{"action":"created","issue":{"url":"https://api.github.com/repos/nservant/HiC-Pro/issues/200","repository_url":"https://api.github.com/repos/nservant/HiC-Pro","labels_url":"https://api.github.com/repos/nservant/HiC-Pro/issues/200/labels{/name}","comments_url":"https://api.github.com/repos/nservant/HiC-Pro/issues/200/comments","events_url":"https://api.github.com/repos/nservant/HiC-Pro/issues/200/events","html_url":"https://github.com/nservant/HiC-Pro/issues/200","id":376484662,"node_id":"MDU6SXNzdWUzNzY0ODQ2NjI=","number":200,"title":"NameError: name 'or1_fragname' is not defined in HiC-Pro-2.11.1","user":{"login":"wangxinbio","id":12146966,"node_id":"MDQ6VXNlcjEyMTQ2OTY2","avatar_url":"https://avatars1.githubusercontent.com/u/12146966?v=4","gravatar_id":"","url":"https://api.github.com/users/wangxinbio","html_url":"https://github.com/wangxinbio","followers_url":"https://api.github.com/users/wangxinbio/followers","following_url":"https://api.github.com/users/wangxinbio/following{/other_user}","gists_url":"https://api.github.com/users/wangxinbio/gists{/gist_id}","starred_url":"https://api.github.com/users/wangxinbio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wangxinbio/subscriptions","organizations_url":"https://api.github.com/users/wangxinbio/orgs","repos_url":"https://api.github.com/users/wangxinbio/repos","events_url":"https://api.github.com/users/wangxinbio/events{/privacy}","received_events_url":"https://api.github.com/users/wangxinbio/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-11-01T17:11:19Z","updated_at":"2018-12-10T16:40:26Z","closed_at":"2018-11-01T20:27:44Z","author_association":"NONE","body":"Hi \r\nWhen I use the lastest Hic-Pro-2.11.1, I faced an error \"NameError: name 'or1_fragname' is not defined\". \r\nHow can I fix it? Thanks.\r\nRun HiC-Pro 2.11.1\r\n--------------------------------------------\r\nThu Nov  1 13:05:49 EDT 2018\r\nBowtie2 alignment step1 ...\r\nLogs: logs/dixon_2M_2/mapping_step1.log\r\nLogs: logs/dixon_2M/mapping_step1.log\r\n\r\n--------------------------------------------\r\nThu Nov  1 13:06:37 EDT 2018\r\nBowtie2 alignment step2 ...\r\nLogs: logs/dixon_2M_2/mapping_step2.log\r\nLogs: logs/dixon_2M/mapping_step2.log\r\n\r\n--------------------------------------------\r\nThu Nov  1 13:06:50 EDT 2018\r\nCombine R1/R2 alignment files ...\r\nLogs: logs/dixon_2M_2/mapping_combine.log\r\nLogs: logs/dixon_2M/mapping_combine.log\r\n\r\n--------------------------------------------\r\nThu Nov  1 13:06:54 EDT 2018\r\nMapping statistics for R1 and R2 tags ...\r\nLogs: logs/dixon_2M_2/mapping_stats.log\r\nLogs: logs/dixon_2M/mapping_stats.log\r\n\r\n--------------------------------------------\r\nThu Nov  1 13:06:56 EDT 2018\r\nPairing of R1 and R2 tags ...\r\nLogs: logs/dixon_2M_2/mergeSAM.log\r\nLogs: logs/dixon_2M/mergeSAM.log\r\n\r\n--------------------------------------------\r\nThu Nov  1 13:07:07 EDT 2018\r\nAssign alignments to restriction fragments ...