{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/1087","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/1087/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/1087/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/1087/events","html_url":"https://github.com/marbl/canu/issues/1087","id":359614817,"node_id":"MDU6SXNzdWUzNTk2MTQ4MTc=","number":1087,"title":"Mhap overlap jobs failed","user":{"login":"nicolasalexandre21","id":21229039,"node_id":"MDQ6VXNlcjIxMjI5MDM5","avatar_url":"https://avatars0.githubusercontent.com/u/21229039?v=4","gravatar_id":"","url":"https://api.github.com/users/nicolasalexandre21","html_url":"https://github.com/nicolasalexandre21","followers_url":"https://api.github.com/users/nicolasalexandre21/followers","following_url":"https://api.github.com/users/nicolasalexandre21/following{/other_user}","gists_url":"https://api.github.com/users/nicolasalexandre21/gists{/gist_id}","starred_url":"https://api.github.com/users/nicolasalexandre21/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nicolasalexandre21/subscriptions","organizations_url":"https://api.github.com/users/nicolasalexandre21/orgs","repos_url":"https://api.github.com/users/nicolasalexandre21/repos","events_url":"https://api.github.com/users/nicolasalexandre21/events{/privacy}","received_events_url":"https://api.github.com/users/nicolasalexandre21/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2018-09-12T19:12:43Z","updated_at":"2018-09-18T17:27:13Z","closed_at":null,"author_association":"NONE","body":"Do you have an idea of what may have happened during the mhap step? I've rerun this a couple of times with the same error message.\r\n\r\n```\r\n    cd correction/1-overlapper\r\n    ./mhap.sh 69 > ./mhap.000069.out 2>&1\r\n    ./mhap.sh 89 > ./mhap.000089.out 2>&1\r\n    ./mhap.sh 90 > ./mhap.000090.out 2>&1\r\n    ./mhap.sh 91 > ./mhap.000091.out 2>&1\r\n    ./mhap.sh 92 > ./mhap.000092.out 2>&1\r\n    ./mhap.sh 93 > ./mhap.000093.out 2>&1\r\n    ./mhap.sh 94 > ./mhap.000094.out 2>&1\r\n    ./mhap.sh 95 > ./mhap.000095.out 2>&1\r\n    ./mhap.sh 96 > ./mhap.000096.out 2>&1\r\n    ./mhap.sh 97 > ./mhap.000097.out 2>&1\r\n    ./mhap.sh 98 > ./mhap.000098.out 2>&1\r\n    ./mhap.sh 99 > ./mhap.000099.out 2>&1\r\n    ./mhap.sh 100 > ./mhap.000100.out 2>&1\r\n    ./mhap.sh 101 > ./mhap.000101.out 2>&1\r\n    ./mhap.sh 102 > ./mhap.000102.out 2>&1\r\n    ./mhap.sh 103 > ./mhap.000103.out 2>&1\r\n    ./mhap.sh 104 > ./mhap.000104.out 2>&1\r\n    ./mhap.sh 105 > ./mhap.000105.out 2>&1\r\n    ./mhap.sh 106 > ./mhap.000106.out 2>&1\r\n    ./mhap.sh 107 > ./mhap.000107.out 2>&1\r\n    ./mhap.sh 108 > ./mhap.000108.out 2>&1\r\n    ./mhap.sh 109 > ./mhap.000109.out 2>&1\r\n    ./mhap.sh 110 > ./mhap.000110.out 2>&1\r\n    ./mhap.sh 111 > ./mhap.000111.out 2>&1\r\n    ./mhap.sh 112 > ./mhap.000112.out 2>&1\r\n    ./mhap.sh 113 > ./mhap.000113.out 2>&1\r\n    ./mhap.sh 114 > ./mhap.000114.out 2>&1\r\n    ./mhap.sh 115 > ./mhap.000115.out 2>&1\r\n    ./mhap.sh 116 > ./mhap.000116.out 2>&1\r\n    ./mhap.sh 117 > ./mhap.000117.out 2>&1\r\n    ./mhap.sh 118 > ./mhap.000118.out 2>&1\r\n    ./mhap.sh 119 > ./mhap.000119.out 2>&1\r\n    ./mhap.sh 