Question: Bowtie2 aligner not generating .sam file.
0
gravatar for pinnintilikithreddy
3 days ago by
pinnintilikithreddy0 wrote:

Hi, I used bowtie2 V2.3.3.1 1st Step- bowtie2-build -f /media/likith/REDDY/CANCERGENOMICS/NewFolder/hg38.fa hg38 Generated a list of files- hg38.1.bt2, hg38.2.bt2,hg38.3.bt2,hg38.4.bt2,hg38.fa, hg38.rev.1.bt2, hg38.rev.2.bt2

2nd Step- bowtie2 -x hg38 -1 /media/likith/REDDY/CANCERGENOMICS/NewFolder/bowtie2/SRR098401testsickle_1.fastq -2 /media/likith/REDDY/CANCERGENOMICS/NewFolder/bowtie2/SRR098401testsickle_2.fastq -s /media/likith/REDDY/CANCERGENOMICS/NewFolder/bowtie2/SRR098401_pebwt.sam

After executing cmd it running for long time.

Result - I'm not able to generate the file "SRR098401_pebwt.sam" (?) The prompt shows( last few lines) like this..... Can any one explain me why it is happening ?

SRR098401.114048463 147 chr9 123652773 8 28M = 123652716 -85 AAAAAAAACGCAAAACAAACAGCAGCAA @@@AACCC6,(<;7FFGGHHHCHHBHHH AS:i:-13 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:8T0T0G2G14 YS:i:-14 YT:Z:CP 92522058 reads; of these: 92522058 (100.00%) were paired; of these: 2035529 (2.20%) aligned concordantly 0 times 73726342 (79.69%) aligned concordantly exactly 1 time 16760187 (18.11%) aligned concordantly >1 times ---- 2035529 pairs aligned concordantly 0 times; of these: 949789 (46.66%) aligned discordantly 1 time ---- 1085740 pairs aligned 0 times concordantly or discordantly; of these: 2171480 mates make up the pairs; of these: 992625 (45.71%) aligned 0 times 387998 (17.87%) aligned exactly 1 time 790857 (36.42%) aligned >1 times 99.46% overall alignment rate SRR098401.114048513 99 chr10 132415511 3 45M1I4M = 132415574 101 ATCCAGACATCCACTGTCACACACACGCACTCTCACACACATTCACCACC HGHFHFHHEFHCHHHHEHEHHFEBHFHHFHHHEHHDHHGHCCEFEAC7BD AS:i:-13 XN:i:0XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:48A0 YS:i:-21 YT:Z:CP SRR098401.114048513 147 chr10 132415574 3 38M = 132415511 -101 CACAACCACCCACACACACCCACCCACAGACACCCACA @<c@2?b>D.DAD@ECE;BBD>D;5<=:-.8>/C;CB AS:i:-21 XS:i:-15 XN:i:0 XM:i:7XO:i:0 XG:i:0 NM:i:7 MD:Z:4T4T13T4T0T0T2T4 YS:i:-13 YT:Z:CP SRR098401.114048581 83 chr10 1816393 24 45M = 1816267 -171 TTTGACTGATATTTGTATAGCCACCGCAGCTCTCTTTTGGTTACT EEDD?CAA>DEBFEBEBDBFFF?AF?GFAG@GGGGGGGGGGGFFG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:45 YS:i:-13 YT:Z:CP SRR098401.114048581 163 chr10 1816267 24 23M = 1816393 171 CGTTTGGTTCTTTTTTTTTGGTG @HHHHGDD9@GGEA?FFF7F6:; AS:i:-13 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:0A7A9A4 YS:i:0 YT:Z:CP SRR098401.114048604 97 chr6 98176005 14 21M1D24M chr17 77085279 0 AATTGAAGGAAATTGAAATATAAAAAAAAAAATTCAAAAGATCAA HHHHHHHHHHHHHHHHHHHEHHHGHHHHHHE6G?:DGD?A2::B= AS:i:-8 XN:i:0 XM:i:0 XO:i:1XG:i:1 NM:i:1 MD:Z:21^A24 YT:Z:UP SRR098401.114048604 145 chr17 77085279 42 25M chr6 98176005 0 