{"action":"created","issue":{"url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/235","repository_url":"https://api.github.com/repos/CGATOxford/UMI-tools","labels_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/235/labels{/name}","comments_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/235/comments","events_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/235/events","html_url":"https://github.com/CGATOxford/UMI-tools/issues/235","id":297437502,"number":235,"title":"Running Whitelist and getting IndexError: list index out of range","user":{"login":"tom-snir","id":16917673,"avatar_url":"https://avatars2.githubusercontent.com/u/16917673?v=4","gravatar_id":"","url":"https://api.github.com/users/tom-snir","html_url":"https://github.com/tom-snir","followers_url":"https://api.github.com/users/tom-snir/followers","following_url":"https://api.github.com/users/tom-snir/following{/other_user}","gists_url":"https://api.github.com/users/tom-snir/gists{/gist_id}","starred_url":"https://api.github.com/users/tom-snir/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tom-snir/subscriptions","organizations_url":"https://api.github.com/users/tom-snir/orgs","repos_url":"https://api.github.com/users/tom-snir/repos","events_url":"https://api.github.com/users/tom-snir/events{/privacy}","received_events_url":"https://api.github.com/users/tom-snir/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-02-15T13:00:39Z","updated_at":"2018-02-25T07:49:17Z","closed_at":null,"author_association":"NONE","body":"I am running the following command:\r\n\r\n>[tom@zelda Melanoma]$ umi_tools whitelist --stdin InvMelanoma_S4_L001_R1_001.fastq \\\r\n>                     --extract-method=regex \\\r\n>                     --bc-pattern=\"(?P<cell_1>.{8,12})(?P<discard_1>GAGTGATTGCTTGTGACGCCTT){s<=2}(?P<cell_2>.{8})(?P<umi_1>.{6})T{3}.*\" \\\r\n>                     --expect-cells=300 \\\r\n>                     --plot-prefix=expect_whitelist \\\r\n>                     --log2stderr > whitelist.txt\r\n\r\n\r\noutput generated by whitelist --stdin InvMelanoma_S4_L001_R1_001.fastq --extract-method=regex --bc-pattern=(?P<cell_1>.{8,12})(?P<discard_1>GAGTGATTGCTTGTGACGCCTT){s<=2}(?P<cell_2>.{8})(?P<umi_1>.{6})T{3}.* --expect-cells=300 --plot-prefix=expect_whitelist --log2stderr\r\njob started at Thu Feb 15 13:44:07 2018 on zelda -- a207a0d7-d0db-429e-8a35-d0816f61ee22\r\npid: 78695, system: Linux 2.6.32-696.6.3.el6.x86_64 #1 SMP Wed Jul 12 14:17:22 UTC 2017 x86_64\r\nblacklist_tsv                           : None\r\ncell_number                             : False\r\ncompresslevel                           : 6\r\nerror_correct_threshold                 : 1\r\nexpect_cells                            : 300\r\nextract_method                          : regex\r\nfilter_cell_barcodes                    : False\r\nlog2stderr                              : True\r\nloglevel                                : 1\r\nmethod                                  : reads\r\npattern                                 : (?P<cell_1>.