>\n"}}
{"actor":{"display_login":"esolares"}}