{"action":"created","issue":{"url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/28","repository_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2","labels_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/28/labels{/name}","comments_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/28/comments","events_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/28/events","html_url":"https://github.com/aquaskyline/SOAPdenovo2/issues/28","id":247865158,"number":28,"title":"SOAPdenovo-127mer going only to kmer of 63","user":{"login":"opatty","id":30707371,"avatar_url":"https://avatars1.githubusercontent.com/u/30707371?v=4","gravatar_id":"","url":"https://api.github.com/users/opatty","html_url":"https://github.com/opatty","followers_url":"https://api.github.com/users/opatty/followers","following_url":"https://api.github.com/users/opatty/following{/other_user}","gists_url":"https://api.github.com/users/opatty/gists{/gist_id}","starred_url":"https://api.github.com/users/opatty/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/opatty/subscriptions","organizations_url":"https://api.github.com/users/opatty/orgs","repos_url":"https://api.github.com/users/opatty/repos","events_url":"https://api.github.com/users/opatty/events{/privacy}","received_events_url":"https://api.github.com/users/opatty/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-08-03T23:40:35Z","updated_at":"2017-08-04T05:57:52Z","closed_at":null,"body":"I am running SOAPdenovo2 v2.04-r214\r\nWhen I run SOAPdenovo-127mer with a -K 67 it will not go over a kmer of\r\n63.\r\nYour guidance will be much appreciated\r\nCheers\r\nOlivia\r\n\r\nexample of portions of output:\r\n\r\n*********************\r\nPregraph\r\n********************\r\nParameters: pregraph -s\r\n../MK_SOAPdenovo.config -K 67 -R -o output/MK \r\nK should not be greater than\r\n63.\r\nIn ../MK_SOAPdenovo.config, 1 lib(s), maximum read length 250, maximum\r\nname length 256\r\n................\r\n********************\r\nMap\r\n*********************\r\nParameters: map -s ../MK_SOAPdenovo.config -g output/MK -K 67 \r\nKmer size:63.\r\nContig length cutoff: 65.\r\n\r\n\r\nMy run command is:\r\n/home/tools/SOAPdenovo2/SOAPdenovo-127mer all -s ../MK_SOAPdenovo.config -o\r\noutput/MK -K 67 -R\r\n\r\nMy config file:\r\n#MKconfig file\r\n#maximal read length\r\nmax_rd_len=250\r\n[LIB]\r\n#average insert size\r\navg_ins=550\r\n#if sequence needs to be reversed\r\nreverse_seq=0\r\n#in which part(s) the reads are used\r\nasm_flags=3\r\n#a pair of fastq file, read 1 file should always be followed by read 2 file\r\nq1=/home/MK_R1_001.paired.fastq.gz\r\nq2=/home/MK_R2_001.paired.fastq.gz"},"comment":{"url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/comments/320163422","html_url":"https://github.com/aquaskyline/SOAPdenovo2/issues/28#issuecomment-320163422","issue_url":"https://api.github.com/repos/aquaskyline/SOAPdenovo2/issues/28","id":320163422,"user":{"login":"phylobase-web","id":1046214,"avatar_url":"https://avatars0.githubusercontent.com/u/1046214?v=4","gravatar_id":"","url":"https://api.github.com/users/phylobase-web","html_url":"https://github.com/phylobase-web","followers_url":"https://api.github.com/users/phylobase-web/followers","following_url":"https://api.github.com/users/phylobase-web/following{/other_user}","gists_url":"https://api.github.com/users/phylobase-web/gists{/gist_id}","starred_url":"https://api.github.com/users/phylobase-web/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/phylobase-web/subscriptions","organizations_url":"https://api.github.com/users/phylobase-web/orgs","repos_url":"https://api.github.com/users/phylobase-web/repos","events_url":"https://api.github.com/users/phylobase-web/events{/privacy}","received_events_url":"https://api.github.com/users/phylobase-web/received_events","type":"User","site_admin":false},"created_at":"2017-08-04T05:57:51Z","updated_at":"2017-08-04T05:57:51Z","body":"opatty,\n\nI had the same problem and fixed lines in Makefile.\nThe fix was committed, so get the latest release and rebuild to solve your\nproblem.\n\nhttps://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/\n\nendo\n\n\n2017-08-04 8:40 GMT+09:00 opatty <notifications@github.com>:\n\n> I am running SOAPdenovo2 v2.04-r214\n> When I run SOAPdenovo-127mer with a -K 67 it will not go over a kmer of\n> 63.\n> Your guidance will be much appreciated\n> Cheers\n> Olivia\n>\n> example of portions of output:\n> ------------------------------\n>\n> Pregraph\n> ------------------------------\n>\n> Parameters: pregraph -s\n> ../MK_SOAPdenovo.config -K 67 -R -o output/MK\n> K should not be greater than\n> 63.\n> In ../MK_SOAPdenovo.config, 1 lib(s), maximum read length 250, maximum\n> name length 256\n> ................\n> ------------------------------\n>\n> Map\n> ------------------------------\n>\n> Parameters: map -s ../MK_SOAPdenovo.config -g output/MK -K 67\n> Kmer size:63.\n> Contig length cutoff: 65.\n>\n> My run command is:\n> /home/tools/SOAPdenovo2/SOAPdenovo-127mer all -s ../MK_SOAPdenovo.config\n> -o\n> output/MK -K 67 -R\n>\n> My config file:\n> #MKconfig file\n> #maximal read length\n> max_rd_len=250\n> [LIB]\n> #average insert size\n> avg_ins=550\n> #if sequence needs to be reversed\n> reverse_seq=0\n> #in which part(s) the reads are used\n> asm_flags=3\n> #a pair of fastq file, read 1 file should always be followed by read 2 file\n> q1=/home/MK_R1_001.paired.fastq.gz\n> q2=/home/MK_R2_001.paired.fastq.gz\n>\n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/aquaskyline/SOAPdenovo2/issues/28>, or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AA_2xnz7QR4p4CqE6Po5YHaWIEnIRr_sks5sUlp0gaJpZM4OtHY0>\n> .\n>\n"}}
{"actor":{"display_login":"phylobase-web"}}