========================================================== Starting on : Sun Aug 25 15:19:34 EDT 2019 Running on node : scc-tr3 Current job ID : 8907816 Current job name : slncky_chrY Task index number : ========================================================== /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/varsha/slncky_19-8-19/annotations/annotations.config Loading annotations for mm9 Loading ortholog annotations for hg19 Starting with 174 transcripts STEP I. FILTER LNCS Checking overlap with coding annotations... min_overlap: 0.0% Removing... ... 158 transcripts that overlap coding or mapped coding transcript ... 0 transcripts that fall inside coding or mapped transcript (likely UTR or intronic fragments) Searching for gene duplications by aligning to commonly duplicated coding genes... learning null distribution of alignment scores self-aligning 1 / 16 genes self-aligning 2 / 16 genes self-aligning 3 / 16 genes self-aligning 4 / 16 genes self-aligning 5 / 16 genes self-aligning 6 / 16 genes self-aligning 7 / 16 genes self-aligning 8 / 16 genes self-aligning 9 / 16 genes self-aligning 10 / 16 genes self-aligning 11 / 16 genes self-aligning 12 / 16 genes self-aligning 13 / 16 genes self-aligning 14 / 16 genes self-aligning 15 / 16 genes self-aligning 16 / 16 genes aligning transcripts to annotated duplications... self-aligning 1 / 16 genes self-aligning 2 / 16 genes self-aligning 3 / 16 genes self-aligning 4 / 16 genes self-aligning 5 / 16 genes self-aligning 6 / 16 genes self-aligning 7 / 16 genes self-aligning 8 / 16 genes self-aligning 9 / 16 genes self-aligning 10 / 16 genes self-aligning 11 / 16 genes self-aligning 12 / 16 genes self-aligning 13 / 16 genes self-aligning 14 / 16 genes self-aligning 15 / 16 genes self-aligning 16 / 16 genes 0 lncs found that align to commonly duplicated coding gene! Searching for gene duplications by aligning lncs to each other... min_cluster: 2 WARNING: too few lncs to accurately find duplications. consider setting the --no_self flag to save time. reusing null distribution from previous step aligning transcripts to each other... self-aligning 1 / 16 genes self-aligning 2 / 16 genes self-aligning 3 / 16 genes self-aligning 4 / 16 genes self-aligning 5 / 16 genes self-aligning 6 / 16 genes self-aligning 7 / 16 genes self-aligning 8 / 16 genes self-aligning 9 / 16 genes self-aligning 10 / 16 genes self-aligning 11 / 16 genes self-aligning 12 / 16 genes self-aligning 13 / 16 genes self-aligning 14 / 16 genes self-aligning 15 / 16 genes self-aligning 16 / 16 genes Removing... ... 1 clusters of 4 trancsripts that share high sequence similarity ... 1 clusters of 2 trancsripts that share high sequence similarity Searching for coding orthologs... learning distribution of coding gene alignment scores WARNING: too few transcripts to accurately learn distribution. Consider setting --min_coding parameter. aligning 1 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 2 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 3 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 4 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 5 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 6 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 7 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 8 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 9 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 10 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 11 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 12 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 13 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 14 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 15 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 16 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 17 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 18 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 19 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 20 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 21 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 22 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 23 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 24 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 25 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 26 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 27 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 28 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 29 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 30 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 31 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 32 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 33 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 34 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 35 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 36 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 37 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 38 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 39 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 40 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 41 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 42 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 43 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 44 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 45 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 46 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 47 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 48 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 49 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 50 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 51 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 52 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 53 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 54 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 55 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 56 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 57 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 58 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 59 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 60 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 61 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 62 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 63 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 64 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 65 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 66 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 67 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 68 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 69 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 70 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 71 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 72 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 73 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 74 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 75 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 76 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 77 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 78 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 79 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 80 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 81 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 82 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 83 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 84 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 85 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 86 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 87 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 88 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 89 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 90 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 91 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 92 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 93 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 94 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 95 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 96 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 97 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 98 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 99 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 100 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 101 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 102 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 103 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 104 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 105 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 106 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 107 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 108 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 109 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 110 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 111 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 112 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 113 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 114 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 115 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 116 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 117 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 118 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 119 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 120 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 121 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 122 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 123 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 124 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 125 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 126 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 127 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 128 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 129 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 130 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 131 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 132 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 133 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 134 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 135 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 136 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 137 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 138 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 139 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 140 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 141 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 142 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 143 / 143 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 1 / 5 genes to ortholog in annotations/hg19.ucsc.pseudogene.bed aligning 2 / 5 genes to ortholog in annotations/hg19.ucsc.pseudogene.bed aligning 3 / 5 genes to ortholog in annotations/hg19.ucsc.pseudogene.bed aligning 4 / 5 genes to ortholog in annotations/hg19.ucsc.pseudogene.bed aligning 5 / 5 genes to ortholog in annotations/hg19.ucsc.pseudogene.bed aligning 1 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 2 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 3 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 4 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 5 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 6 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 7 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 8 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 9 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 10 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 11 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 12 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 13 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 14 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 15 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 16 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 17 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 18 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 19 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 20 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 21 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 22 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 23 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 24 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 25 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 26 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 27 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 28 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 29 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 30 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 31 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 32 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 33 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 34 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 35 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 36 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 37 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 38 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 39 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 40 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 41 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 42 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 43 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 44 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 45 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 46 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 47 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 48 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 49 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 50 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 51 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 52 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 53 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 54 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 55 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 56 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 57 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 58 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 59 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 60 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 61 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 62 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 63 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 64 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 65 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 66 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 67 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 68 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 69 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 70 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 71 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 72 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 73 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 74 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 75 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 76 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 77 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 78 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 79 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 80 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 81 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 82 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 83 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 84 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 85 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 86 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 87 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 88 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 89 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 90 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 91 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 92 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 93 / 93 genes to ortholog in annotations/hg19.refseq.coding.bed setting cutoff for positive coding alignment at exonic id = 0.210 aligning 1 / 8 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 2 / 8 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 3 / 8 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 4 / 8 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 5 / 8 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 6 / 8 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 7 / 8 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 8 / 8 genes to ortholog in annotations/hg19.ucsc.coding.bed aligning 1 / 7 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 2 / 7 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 3 / 7 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 4 / 7 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 5 / 7 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 6 / 7 genes to ortholog in annotations/hg19.refseq.coding.bed aligning 7 / 7 genes to ortholog in annotations/hg19.refseq.coding.bed Removing... ... 1 transcripts that aligns >21.0% to ortholog coding transcript Writing final lncs file. STEP II. FIND LNC ORTHOLOGS Searching for orthologs... aligning 1 / 4 genes to ortholog in annotations/hg19.ucsc.noncoding.bed aligning 2 / 4 genes to ortholog in annotations/hg19.ucsc.noncoding.bed aligning 3 / 4 genes to ortholog in annotations/hg19.ucsc.noncoding.bed aligning 4 / 4 genes to ortholog in annotations/hg19.ucsc.noncoding.bed Found... ... 2 transcripts with noncoding ortholog! ... 0 conserved small ORF with kN/kS < 1! Finished .............. Sun Aug 25 15:24:26 EDT 2019