AAAAAAAATAAAACCCAAAAAAAGA @@@@-<<<&?56@@EEEE7CCC@C AS:i:-2 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:8A16 YT:Z:UP SRR098401.114048637 99 chr15 33685784 7 50M = 33685888 124 AAACTCACTCAAAACCGCACAACTACATGGAAACCGAACAATCTGCTCCT EDBGGGGGFEGGGGGGGGGGGGGEGGGFGFGGBGGGAEDCGGGGG7DCDC AS:i:0 XS:i:-5 XN:i:0XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YS:i:-11 YT:Z:CP SRR098401.114048637 147 chr15 33685888 7 20M = 33685784 -124 AACCAAAAAAAACAAAAACA CBA@@<%.<4;<;6<>-@=> AS:i:-11 XS:i:0 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:6T0G1G6G3 YS:i:0YT:Z:CP SRR098401.114048738 89 chr3 175315939 42 45M = 175315939 0 TTCATATATGACCCTATATTTAAAAATGCAATTAATGTGTCTTTG EEEBEGEGGGFBEEGGDGGBGFFGGGGGFGGGEGGGGFGGGGGFG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0NM:i:0 MD:Z:45 YT:Z:UP SRR098401.114048738 165 chr3 175315939 0 * = 175315939 0 TGTTTGTGTTTTTTTTTTGTTGTGG C8@AA1<>@<;)<;@1@1@<<9?9 YT:Z:UP SRR098401.114048748 73 chr7 20086531 15 54M = 20086531 0 CCACACCCAGCTAATTTTTGTATTATTAGTAGAGACAAGGTTTTACCCTGTTGG HHHHHHHGGHHGGGHHGHHHBEGBEGGFGFHGDHDHHDHHEHHHF@@B@@>B@@ AS:i:-5 XN:i:0XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:47A6 YT:Z:UP SRR098401.114048748 133 chr7 20086531 0 * = 20086531 0 GGGTGGTTTTTTTGGGGTTGGGTGT HHHHH@2C24-<<<1?8894CB9B? YT:Z:UP SRR098401.114048920 89 chr5 70946170 1 45M = 70946170 0 GTATATGGTAAGTAATCACTCAGCATCTTTTCCTGACAATTTTTT ?EGGFDHHHHHHHHHHHHHHHHGHHHBHHHHHHHHHHEHHHHHHH AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0NM:i:1 MD:Z:0T44 YT:Z:UP SRR098401.114048920 165 chr5 70946170 0 * = 70946170 0 TCGGGGGTTTGGTTTTTTGTTTGGTGG @,68@02@@@21A@ADDBBBBB%8D=> YT:Z:UP SRR098401.114048974 97 chr20 43139895 42 45M chr7 39680385 0 AAAGCCTCCAAGGGACTTACCACAAAACAGAAGCAATATTTTAAC FEEDEBGGGAAFFB@EFEEEFGFF?FDGEE>@;DC;:DDAD=?DB AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0NM:i:1 MD:Z:44A0 YT:Z:UP SRR098401.114048974 145 chr7 39680385 1 20M chr20 43139895 0 ACAAAAACAAAAAAAACACA ?79??<@<<4471B>5-5@@ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:20 YT:Z:UP SRR098401.114048986 89 chr10 84627148 42 38M = 84627148 0 CCTGCCATTATGTTACATGATGTTCTTTGCCTGTTACA EEB?HHHFFGFFCBEEFHHAHFDGHGFHEGFGFGFFGG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0MD:Z:38 YT:Z:UP SRR098401.114048986 165 chr10 84627148 0 * = 84627148 0 GGGTTTTTTTGGTTGGTTTGTGTGTGGTGTTTTTTG ??=643?>;<.41;?=94?<>>;.@BA:1AGDBB?: YT:Z:UP SRR098401.114049008 99 chrX 25575707 40 44M = 25575835 148 TGGGAATAAGAGGCTAATAGGAGAGGACAAGTAGTGCCAAAGTA HHHHFHHHHHHGHHHHDHHHEHGEHHFHHHGCGFBFFFED<c6b as:i:0="" xn:i:0="" xm:i:0="" xo:i:0="" xg:i:0nm:i:0="" md:z:44="" ys:i:-11="" yt:z:cp="" srr098401.114049008="" 147="" chrx="" 25575835="" 40="" 20m="25575707" -148="" aaaaaaacaaaaacaaaaaa="" @@@@@@'-@@ee7eegg(gd="" as:i:-11="" xs:i:0="" xn:i:0="" xm:i:4="" xo:i:0="" xg:i:0="" nm:i:4="" md:z:6t0g4g4t2="" ys:i:0yt:z:cp="" srr098401.114049024="" 