cat tophat_00*/ali* Reads: Input : 3179715 3124159 uniq. mapped reads (/ 3124159 31797.15) 98.25279938610849 Mapped : 1439420 (45.3% of input) of these: 96914 ( 6.7%) have multiple alignments (937 have >20) 45.3% overall read mapping rate. Reads: Input : 3472686 3415537 uniq. mapped reads (/ 3415537 34726.86) 98.35432860903634 Mapped : 1535914 (44.2% of input) of these: 95744 ( 6.2%) have multiple alignments (1012 have >20) 44.2% overall read mapping rate. Reads: Input : 2910888 2864563 uniq. mapped reads (/ 2864563 29108.88) 98.40856123629628 Mapped : 1286405 (44.2% of input) of these: 79239 ( 6.2%) have multiple alignments (765 have >20) 44.2% overall read mapping rate. Reads: Input : 4743271 4673704 uniq. mapped reads (/ 4673704 47432.71) 98.5333538817411 Mapped : 2216556 (46.7% of input) of these: 141749 ( 6.4%) have multiple alignments (1565 have >20) 46.7% overall read mapping rate. reczko@filia:/data/images/proton/run268$ pip.log: 1740295 reads; of these: 1740295 (100.00%) were unpaired; of these: 55555 (3.19%) aligned 0 times 596667 (34.29%) aligned exactly 1 time 1088073 (62.52%) aligned >1 times 96.81% overall alignment rate [sam_header_read2] 22 sequences loaded. 3124159 uniq. mapped reads [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 22 sequences. 1936772 reads; of these: 1936772 (100.00%) were unpaired; of these: 57148 (2.95%) aligned 0 times 669877 (34.59%) aligned exactly 1 time 1209747 (62.46%) aligned >1 times 97.05% overall alignment rate [sam_header_read2] 22 sequences loaded. 3415537 uniq. mapped reads [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 22 sequences. 1624483 reads; of these: 1624483 (100.00%) were unpaired; of these: 46324 (2.85%) aligned 0 times 590607 (36.36%) aligned exactly 1 time 987552 (60.79%) aligned >1 times 97.15% overall alignment rate [sam_header_read2] 22 sequences loaded. 2864563 uniq. mapped reads [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 22 sequences. 2526715 reads; of these: 2526715 (100.00%) were unpaired; of these: 69566 (2.75%) aligned 0 times 924990 (36.61%) aligned exactly 1 time 1532159 (60.64%) aligned >1 times 97.25% overall alignment rate [bam_sort_core] merging from 2 files... [sam_header_read2] 22 sequences loaded. 4673704 uniq. mapped reads [bam_header_read] EOF marker is absent. The input is probably truncated. [samopen] SAM header is present: 22 sequences. 6625600 reads; of these: 6625600 (100.00%) were unpaired; of these: 1751291 (26.43%) aligned 0 times 2106907 (31.80%) aligned exactly 1 time 2767402 (41.77%) aligned >1 times 73.57% overall alignment rate [bam_sort_core] merging from 3 files... [bam_sort_core] merging from 24 files... [sam_header_read2] 22 sequences loaded. 44487703 uniq. mapped reads #@ reczko@filia:/data/images/proton/run268$ /data/results/tools/align/adapter/minion search-adapter -i R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GKLex1-4382Sal.IonXpressRNA_001.fastq [minion] reading reads ................................................. 1 ................................................. 2 [minion] connected component analysis [minion] building consensus sequences criterion=sequence-density sequence-density=1.09 sequence-density-rank=1 fanout-score=2.28 fanout-score-rank=29 prefix-density=1.22 prefix-fanout=2.0 sequence=TTCTCCCAGTACGAAAGGACAAGAGAAATAGAGCCACCTTACAAATAAGCGCTCTCAACTTAATTTATGAATAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=380.58 fanout-score-rank=1 prefix-density=0.60 prefix-fanout=5.5 sequence=ATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACATGATAATACATAAA reczko@filia:/data/images/proton/run268$ reczko@filia:/data/images/proton/run268$ /data/results/tools/align/adapter/minion search-adapter -i R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GKLex2-4383Sal.IonXpressRNA_002.fastq [minion] reading reads ................................................. 1 ................................................. 2 [minion] connected component analysis [minion] building consensus sequences criterion=sequence-density sequence-density=0.96 sequence-density-rank=1 fanout-score=2.40 fanout-score-rank=25 prefix-density=1.10 prefix-fanout=2.1 sequence=TTCTCCCAGTACGAAAGGACAAGAGAAATAGAGCCACCTTACAAATAAGCGCTCTCAACTTAATTTATGAATAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=312.24 fanout-score-rank=1 prefix-density=0.68 prefix-fanout=4.8 sequence=ATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACATGATAATACATAAA reczko@filia:/data/images/proton/run268$ /data/results/tools/align/adapter/minion search-adapter -i R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GKLex3-43819Hum.IonXpressRNA_003.fastq [minion] reading reads ................................................. 1 ................................................. 2 [minion] connected component analysis [minion] building consensus sequences criterion=sequence-density sequence-density=1.14 sequence-density-rank=1 fanout-score=2.37 fanout-score-rank=26 prefix-density=1.29 prefix-fanout=2.1 sequence=TTCTCCCAGTACGAAAGGACAAGAGAAATAGAGCCACCTTACAAATAAGCGCTCTCAACTTAATTTATGAATAAAAATCTAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=26 fanout-score=258.12 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=4.7 sequence=ATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACATGATAATACATAAA reczko@filia:/data/images/proton/run268$ /data/results/tools/align/adapter/minion search-adapter -i R_2016_01_29_13_01_36_user_IONAS-268-GSR9_GSkP4-5_GKLex1-4_160129.GKLex4-43823Hum.IonXpressRNA_004.fastq [minion] reading reads ................................................. 1 ................................................. 2 [minion] connected component analysis [minion] building consensus sequences criterion=sequence-density sequence-density=1.00 sequence-density-rank=1 fanout-score=2.96 fanout-score-rank=19 prefix-density=1.15 prefix-fanout=2.6 sequence=AGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=23 fanout-score=285.88 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=4.8 sequence=ATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACATGATAATACATAA reczko@filia:/data/images/proton/run268$