{"action":"created","issue":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/117","repository_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq","labels_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/117/labels{/name}","comments_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/117/comments","events_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/117/events","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/117","id":145179340,"number":117,"title":"bowtie2-align exited with value 1","user":{"login":"bimbam23","id":2727580,"avatar_url":"https://avatars.githubusercontent.com/u/2727580?v=3","gravatar_id":"","url":"https://api.github.com/users/bimbam23","html_url":"https://github.com/bimbam23","followers_url":"https://api.github.com/users/bimbam23/followers","following_url":"https://api.github.com/users/bimbam23/following{/other_user}","gists_url":"https://api.github.com/users/bimbam23/gists{/gist_id}","starred_url":"https://api.github.com/users/bimbam23/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bimbam23/subscriptions","organizations_url":"https://api.github.com/users/bimbam23/orgs","repos_url":"https://api.github.com/users/bimbam23/repos","events_url":"https://api.github.com/users/bimbam23/events{/privacy}","received_events_url":"https://api.github.com/users/bimbam23/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2016-04-01T13:21:01Z","updated_at":"2016-08-17T17:05:06Z","closed_at":null,"body":"Hi, I installed the new Version 2.2.0 and got the following error:\r\n\r\n`* Running CMD: bash -c \" set -o pipefail;bowtie2 --local -a --threads 24 -f /cluster/scratch/bickj/trinity_run_8_endo_cor_pb_NEW//chrysalis/inchworm.K25.L25.fa.min100 both.fa  | samtools view -@ 24 -F4 -Sb - | samtools sort -m 5816101546 -@ 24 -no - - > /cluster/scratch/bickj/trinity_run_8_endo_cor_pb_NEW//chrysalis/iworm.bowtie.nameSorted.bam\" \r\n[bam_header_read] EOF marker is absent. The input is probably truncated.\r\nNo index, query, or output file specified!\r\nBowtie 2 version 2.2.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)\r\nUsage: \r\n  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]\r\n\r\n  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).\r\n             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.\r\n  <m1>       Files with #1 mates, paired with files in <m2>.\r\n             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).\r\n  <m2>       Files with #2 mates, paired with files in <m1>.\r\n             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).\r\n  <r>        Files with unpaired reads.\r\n             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).\r\n  <sam>      File for SAM output (default: stdout)\r\n\r\n  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be\r\n  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.\r\n\r\nOptions (defaults in parentheses):\r\n\r\n Input:\r\n  -q                 query input files are FASTQ .fq/.fastq (default)\r\n  --qseq             query input files are in Illumina's qseq format\r\n  -f                 query input files are (multi-)FASTA .fa/.mfa\r\n  -r                 query input files are raw one-sequence-per-line\r\n  -c                 <m1>, <m2>, <r> are sequences themselves, not files\r\n  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)\r\n  -u/--upto <int>    stop after first <int> reads/pairs (no limit)\r\n  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)\r\n  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)\r\n  --phred33          qualities are Phred+33 (default)\r\n  --phred64          qualities are Phred+64\r\n  --int-quals        qualities encoded as space-delimited integers\r\n\r\n Presets:                 Same as:\r\n  For --end-to-end:\r\n   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50\r\n   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50\r\n   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)\r\n   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50\r\n\r\n  For --local:\r\n   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00\r\n   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75\r\n   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)\r\n   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50\r\n\r\n Alignment:\r\n  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)\r\n  -L <int>           length of seed substrings; must be >3, <32 (22)\r\n  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)\r\n  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)\r\n  --dpad <int>       include <int> extra ref chars on sides of DP table (15)\r\n  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)\r\n  --ignore-quals     treat all quality values as 30 on Phred scale (off)\r\n  --nofw             do not align forward (original) version of read (off)\r\n  --norc             do not align reverse-complement version of read (off)\r\n  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to\r\n                     scan for the optimal seeded alignments\r\n  --end-to-end       entire read must align; no clipping (on)\r\n   OR\r\n  --local            local alignment; ends might be soft clipped (off)\r\n\r\n Scoring:\r\n  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) \r\n  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)\r\n  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)\r\n  --rdg <int>,<int>  read gap open, extend penalties (5,3)\r\n  --rfg <int>,<int>  reference gap open, extend penalties (5,3)\r\n  --score-min <func> min acceptable alignment score w/r/t read length\r\n                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)\r\n\r\n Reporting:\r\n  (default)          look for multiple alignments, report best, with MAPQ\r\n   OR\r\n  -k <int>           report up to <int> alns per read; MAPQ not meaningful\r\n   OR\r\n  -a/--all           report all alignments; very slow, MAPQ not meaningful\r\n\r\n Effort:\r\n  -D <int>           give up extending after <int> failed extends in a row (15)\r\n  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)\r\n\r\n Paired-end:\r\n  -I/--minins <int>  minimum fragment length (0)\r\n  -X/--maxins <int>  maximum fragment length (500)\r\n  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)\r\n  --no-mixed         suppress unpaired alignments for paired reads\r\n  --no-discordant    suppress discordant alignments for paired reads\r\n  --no-dovetail      not concordant when mates extend past each other\r\n  --no-contain       not concordant when one mate alignment contains other\r\n  --no-overlap       not concordant when mates overlap at all\r\n\r\n Output:\r\n  -t/--time          print wall-clock time taken by search phases\r\n  --un <path>           write unpaired reads that didn't align to <path>\r\n  --al <path>           write unpaired reads that aligned at least once to <path>\r\n  --un-conc <path>      write pairs that didn't align concordantly to <path>\r\n  --al-conc <path>      write pairs that aligned concordantly at least once to <path>\r\n  (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.\r\n  --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)\r\n  --quiet            print nothing to stderr except serious errors\r\n  --met-file <path>  send metrics to file at <path> (off)\r\n  --met-stderr       send metrics to stderr (off)\r\n  --met <int>        report internal counters & metrics every <int> secs (1)\r\n  --no-head          supppress header lines, i.e. lines starting with @\r\n  --no-sq            supppress @SQ header lines\r\n  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field\r\n  --rg <text>        add <text> (\"lab:value\") to @RG line of SAM header.\r\n                     Note: @RG line only printed when --rg-id is set.\r\n  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.\r\n\r\n Performance:\r\n  -p/--threads <int> number of alignment threads to launch (1)\r\n  --reorder          force SAM output order to match order of input reads\r\n  --mm               use memory-mapped I/O for index; many 'bowtie's can share\r\n\r\n Other:\r\n  --qc-filter        filter out reads that are bad according to QSEQ filter\r\n  --seed <int>       seed for random number generator (0)\r\n  --non-deterministic seed rand. gen. arbitrarily instead of using read attributes\r\n  --version          print version information and quit\r\n  -h/--help          print this usage message\r\n(ERR): bowtie2-align exited with value 1\r\n[samopen] no @SQ lines in the header.\r\n[sam_read1] missing header? Abort!\r\nTrinity run failed. Must investigate error above.`\r\n\r\n\r\nSomehow bowtie2 does not have an index file?\r\nDo you need more info about my executed  command?\r\n\r\nCheers Jochen"},"comment":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/comments/240478395","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/117#issuecomment-240478395","issue_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/117","id":240478395,"user":{"login":"roberthaney","id":15001530,"avatar_url":"https://avatars.githubusercontent.com/u/15001530?v=3","gravatar_id":"","url":"https://api.github.com/users/roberthaney","html_url":"https://github.com/roberthaney","followers_url":"https://api.github.com/users/roberthaney/followers","following_url":"https://api.github.com/users/roberthaney/following{/other_user}","gists_url":"https://api.github.com/users/roberthaney/gists{/gist_id}","starred_url":"https://api.github.com/users/roberthaney/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roberthaney/subscriptions","organizations_url":"https://api.github.com/users/roberthaney/orgs","repos_url":"https://api.github.com/users/roberthaney/repos","events_url":"https://api.github.com/users/roberthaney/events{/privacy}","received_events_url":"https://api.github.com/users/roberthaney/received_events","type":"User","site_admin":false},"created_at":"2016-08-17T17:05:06Z","updated_at":"2016-08-17T17:05:06Z","body":"Thanks! Will go with (a) first and then see about trying (b) later. "}}
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