{"action":"created","issue":{"url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/141","repository_url":"https://api.github.com/repos/BenLangmead/bowtie2","labels_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/141/labels{/name}","comments_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/141/comments","events_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/141/events","html_url":"https://github.com/BenLangmead/bowtie2/issues/141","id":258230267,"number":141,"title":"Error in Bowtie2 \"isn't numeric in bitwise and (&) at \"","user":{"login":"hasnahana","id":6950692,"avatar_url":"https://avatars3.githubusercontent.com/u/6950692?v=4","gravatar_id":"","url":"https://api.github.com/users/hasnahana","html_url":"https://github.com/hasnahana","followers_url":"https://api.github.com/users/hasnahana/followers","following_url":"https://api.github.com/users/hasnahana/following{/other_user}","gists_url":"https://api.github.com/users/hasnahana/gists{/gist_id}","starred_url":"https://api.github.com/users/hasnahana/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hasnahana/subscriptions","organizations_url":"https://api.github.com/users/hasnahana/orgs","repos_url":"https://api.github.com/users/hasnahana/repos","events_url":"https://api.github.com/users/hasnahana/events{/privacy}","received_events_url":"https://api.github.com/users/hasnahana/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":16,"created_at":"2017-09-16T13:00:31Z","updated_at":"2018-03-28T00:11:57Z","closed_at":null,"author_association":"NONE","body":"Hi All and @BenLangmead ,\r\n \r\nI am trying to align and then remove rrna sequences from my RNA-Seq data.\r\nI built index for my rrna fasta files using the following command\r\n**bowtie2-build -f --threads 24 --quiet rrna.fasta index_rrna**\r\n\r\nNow, i am trying to align my paired-end fastq files to the rrna files using the following command-\r\n**bowtie2 --very-sensitive-local --phred33  -x index_rrna -1 file_R1.fastq  -2 file_R2.fastq --threads 24 --met-file summary_rrna.txt --al-conc-gz paired_matches_file --un-conc-gz paired_unmatched_file --al-gz single_matches_file --un-gz single_unmatched_file**\r\n\r\nHowever, on running the script with slurm, my job gets killed and I am getting multiple errors of similar kind. See below-\r\n****Argument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42321883.\r\nArgument \"\\0:1214:7890:64386 2:N:0:TGACCA%0ACATCGCATTCTACATTATTTGC...\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42323448.\r\nArgument \"DDDDDDDD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42333056.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42339084.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42351116.\r\nArgument \"\\0BCC%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42360088.\r\nArgument \"%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42367614.\r\nArgument \"CDBDDDDDDDDDDDDC%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42387194.\r\nArgument \"%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42397563.\r\nArgument \"\\0JIIIJIIJIJIJJJIJIJJJJFGIJJJJJJIJJJJJJJJJJJIJJHHHHFDFFF...\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42400464.\r\nArgument \"%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42401981.\r\nArgument \"FFFFFEEEEEDDDDDDDEDD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42403454.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42403463.\r\nArgument \"\\0CAB?@<C%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42407951.\r\nArgument \"EACD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42411008.\r\nArgument \"\\0FFECCEEEDDDDDDDDDDDDDDD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42411013.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42426317.\r\nArgument \"\\0GACAAGTTTCAACATATACTTCGTATTATGAATACGAATA%0A+%0AHB?E>FF...\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42429058.\r\nArgument \"\\0DDDDDDDDBDD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42430603.\r\nArgument \"%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42447041.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42454466.\r\nArgument \"\\0DDD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42462019.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42463580.\r\nArgument \"\\0CC<>@BBBB>>:>CB%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42469559.\r\nArgument \"\\0CCC%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42475460.\r\nArgument \"\\0EDEDDDD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42475477.\r\nArgument \"\\0FFDECCE%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42479966.\r\nArgument \"\\0A%0AAAACACAAATAAAAAACTTTGGCGTCCTTTCTCTATACAATTTGATATTT...\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42487379.\r\nArgument \"DDCD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42545351.\r\nArgument \"\\0BCD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42556600.\r\nArgument \"DDDDDDDDDCCDDDDD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42601991.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42606424.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42613837.\r\nArgument \"%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42620040.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42620093.\r\nArgument \"\\0DDA%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42623154.\r\nArgument \"\\0TTCATGGCATCTACACTACGGTTATTCCTAGTTCTAGTAAATTCTATGTAGCCA...\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42626621.\r\nArgument \"DDDDDDDD%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42632202.\r\nArgument \"\\00\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42636822.\r\nArgument \"%0\" isn't numeric in bitwise and (&) at  bowtie2-2.3.3/bowtie2 line 556, <BT> line 42659081.\r\nslurmstepd: *** JOB 141619 ON cn069 CANCELLED AT 2017-09-16T18:09:48 ***\r\n\r\nPlease help."},"comment":{"url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/comments/376716222","html_url":"https://github.com/BenLangmead/bowtie2/issues/141#issuecomment-376716222","issue_url":"https://api.github.com/repos/BenLangmead/bowtie2/issues/141","id":376716222,"user":{"login":"tomas-pluskal","id":1796692,"avatar_url":"https://avatars0.githubusercontent.com/u/1796692?v=4","gravatar_id":"","url":"https://api.github.com/users/tomas-pluskal","html_url":"https://github.com/tomas-pluskal","followers_url":"https://api.github.com/users/tomas-pluskal/followers","following_url":"https://api.github.com/users/tomas-pluskal/following{/other_user}","gists_url":"https://api.github.com/users/tomas-pluskal/gists{/gist_id}","starred_url":"https://api.github.com/users/tomas-pluskal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tomas-pluskal/subscriptions","organizations_url":"https://api.github.com/users/tomas-pluskal/orgs","repos_url":"https://api.github.com/users/tomas-pluskal/repos","events_url":"https://api.github.com/users/tomas-pluskal/events{/privacy}","received_events_url":"https://api.github.com/users/tomas-pluskal/received_events","type":"User","site_admin":false},"created_at":"2018-03-28T00:11:57Z","updated_at":"2018-03-28T00:11:57Z","author_association":"NONE","body":"Hi, \r\nI am seeing the same error message during our Trinity runs on a LSF computing cluster running Ubuntu 14.04. We are using bowtie2-2.3.3.1-linux-x86_64 in 2 threads. Just letting you know.\r\n"}}
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