{8,12})(?P<discard_1>GAGTGATTGCTTGTGACGCCTT){s<=2}(?P<cell_2>.{8})(?P<umi_1>.{6})T{3}.*\r\npattern2                                : None\r\nplot_prefix                             : expect_whitelist\r\nprime3                                  : None\r\nrandom_seed                             : None\r\nread2_in                                : None\r\nshort_help                              : None\r\nstderr                                  : <open file '<stderr>', mode 'w' at 0x7f8523b601e0>\r\nstdin                                   : <open file 'InvMelanoma_S4_L001_R1_001.fastq', mode 'r' at 0x7f851ab5c150>\r\nstdlog                                  : <open file '<stderr>', mode 'w' at 0x7f8523b601e0>\r\nstdout                                  : <open file '<stdout>', mode 'w' at 0x7f8523b60150>\r\nsubset_reads                            : 100000000\r\ntimeit_file                             : None\r\ntimeit_header                           : None\r\ntimeit_name                             : all\r\nwhitelist_tsv                           : None\r\n\r\nAnd I get the following output, ending with an error:\r\n\r\n2018-02-15 13:44:07,518 INFO Starting barcode extraction\r\n2018-02-15 13:44:07,518 INFO Parsed 0 reads\r\n2018-02-15 13:44:08,090 INFO Parsed 100000 reads\r\n2018-02-15 13:44:08,658 INFO Parsed 200000 reads\r\n2018-02-15 13:44:09,226 INFO Parsed 300000 reads\r\n2018-02-15 13:44:09,796 INFO Parsed 400000 reads\r\n2018-02-15 13:44:10,362 INFO Parsed 500000 reads\r\n2018-02-15 13:44:10,931 INFO Parsed 600000 reads\r\n2018-02-15 13:44:11,500 INFO Parsed 700000 reads\r\n2018-02-15 13:44:12,069 INFO Parsed 800000 reads\r\n2018-02-15 13:44:12,638 INFO Parsed 900000 reads\r\n2018-02-15 13:44:13,205 INFO Parsed 1000000 reads\r\n2018-02-15 13:44:13,773 INFO Parsed 1100000 reads\r\n2018-02-15 13:44:14,342 INFO Parsed 1200000 reads\r\n2018-02-15 13:44:14,911 INFO Parsed 1300000 reads\r\n2018-02-15 13:44:15,479 INFO Parsed 1400000 reads\r\n2018-02-15 13:44:16,046 INFO Parsed 1500000 reads\r\n2018-02-15 13:44:16,614 INFO Parsed 1600000 reads\r\n2018-02-15 13:44:17,181 INFO Parsed 1700000 reads\r\n2018-02-15 13:44:17,748 INFO Parsed 1800000 reads\r\n2018-02-15 13:44:18,315 INFO Parsed 1900000 reads\r\n2018-02-15 13:44:18,884 INFO Parsed 2000000 reads\r\n2018-02-15 13:44:19,453 INFO Parsed 2100000 reads\r\n2018-02-15 13:44:20,022 INFO Parsed 2200000 reads\r\n2018-02-15 13:44:20,593 INFO Parsed 2300000 reads\r\n2018-02-15 13:44:21,161 INFO Parsed 2400000 reads\r\n2018-02-15 13:44:21,732 INFO Parsed 2500000 reads\r\n2018-02-15 13:44:22,301 INFO Parsed 2600000 reads\r\n2018-02-15 13:44:22,870 INFO Parsed 2700000 reads\r\n2018-02-15 13:44:23,437 INFO Parsed 2800000 reads\r\n2018-02-15 13:44:24,007 INFO Parsed 2900000 reads\r\n2018-02-15 13:44:24,575 INFO Parsed 3000000 reads\r\n2018-02-15 13:44:25,145 INFO Parsed 3100000 reads\r\n2018-02-15 13:44:25,714 INFO Parsed 3200000 reads\r\n2018-02-15 13:44:26,283 INFO Parsed 3300000 reads\r\n2018-02-15 13:44:26,851 INFO Parsed 3400000 reads\r\n2018-02-15 13:44:27,420 INFO Parsed 3500000 