83="" chr2="" 51191331="" 8="" 45m="51191234" -142="" gttgttaacttgagatatttctagcttttcagtgtgggcaattag="" bfbgfhhhhfhbhhhhhhghhfhhhhhhhhhhhhhhhhhhhhghh="" as:i:-5="" xs:i:-20="" xn:i:0="" xm:i:1xo:i:0="" xg:i:0="" nm:i:1="" md:z:0t44="" ys:i:-33="" yt:z:cp="" srr098401.114049024="" 163="" chr2="" 51191234="" 8="" 69m="51191331" 142="" tcttgtgttttggtggttttggggtttgtttgtttttggttttgttttggtttggtttgttgttggttg="" c,ccc@ccc2@;4="">/A4CCAEGGECHHHFH==2?2?=?@@A'@9=;<7'>?CC'C?CAC.@%BBA>>@> AS:i:-33 XN:i:0 XM:i:12 XO:i:0 XG:i:0 NM:i:12 MD:Z:9C2A1A1C15C1C6C1C4A4A5C1C7 YS:i:-5 YT:Z:CP SRR098401.114049028 147 chr9 63254389 1 32M = 63254344 -77 CAAAACAAAACACACACCCCCACACAAACACA 7;@?@%@EGDGDFCFEEGFFGFHHGHHHHHHH AS:i:-2 XS:i:-2 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1MD:Z:5T26 YS:i:0 YT:Z:CP SRR098401.114049061 89 chr2 106552997 42 45M = 106552997 0 GGCACTGTAATATTTTGGGAATCTTGCTTTTCTGCACTTTTCCCT BFGGCGHHFHEGGGGGECGHHHHGGHHDHHEGGEGDFFHGHHHHG AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0NM:i:1 MD:Z:17T27 YT:Z:UP SRR098401.114049061 165 chr2 106552997 0 * = 106552997 0 TTGTGGTTGGTTATGTTTTGTGT <,::?74=6<<,?;@@B<4??A YT:Z:UP SRR098401.114049095 113 chr12 104805213 42 50M chr17 30910349 0 AACAGAGCTGTCCCGAGCAGATCACCCAATGCTGTTAGGTAGGGGATGGA 89;68EFFEEFCBF?FFEFFB<ecefe@fefff?fffffffff@faefff as:i:0="" xn:i:0="" xm:i:0xo:i:0="" xg:i:0="" nm:i:0="" md:z:50="" yt:z:up="" srr098401.114049095="" 177="" chr17="" 30910349="" 1="" 21m="" chr12="" 104805213="" 0="" accaaaaaaaaaaaaacacca="" @c?@@24&lt;:'7;@@5="">7>81: AS:i:-2 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:9C11 YT:Z:UP SRR098401.114049150 65 chr11 101643970 0 42M chr8 73321970 0 AGGCATGGGCAAGGACTTCATGACTACCGCACGAAAAGCAAT FEDGGFGBDGGGFFCFFFFDGBFDGB;<<:<<<<<eb8ed@c as:i:-16="" xn:i:0="" xm:i:4="" xo:i:0xg:i:0="" nm:i:4="" md:z:26a0a0a3c9="" yt:z:up="" srr098401.114049150="" 129="" chr8="" 73321970="" 40="" 24m="" chr11="" 101643970="" 0="" gtgttggtggtttgttttgttgtg="" dgd<gdda7cegeeefeff4=""><;@ AS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21T2 YT:Z:UP SRR098401.114049247 89 chr9 41024476 0 45M = 41024476 0 GGGCGGTGCGGGGGTGTGAGGCTTTTGGCCAGCATACAGAGACAC BDD8DDHFGHEEEEEAFFEDFFHHHHHHHHHHHHHHHHHHHHHHH AS:i:-20 XN:i:0 XM:i:4 XO:i:0XG:i:0 NM:i:4 MD:Z:2T1T2T7T29 YT:Z:UP SRR098401.114049247 165 chr9 41024476 0 * = 41024476 0 TTGTATTTTGTTGGTTTTGGTTGG CC,/&CAA@@GIG7IDDDDD1CC6 YT:Z:UP SRR098401.114049279 83 chr4 123028176 0 37M = 123028112 -101 TAGGTTGCAGGTATCCTGGTCAGATATAGGAGGACTG A>B@@BABDECEFEHGGHHHHHGHFHGHGHHGHHHGH AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3MD:Z:2T0T2T30 YS:i:-16 YT:Z:CP SRR098401.114049279 163 chr4 123028112 0 34M = 123028176 101 TTTGTTTTTTTTTTTTTTTTGGTTGTGTGTTTGT D6DDCBBBBB4FFFFCCBAB-BCA,?3?