120 > ./mhap.000120.out 2>&1\r\n    ./mhap.sh 121 > ./mhap.000121.out 2>&1\r\n    ./mhap.sh 122 > ./mhap.000122.out 2>&1\r\n    ./mhap.sh 123 > ./mhap.000123.out 2>&1\r\n    ./mhap.sh 124 > ./mhap.000124.out 2>&1\r\n    ./mhap.sh 125 > ./mhap.000125.out 2>&1\r\n    ./mhap.sh 126 > ./mhap.000126.out 2>&1\r\n    ./mhap.sh 127 > ./mhap.000127.out 2>&1\r\n    ./mhap.sh 128 > ./mhap.000128.out 2>&1\r\n    ./mhap.sh 129 > ./mhap.000129.out 2>&1\r\n    ./mhap.sh 130 > ./mhap.000130.out 2>&1\r\n    ./mhap.sh 131 > ./mhap.000131.out 2>&1\r\n    ./mhap.sh 132 > ./mhap.000132.out 2>&1\r\n    ./mhap.sh 133 > ./mhap.000133.out 2>&1\r\n    ./mhap.sh 134 > ./mhap.000134.out 2>&1\r\n    ./mhap.sh 135 > ./mhap.000135.out 2>&1\r\n    ./mhap.sh 136 > ./mhap.000136.out 2>&1\r\n    ./mhap.sh 137 > ./mhap.000137.out 2>&1\r\n    ./mhap.sh 138 > ./mhap.000138.out 2>&1\r\n    ./mhap.sh 139 > ./mhap.000139.out 2>&1\r\n    ./mhap.sh 140 > ./mhap.000140.out 2>&1\r\n    ./mhap.sh 141 > ./mhap.000141.out 2>&1\r\n    ./mhap.sh 142 > ./mhap.000142.out 2>&1\r\n    ./mhap.sh 143 > ./mhap.000143.out 2>&1\r\n    ./mhap.sh 144 > ./mhap.000144.out 2>&1\r\n    ./mhap.sh 145 > ./mhap.000145.out 2>&1\r\n    ./mhap.sh 146 > ./mhap.000146.out 2>&1\r\n    ./mhap.sh 147 > ./mhap.000147.out 2>&1\r\n    ./mhap.sh 148 > ./mhap.000148.out 2>&1\r\n    ./mhap.sh 149 > ./mhap.000149.out 2>&1\r\n    ./mhap.sh 150 > ./mhap.000150.out 2>&1\r\n    ./mhap.sh 151 > ./mhap.000151.out 2>&1\r\n    ./mhap.sh 152 > ./mhap.000152.out 2>&1\r\n    ./mhap.sh 153 > ./mhap.000153.out 2>&1\r\n    ./mhap.sh 154 > ./mhap.000154.out 2>&1\r\n    ./mhap.sh 155 > ./mhap.000155.out 2>&1\r\n    ./mhap.sh 156 > ./mhap.000156.out 2>&1\r\n    ./mhap.sh 157 > ./mhap.000157.out 2>&1\r\n    ./mhap.sh 158 > ./mhap.000158.out 2>&1\r\n    ./mhap.sh 159 > ./mhap.000159.out 2>&1\r\n    ./mhap.sh 160 > ./mhap.000160.out 2>&1\r\n    ./mhap.sh 161 > ./mhap.000161.out 2>&1\r\n    ./mhap.sh 162 > ./mhap.000162.out 2>&1\r\n    ./mhap.sh 163 > ./mhap.000163.out 2>&1\r\n    ./mhap.sh 164 > ./mhap.000164.out 2>&1\r\n    ./mhap.sh 165 > ./mhap.000165.out 2>&1\r\n    ./mhap.sh 166 > ./mhap.000166.out 2>&1\r\n    ./mhap.sh 167 > ./mhap.000167.out 2>&1\r\n    ./mhap.sh 168 > ./mhap.000168.out 2>&1\r\n    ./mhap.sh 169 > ./mhap.000169.out 2>&1\r\n    ./mhap.sh 170 > ./mhap.000170.out 2>&1\r\n    ./mhap.sh 171 > ./mhap.000171.out 2>&1\r\n    ./mhap.sh 172 > ./mhap.000172.out 2>&1\r\n    ./mhap.sh 173 > ./mhap.000173.out 2>&1\r\n    ./mhap.sh 174 > ./mhap.000174.out 2>&1\r\n    ./mhap.sh 175 > ./mhap.000175.out 2>&1\r\n    ./mhap.sh 176 > ./mhap.000176.out 2>&1\r\n    ./mhap.sh 177 > ./mhap.000177.out 2>&1\r\n    ./mhap.sh 178 > ./mhap.000178.out 2>&1\r\n    ./mhap.sh 179 > ./mhap.000179.out 2>&1\r\n    ./mhap.sh 180 > ./mhap.000180.out 2>&1\r\n    ./mhap.sh 181 > ./mhap.000181.out 2>&1\r\n    ./mhap.sh 182 > ./mhap.000182.out 2>&1\r\n    ./mhap.sh 183 > ./mhap.000183.out 2>&1\r\n    ./mhap.sh 184 > ./mhap.000184.out 2>&1\r\n    ./mhap.sh 185 > ./mhap.000185.out 2>&1\r\n    ./mhap.sh 186 > ./mhap.000186.out 2>&1\r\n    ./mhap.sh 187 > ./mhap.000187.out 2>&1\r\n    ./mhap.sh 188 > ./mhap.000188.out 2>&1\r\n    ./mhap.sh 189 > ./mhap.000189.out 2>&1\r\n    ./mhap.sh 190 > ./mhap.000190.out 2>&1\r\n    ./mhap.sh 191 > ./mhap.000191.out 2>&1\r\n    ./mhap.sh 192 > ./mhap.000192.out 2>&1\r\n    ./mhap.sh 193 > ./mhap.000193.out 2>&1\r\n    ./mhap.sh 194 > ./mhap.000194.out 2>&1\r\n    ./mhap.sh 195 > ./mhap.000195.out 2>&1\r\n    ./mhap.sh 196 > ./mhap.000196.out 2>&1\r\n    ./mhap.sh 197 > ./mhap.000197.out 2>&1\r\n    ./mhap.sh 198 > ./mhap.000198.out 2>&1\r\n    ./mhap.sh 199 > ./mhap.000199.out 2>&1\r\n    ./mhap.sh 200 > ./mhap.000200.out 2>&1\r\n    ./mhap.sh 201 > ./mhap.000201.out 2>&1\r\n    ./mhap.sh 202 > ./mhap.000202.out 2>&1\r\n    ./mhap.sh 203 > ./mhap.000203.out 2>&1\r\n    ./mhap.sh 204 > ./mhap.000204.out 2>&1\r\n    ./mhap.sh 205 > ./mhap.000205.out 2>&1\r\n    ./mhap.sh 206 > ./mhap.000206.out 2>&1\r\n    ./mhap.sh 207 > ./mhap.000207.out 2>&1\r\n    ./mhap.sh 208 > ./mhap.000208.out 2>&1\r\n    ./mhap.sh 209 > ./mhap.000209.out 2>&1\r\n    ./mhap.sh 210 > ./mhap.000210.out 2>&1\r\n    ./mhap.sh 211 > ./mhap.000211.out 2>&1\r\n    ./mhap.sh 212 > ./mhap.000212.out 2>&1\r\n    ./mhap.sh 213 > ./mhap.000213.out 2>&1\r\n    ./mhap.sh 214 > ./mhap.000214.out 2>&1\r\n    ./mhap.sh 215 > ./mhap.000215.out 2>&1\r\n    ./mhap.sh 216 > ./mhap.000216.out 2>&1\r\n    ./mhap.sh 217 > ./mhap.000217.out 2>&1\r\n    ./mhap.sh 218 > ./mhap.000218.out 2>&1\r\n    ./mhap.sh 219 > ./mhap.000219.out 2>&1\r\n    ./mhap.sh 220 > ./mhap.000220.out 2>&1\r\n    ./mhap.sh 221 > ./mhap.000221.out 2>&1\r\n    ./mhap.sh 222 > ./mhap.000222.out 2>&1\r\n    ./mhap.sh 223 > ./mhap.000223.out 2>&1\r\n\r\n-- Finished on Wed Sep 12 12:50:59 2018 (1032001 seconds) with 1691733.687 GB free disk space\r\n----------------------------------------\r\n--\r\n-- Mhap overlap jobs failed, retry.\r\n--   job correction/1-overlapper/results/000139.ovb FAILED.\r\n--   job correction/1-overlapper/results/000149.ovb FAILED.\r\n--\r\n--\r\n-- Running jobs.  Second attempt out of 2.\r\n----------------------------------------\r\n-- Starting 'cormhap' concurrent execution on Wed Sep 12 12:51:05 2018 with 1691737.839 GB free disk space (2 processes; 4 concurrently)\r\n\r\n    cd correction/1-overlapper\r\n    ./mhap.sh 139 > ./mhap.000139.out 2>&1\r\n    ./mhap.sh 149 > ./mhap.000149.out 2>&1\r\n\r\n-- Finished on Wed Sep 12 12:52:48 2018 (103 seconds) with 1691795.666 GB free disk space\r\n----------------------------------------\r\n--\r\n-- Mhap overlap jobs failed, tried 2 times, giving up.\r\n--   job correction/1-overlapper/results/000139.ovb FAILED.\r\n--   job correction/1-overlapper/results/000149.ovb FAILED.\r\n--\r\n\r\nABORT:\r\nABORT: Canu 1.7\r\nABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.\r\nABORT: Try restarting.  If that doesn't work, ask for help.