reads\r\n2018-02-15 13:44:27,989 INFO Parsed 3600000 reads\r\n2018-02-15 13:44:28,558 INFO Parsed 3700000 reads\r\n2018-02-15 13:44:29,127 INFO Parsed 3800000 reads\r\n2018-02-15 13:44:29,695 INFO Parsed 3900000 reads\r\n2018-02-15 13:44:30,263 INFO Parsed 4000000 reads\r\n2018-02-15 13:44:30,832 INFO Parsed 4100000 reads\r\n2018-02-15 13:44:31,399 INFO Parsed 4200000 reads\r\n2018-02-15 13:44:31,969 INFO Parsed 4300000 reads\r\n2018-02-15 13:44:32,539 INFO Parsed 4400000 reads\r\n2018-02-15 13:44:33,107 INFO Parsed 4500000 reads\r\n2018-02-15 13:44:33,676 INFO Parsed 4600000 reads\r\n2018-02-15 13:44:34,246 INFO Parsed 4700000 reads\r\n2018-02-15 13:44:34,814 INFO Parsed 4800000 reads\r\n2018-02-15 13:44:35,382 INFO Parsed 4900000 reads\r\n2018-02-15 13:44:35,950 INFO Parsed 5000000 reads\r\n2018-02-15 13:44:36,518 INFO Parsed 5100000 reads\r\n2018-02-15 13:44:37,086 INFO Parsed 5200000 reads\r\n2018-02-15 13:44:37,654 INFO Parsed 5300000 reads\r\n2018-02-15 13:44:38,221 INFO Parsed 5400000 reads\r\n2018-02-15 13:44:38,790 INFO Parsed 5500000 reads\r\n2018-02-15 13:44:39,358 INFO Parsed 5600000 reads\r\n2018-02-15 13:44:39,928 INFO Parsed 5700000 reads\r\n2018-02-15 13:44:40,498 INFO Parsed 5800000 reads\r\n2018-02-15 13:44:41,066 INFO Parsed 5900000 reads\r\n2018-02-15 13:44:41,634 INFO Parsed 6000000 reads\r\n2018-02-15 13:44:42,205 INFO Parsed 6100000 reads\r\n2018-02-15 13:44:42,773 INFO Parsed 6200000 reads\r\n2018-02-15 13:44:43,345 INFO Parsed 6300000 reads\r\n2018-02-15 13:44:43,916 INFO Parsed 6400000 reads\r\n2018-02-15 13:44:44,485 INFO Parsed 6500000 reads\r\n2018-02-15 13:44:45,054 INFO Parsed 6600000 reads\r\n2018-02-15 13:44:45,623 INFO Parsed 6700000 reads\r\n2018-02-15 13:44:46,192 INFO Parsed 6800000 reads\r\n2018-02-15 13:44:46,761 INFO Parsed 6900000 reads\r\n2018-02-15 13:44:47,330 INFO Parsed 7000000 reads\r\n2018-02-15 13:44:47,898 INFO Parsed 7100000 reads\r\n2018-02-15 13:44:48,466 INFO Parsed 7200000 reads\r\n2018-02-15 13:44:49,035 INFO Parsed 7300000 reads\r\n2018-02-15 13:44:49,604 INFO Parsed 7400000 reads\r\n2018-02-15 13:44:50,173 INFO Parsed 7500000 reads\r\n2018-02-15 13:44:50,743 INFO Parsed 7600000 reads\r\n2018-02-15 13:44:51,312 INFO Parsed 7700000 reads\r\n2018-02-15 13:44:51,882 INFO Parsed 7800000 reads\r\n2018-02-15 13:44:52,450 INFO Parsed 7900000 reads\r\n2018-02-15 13:44:53,018 INFO Parsed 8000000 reads\r\n2018-02-15 13:44:53,587 INFO Parsed 8100000 reads\r\n2018-02-15 13:44:54,155 INFO Parsed 8200000 reads\r\n2018-02-15 13:44:54,728 INFO Parsed 8300000 reads\r\n2018-02-15 13:44:55,297 INFO Parsed 8400000 reads\r\n2018-02-15 13:44:55,864 INFO Parsed 8500000 reads\r\n2018-02-15 13:44:56,432 INFO Parsed 8600000 reads\r\n2018-02-15 13:44:57,001 INFO Parsed 8700000 reads\r\n2018-02-15 13:44:57,572 INFO Parsed 8800000 reads\r\n2018-02-15 13:44:58,143 INFO Parsed 8900000 reads\r\n2018-02-15 13:44:58,712 INFO Parsed 9000000 reads\r\n2018-02-15 13:44:59,281 INFO Parsed 9100000 reads\r\n2018-02-15 13:44:59,848 INFO Parsed 9200000 reads\r\n2018-02-15 13:45:00,417 INFO Parsed 9300000 