\r\nLogs: logs/dixon_2M_2/mapped_2hic_fragments.log\r\nmake: *** [/home/xinwang/local/HiC-Pro_2.11.1/HiC-Pro_2.11.1/bin/../scripts//Makefile:152: mapped_2hic_fragments] Error 1\r\n\r\n\r\n/home/xinwang/local/python-2.7.5/bin/python /home/xinwang/local/HiC-Pro_2.11.1/HiC-Pro_2.11.1/scripts/mapped_2hic_fragments.py -v -S -t 100 -m 100000 -s 100 -l 600 -a -f /home/xinwang/local/HiC-Pro_2.11.1/HiC-Pro_2.11.1/annotation/HindIII_resfrag_hg19.bed -r bowtie_results/bwt2/dixon_2M_2/SRR400264_01_GRCh38_latest_genomic.bwt2pairs.bam -o hic_results/data/dixon_2M_2\r\n## overlapMapped2HiCFragments.py\r\n## mappedReadsFile= bowtie_results/bwt2/dixon_2M_2/SRR400264_01_GRCh38_latest_genomic.bwt2pairs.bam\r\n## fragmentFile= /home/xinwang/local/HiC-Pro_2.11.1/HiC-Pro_2.11.1/annotation/HindIII_resfrag_hg19.bed\r\n## minInsertSize= 100\r\n## maxInsertSize= 600\r\n## minFragSize= 100\r\n## maxFragSize= 100000\r\n## allOuput= True\r\n## SAM ouput= True\r\n## verbose= True \r\n\r\n## Loading Restriction File Intervals ' /home/xinwang/local/HiC-Pro_2.11.1/HiC-Pro_2.11.1/annotation/HindIII_resfrag_hg19.bed '...\r\nWarning :  28576 fragment(s) outside of range and discarded.  809075  remaining.\r\nload_restriction_fragment function took 7994.759 ms\r\n## Opening SAM/BAM file ' bowtie_results/bwt2/dixon_2M_2/SRR400264_01_GRCh38_latest_genomic.bwt2pairs.bam '...\r\n## Classifying Interactions ...\r\nWarning - no restriction fragments for  SRR400264.250001  at  NC_000004.12 : 80314548\r\nWarning - no restriction fragments for  SRR400264.250001  at  NC_000015.10 : 39621593\r\nTraceback (most recent call last):\r\n  File \"/home/xinwang/local/HiC-Pro_2.11.1/HiC-Pro_2.11.1/scripts/mapped_2hic_fragments.py\", line 744, in <module>\r\n    str(htag) + \"\\n\")\r\nNameError: name 'or1_fragname' is not defined\r\nhicpro_latest_test/logs/dixon_2M_2/mapped_2hic_fragments.log (END)\r\n\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/nservant/HiC-Pro/issues/comments/445882848","html_url":"https://github.com/nservant/HiC-Pro/issues/200#issuecomment-445882848","issue_url":"https://api.github.com/repos/nservant/HiC-Pro/issues/200","id":445882848,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NTg4Mjg0OA==","user":{"login":"wangxinbio","id":12146966,"node_id":"MDQ6VXNlcjEyMTQ2OTY2","avatar_url":"https://avatars1.githubusercontent.com/u/12146966?v=4","gravatar_id":"","url":"https://api.github.com/users/wangxinbio","html_url":"https://github.com/wangxinbio","followers_url":"https://api.github.com/users/wangxinbio/followers","following_url":"https://api.github.com/users/wangxinbio/following{/other_user}","gists_url":"https://api.github.com/users/wangxinbio/gists{/gist_id}","starred_url":"https://api.github.com/users/wangxinbio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wangxinbio/subscriptions","organizations_url":"https://api.github.com/users/wangxinbio/orgs","repos_url":"https://api.github.com/users/wangxinbio/repos","events_url":"https://api.github.com/users/wangxinbio/events{/privacy}","received_events_url":"https://api.github.com/users/wangxinbio/received_events","type":"User","site_admin":false},"created_at":"2018-12-10T16:40:26Z","updated_at":"2018-12-10T16:40:26Z","author_association":"NONE","body":"> Hi dear wangxinbio,\r\n> I meet the same issue, how do your solve it? Thank you!\r\n\r\nI update to the lastest version and it is OK."}}
{"actor":{"display_login":"wangxinbio"}}