\r\nABORT:\r\n```"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/422479201","html_url":"https://github.com/marbl/canu/issues/1087#issuecomment-422479201","issue_url":"https://api.github.com/repos/marbl/canu/issues/1087","id":422479201,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMjQ3OTIwMQ==","user":{"login":"nicolasalexandre21","id":21229039,"node_id":"MDQ6VXNlcjIxMjI5MDM5","avatar_url":"https://avatars0.githubusercontent.com/u/21229039?v=4","gravatar_id":"","url":"https://api.github.com/users/nicolasalexandre21","html_url":"https://github.com/nicolasalexandre21","followers_url":"https://api.github.com/users/nicolasalexandre21/followers","following_url":"https://api.github.com/users/nicolasalexandre21/following{/other_user}","gists_url":"https://api.github.com/users/nicolasalexandre21/gists{/gist_id}","starred_url":"https://api.github.com/users/nicolasalexandre21/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nicolasalexandre21/subscriptions","organizations_url":"https://api.github.com/users/nicolasalexandre21/orgs","repos_url":"https://api.github.com/users/nicolasalexandre21/repos","events_url":"https://api.github.com/users/nicolasalexandre21/events{/privacy}","received_events_url":"https://api.github.com/users/nicolasalexandre21/received_events","type":"User","site_admin":false},"created_at":"2018-09-18T17:27:13Z","updated_at":"2018-09-18T17:27:13Z","author_association":"NONE","body":"Here is the output of results:\n\n000001.counts  000057.counts  000113.counts            000169.counts\n000001.ovb     000057.ovb     000113.ovb               000169.ovb\n000002.counts  000058.counts  000114.counts            000170.counts\n000002.ovb     000058.ovb     000114.ovb               000170.ovb\n000003.counts  000059.counts  000115.counts            000171.counts\n000003.ovb     000059.ovb     000115.ovb               000171.ovb\n000004.counts  000060.counts  000116.counts            000172.counts\n000004.ovb     000060.ovb     000116.ovb               000172.ovb\n000005.counts  000061.counts  000117.counts            000173.counts\n000005.ovb     000061.ovb     000117.ovb               000173.ovb\n000006.counts  000062.counts  000118.counts            000174.counts\n000006.ovb     000062.ovb     000118.ovb               000174.ovb\n000007.counts  000063.counts  000119.counts            000175.counts\n000007.ovb     000063.ovb     000119.ovb               000175.ovb\n000008.counts  000064.counts  000120.counts            000176.counts\n000008.ovb     000064.ovb     000120.ovb               000176.ovb\n000009.counts  000065.counts  000121.counts            000177.counts\n000009.ovb     000065.ovb     000121.ovb               000177.ovb\n000010.counts  000066.counts  000122.counts            000178.counts\n000010.ovb     000066.ovb     000122.ovb               000178.ovb\n000011.counts  000067.counts  000123.counts            000179.counts\n000011.ovb     000067.ovb     000123.ovb               000179.ovb\n000012.counts  000068.counts  000124.counts            000180.counts\n000012.ovb     000068.ovb     000124.ovb               000180.ovb\n000013.counts  000069.counts  000125.counts            000181.counts\n000013.ovb     000069.ovb     000125.ovb               000181.ovb\n000014.counts  000070.counts  000126.counts            000182.counts\n000014.ovb     000070.ovb     000126.ovb               000182.ovb\n000015.counts  000071.counts  000127.counts            000183.counts\n000015.ovb     000071.ovb     000127.ovb               000183.ovb\n000016.counts  000072.counts  000128.counts            