=;AAA< AS:i:-16 XS:i:-10 XN:i:0 XM:i:5 XO:i:0XG:i:0 NM:i:5 MD:Z:1A8A9A3C1C7 YS:i:-15 YT:Z:CP SRR098401.114049304 99 chr15 89496360 24 25M = 89496459 121 CTTGGGTAGCGATAGTAGAATTCGT ><<>9:@BA,EEF=FC@BE8B<@CB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:25 YS:i:-10 YT:Z:CP SRR098401.114049304 147 chr15 89496459 24 22M = 89496360 -121 AACACCCCAAAAAAAACCACCA ?>@9@CC@'@@2A'CB+>>>>@ AS:i:-10 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:8G2G1G2T5 YS:i:0YT:Z:CP SRR098401.114049405 77 * 0 0 * * 0 0 AATGAGCTGAGGCCAGGGCCGCTCCCGGCTGC GHHHEHGFHEGHHHGGFGFECB@CC;><>:=A YT:Z:UP SRR098401.114049405 141 * 0 0 * * 0 0 TCTGTTTTGGTTGGTCTGGTTT @,00@=;:%4>=<1=,0@@<6@ YT:Z:UP SRR098401.114049415 137 chr3 126560201 7 24M = 126560201 0 TGTTGGTTTTTTTTTTTTGTGTTT C,CCCC>CBC:FFFF<,9*@:8;; AS:i:-2 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:18T5 YT:Z:UP SRR098401.114049415 69 chr3 126560201 0 * = 126560201 0 AAAAGGAAATCTCCACAACCGTGCTCCCCCCGGTTCTTGTTTTCGTTG GGGGGFBGBGGFGGGEEEE>80653CACB>B=?A?DDBEA9><9:;>@ YT:Z:UP SRR098401.114049439 153 chr5 131847986 6 21M = 131847986 0 CAAAACCACAACAAAACCAAA @EGE9EB?@<@-@-6@651@@ AS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:13T7 YT:Z:UP SRR098401.114049439 101 chr5 131847986 0 * = 131847986 0 GCCACTGTCCTCCAAAACCCCGCCTGGTCGCTCCCCCGCCCGCTT HGHDGHHHHHHHGHHHECH@BE:2@C@>>B9<<:04?B;B9?BA? YT:Z:UP SRR098401.114049460 73 chr4 28211665 0 20M = 28211665 0 CCCCACCATCTAACCCAGTT FHHHHGHEGGGFFEGGFGGG AS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:14A5 YT:Z:UP SRR098401.114049460 133 chr4 28211665 0 * = 28211665 0 TGTTGTGTGTTTGGGGTGTTTGGTGGTTGG CA11B@C@AC9>2?3B=@79@-@;-@,=@< YT:Z:UP SRR098401.114049495 77 * 0 0 * * 0 0 GCATATAGTAAATACCCTATCCCTCCCTCTGGCCTCCCCC HHHHHHHHHGHHHHHGEGGGCCFFDEEFDFHFEEHFGFGE YT:Z:UP SRR098401.114049495 141 * 0 0 * * 0 0 GGGTTTGGTTGGTGGTTGGGTTTGTTTGTTTGTTT C6C0CCCC6C@84/1@@@@@HHHHHE@%GE?BC?? YT:Z:UP SRR098401.114049544 137 chr5 158711659 1 20M = 158711659 0 GGGTTTTTTTGTTTGCTTTT ?29.??.>@@%@%@@,>@?> AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:20 YT:Z:UP SRR098401.114049544 69 chr5 158711659 0 * = 158711659 0 TATAGGAAATCAATGTGTTGCCCGTTGTCTTCGTCCCCCCCG HHHHGHHHHHHHFHHFGGGG@DADD>>//>6-9<7CFFG?=? YT:Z:UP SRR098401.114049553 89 chr3 196238676 42 25M = 196238676 0 AGGGAGGAAACATTAGTCTTCTTCA B8@4C?GFGGGGGFGGGGGEGGFGG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:25 YT:Z:UP SRR098401.114049553 165 chr3 196238676 0 * = 196238676 0 TGGTTTGTTGTTGTGTTTGGGTTTGGTGTTGGGGT @6,@>?<>1<1ABA15@>1@C?CB2GDGEGEEGEC YT:Z:UP SRR098401.114049628 153 chr6 4420767 7 21M = 4420767 0 CACCAAAACCAAACCAAACAA BCDDDG6<@@@1D1BB<gggg as:i:-3="" xn:i:0="" xm:i:1="" xo:i:0="" xg:i:0="" nm:i:1="" md:z:13a7="" yt:z:up="" srr098401.114049628="" 101="" chr6="" 4420767="" 0="" *="4420767" 0="" ttaaatatttcatttcccttgttttctttttgccgcc="" hhhhhhhhhhhhhhhhdfhhghhhh6="">@<':@<<