reads\r\n2018-02-15 13:45:00,987 INFO Parsed 9400000 reads\r\n2018-02-15 13:45:01,555 INFO Parsed 9500000 reads\r\n2018-02-15 13:45:02,124 INFO Parsed 9600000 reads\r\n2018-02-15 13:45:02,693 INFO Parsed 9700000 reads\r\n2018-02-15 13:45:03,263 INFO Parsed 9800000 reads\r\n2018-02-15 13:45:03,829 INFO Parsed 9900000 reads\r\n2018-02-15 13:45:04,399 INFO Parsed 10000000 reads\r\n2018-02-15 13:45:04,967 INFO Parsed 10100000 reads\r\n2018-02-15 13:45:05,537 INFO Parsed 10200000 reads\r\n2018-02-15 13:45:06,106 INFO Parsed 10300000 reads\r\n2018-02-15 13:45:06,676 INFO Parsed 10400000 reads\r\n2018-02-15 13:45:06,910 INFO Starting - whitelist determination\r\nTraceback (most recent call last):\r\n  File \"/usr/local/bin/umi_tools\", line 11, in <module>\r\n    load_entry_point('umi-tools==0.5.3', 'console_scripts', 'umi_tools')()\r\n  File \"/usr/local/lib/python2.7/site-packages/umi_tools-0.5.3-py2.7-linux-x86_64.egg/umi_tools/umi_tools.py\", line 59, in main\r\n    module.main(sys.argv)\r\n  File \"/usr/local/lib/python2.7/site-packages/umi_tools-0.5.3-py2.7-linux-x86_64.egg/umi_tools/whitelist.py\", line 371, in main\r\n    options.plot_prefix)\r\n  File \"/usr/local/lib/python2.7/site-packages/umi_tools-0.5.3-py2.7-linux-x86_64.egg/umi_tools/umi_methods.py\", line 400, in getCellWhitelist\r\n    cell_barcode_counts, expect_cells, cell_number, plotfile_prefix)\r\n  File \"/usr/local/lib/python2.7/site-packages/umi_tools-0.5.3-py2.7-linux-x86_64.egg/umi_tools/umi_methods.py\", line 160, in getKneeEstimate\r\n    threshold = 0.001 * cell_barcode_counts.most_common(1)[0][1]\r\nIndexError: list index out of range\r\n\r\nAny idea what the problem is?"},"comment":{"url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/comments/368290348","html_url":"https://github.com/CGATOxford/UMI-tools/issues/235#issuecomment-368290348","issue_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/235","id":368290348,"user":{"login":"tom-snir","id":16917673,"avatar_url":"https://avatars2.githubusercontent.com/u/16917673?v=4","gravatar_id":"","url":"https://api.github.com/users/tom-snir","html_url":"https://github.com/tom-snir","followers_url":"https://api.github.com/users/tom-snir/followers","following_url":"https://api.github.com/users/tom-snir/following{/other_user}","gists_url":"https://api.github.com/users/tom-snir/gists{/gist_id}","starred_url":"https://api.github.com/users/tom-snir/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tom-snir/subscriptions","organizations_url":"https://api.github.com/users/tom-snir/orgs","repos_url":"https://api.github.com/users/tom-snir/repos","events_url":"https://api.github.com/users/tom-snir/events{/privacy}","received_events_url":"https://api.github.com/users/tom-snir/received_events","type":"User","site_admin":false},"created_at":"2018-02-25T07:49:17Z","updated_at":"2018-02-25T07:49:17Z","author_association":"NONE","body":"Anyone experienced something similar? Looking for any advice regarding this issue.\r\n\r\nThank you!"}}
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