000184.counts\n000016.ovb     000072.ovb     000128.ovb               000184.ovb\n000017.counts  000073.counts  000129.counts            000185.counts\n000017.ovb     000073.ovb     000129.ovb               000185.ovb\n000018.counts  000074.counts  000130.counts            000186.counts\n000018.ovb     000074.ovb     000130.ovb               000186.ovb\n000019.counts  000075.counts  000131.counts            000187.counts\n000019.ovb     000075.ovb     000131.ovb               000187.ovb\n000020.counts  000076.counts  000132.counts            000188.counts\n000020.ovb     000076.ovb     000132.ovb               000188.ovb\n000021.counts  000077.counts  000133.counts            000189.counts\n000021.ovb     000077.ovb     000133.ovb               000189.ovb\n000022.counts  000078.counts  000134.counts            000190.counts\n000022.ovb     000078.ovb     000134.ovb               000190.ovb\n000023.counts  000079.counts  000135.counts            000191.counts\n000023.ovb     000079.ovb     000135.ovb               000191.ovb\n000024.counts  000080.counts  000136.counts            000192.counts\n000024.ovb     000080.ovb     000136.ovb               000192.ovb\n000025.counts  000081.counts  000137.counts            000193.counts\n000025.ovb     000081.ovb     000137.ovb               000193.ovb\n000026.counts  000082.counts  000138.counts            000194.counts\n000026.ovb     000082.ovb     000138.ovb               000194.ovb\n000027.counts  000083.counts  000139.mhap              000195.counts\n000027.ovb     000083.ovb     000139.mhap.ovb.WORKING  000195.ovb\n000028.counts  000084.counts  000140.counts            000196.counts\n000028.ovb     000084.ovb     000140.ovb               000196.ovb\n000029.counts  000085.counts  000141.counts            000197.counts\n000029.ovb     000085.ovb     000141.ovb               000197.ovb\n000030.counts  000086.counts  000142.counts            000198.counts\n000030.ovb     000086.ovb     000142.ovb               000198.ovb\n000031.counts  000087.counts  000143.counts            000199.counts\n000031.ovb     000087.ovb     000143.ovb               000199.ovb\n000032.counts  000088.counts  000144.counts            000200.counts\n000032.ovb     000088.ovb     000144.ovb               000200.ovb\n000033.counts  000089.counts  000145.counts            000201.counts\n000033.ovb     000089.ovb     000145.ovb               000201.ovb\n000034.counts  000090.counts  000146.counts            000202.counts\n000034.ovb     000090.ovb     000146.ovb               000202.ovb\n000035.counts  000091.counts  000147.counts            000203.counts\n000035.ovb     000091.ovb     000147.ovb               000203.ovb\n000036.counts  000092.counts  000148.counts            000204.counts\n000036.ovb     000092.ovb     000148.ovb               000204.ovb\n000037.counts  000093.counts  000149.mhap              000205.counts\n000037.ovb     000093.ovb     000149.mhap.ovb.WORKING  000205.ovb\n000038.counts  000094.counts  000150.counts            000206.counts\n000038.ovb     000094.ovb     000150.ovb               000206.ovb\n000039.counts  000095.counts  000151.counts            000207.counts\n000039.ovb     000095.ovb     