SRR098401.114050028 163 chr16 88249434 0 35M = 88249587 175 TTTCTTTTTTTTTTTTTTTTTGGGTTGGGGTTTTG GGG(GCC%CCFFFFFHHHHHBB8G6;=;)?C7CBC AS:i:-17 XS:i:-12 XN:i:0 XM:i:5 XO:i:0XG:i:0 NM:i:5 MD:Z:3T18A5A0A1C3 YS:i:-5 YT:Z:CP SRR098401.114051567 97 chr2 172534392 1 20M chr4 48927903 0 CTGGGTGGGGGGGGGGGGGG >>>>*=>;;;0DDCD@11@; AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:20 YT:Z:UP SRR098401.114051567 145 chr4 48927903 1 20M chr2 172534392 0 ACAAAACAAAACCCCCCCAC @9<@@@71CC+<><<cc:6b as:i:0="" xn:i:0="" xm:i:0="" xo:i:0="" xg:i:0="" nm:i:0="" md:z:20="" yt:z:up<="" p="">

alignment • 94 views
ADD COMMENTlink modified 3 days ago by Seigfried30 • written 3 days ago by pinnintilikithreddy0
1
gravatar for Suraj Mahendra Metha
3 days ago by
Suraj Mahendra Metha20 wrote:

There is small mistake in your command, you should use "-S" instead of "-s".

ADD COMMENTlink written 3 days ago by Suraj Mahendra Metha20
1
gravatar for Seigfried
3 days ago by
Seigfried30
Seigfried30 wrote:

The difference between -S and -s

-s/--skip <int> Skip (i.e. do not align) the first <int> reads or pairs in the input.

-S <sam> File to write SAM alignments to. By default, alignments are written to the "standard out" or "stdout" filehandle (i.e. the console).

ADD COMMENTlink written 3 days ago by Seigfried30
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