000151.ovb               000207.ovb\n000040.counts  000096.counts  000152.counts            000208.counts\n000040.ovb     000096.ovb     000152.ovb               000208.ovb\n000041.counts  000097.counts  000153.counts            000209.counts\n000041.ovb     000097.ovb     000153.ovb               000209.ovb\n000042.counts  000098.counts  000154.counts            000210.counts\n000042.ovb     000098.ovb     000154.ovb               000210.ovb\n000043.counts  000099.counts  000155.counts            000211.counts\n000043.ovb     000099.ovb     000155.ovb               000211.ovb\n000044.counts  000100.counts  000156.counts            000212.counts\n000044.ovb     000100.ovb     000156.ovb               000212.ovb\n000045.counts  000101.counts  000157.counts            000213.counts\n000045.ovb     000101.ovb     000157.ovb               000213.ovb\n000046.counts  000102.counts  000158.counts            000214.counts\n000046.ovb     000102.ovb     000158.ovb               000214.ovb\n000047.counts  000103.counts  000159.counts            000215.counts\n000047.ovb     000103.ovb     000159.ovb               000215.ovb\n000048.counts  000104.counts  000160.counts            000216.counts\n000048.ovb     000104.ovb     000160.ovb               000216.ovb\n000049.counts  000105.counts  000161.counts            000217.counts\n000049.ovb     000105.ovb     000161.ovb               000217.ovb\n000050.counts  000106.counts  000162.counts            000218.counts\n000050.ovb     000106.ovb     000162.ovb               000218.ovb\n000051.counts  000107.counts  000163.counts            000219.counts\n000051.ovb     000107.ovb     000163.ovb               000219.ovb\n000052.counts  000108.counts  000164.counts            000220.counts\n000052.ovb     000108.ovb     000164.ovb               000220.ovb\n000053.counts  000109.counts  000165.counts            000221.counts\n000053.ovb     000109.ovb     000165.ovb               000221.ovb\n000054.counts  000110.counts  000166.counts            000222.counts\n000054.ovb     000110.ovb     000166.ovb               000222.ovb\n000055.counts  000111.counts  000167.counts            000223.counts\n000055.ovb     000111.ovb     000167.ovb               000223.ovb\n000056.counts  000112.counts  000168.counts\n000056.ovb     000112.ovb     000168.ovb\n\n\nOn Mon, Sep 17, 2018 at 2:08 PM Sergey Koren <notifications@github.com>\nwrote:\n\n> No, the parameters are already in the shell script but if you have\n> intermediate files it will skip this step and continue onto the next part.\n> Your output implies your results folder still has intermediate results that\n> should be removed. Run ls on the results folder first and post that output.\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/marbl/canu/issues/1087#issuecomment-422171992>, or mute\n> the thread\n> <https://github.com/notifications/unsubscribe-auth/AUPt7z7oC-xlhFwDeLKX2q-WByvcilkCks5ucA9LgaJpZM4Wl_yc>\n> .\n>\n\n\n-- \nThank you,\n\nNicolas Alexandre\nPhD Candidate, Integrative Biology\nWhiteman Lab\nUniversity of California - Berkeley\nnalexandre@berkeley.edu <kiv@berkeley.edu>\n"}}
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