test bg_sortmerna 2.1b.6

[jennaj]

toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6

no indexes at ORG

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.6

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	6
Passed	3
Error	0
Failure	3
Skipped	0

Failed s

• ❌ toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna (Test Test Prokka 1.14.6+galaxy1 #3)

  Problems:

  • Output aligned_forward:  different than expected, difference (using diff):
    ( /tmp/tmpaz5i9_sntest3_aligned_forward.fastq v. /tmp/tmpbtiros1dtest3_aligned_forward.fastq )
    --- local_file
    +++ history_data
    @@ -1,3812 +0,0 @@
    [email protected] M03099:23:000000000-APTLR:1:1101:19252:1849/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATTCCCCGTGTGTGCTGCTTGCCTTCGGTTTGTATATCACTTTCTTTTTTGACGACTCTCTTTTTTTTATTACCTTTCTTTTTTTACTTTACCTACATTTTCTGCTCCGTCTTTCTTCTTTCCTTCTTCCTCTCTCATCCGTATGTTGCAACCTTTTTTCTTTTTTCCTTTTCTTTTATCTCTCTTTTTTGTTTCTTCACGTTTTCTTTTACCTCCCCTTTCTCTTCCTGTTAACTTCCTCCTAT
    -+
    -@CCCCGGGCGGGGGGGGGGGGGGGGGGF9FGGFGFEFG<F+6@+C6CC,;6C,,69,9,9C,:+8,C,C,,,,,,,,,:6C<,,,8=,:,,,,5,99CC,,,<5,+++,+++++,5,,9,,+8>,,:,,,55,88,558=+,3,8=,8,,,,,,,,8,,,3,73++,8+,8@,8,7,7,,,3,,,,,3,,7,,6,2**,,,,7,2,,,4,7<,,40,,,,63,23++,+35+,++1+4+++1+++/*+20++++*+*22****+03*+*228*/**+20+++305*++***1*.)0*,)**
    [email protected] M03099:23:000000000-APTLR:1:1101:15851:1971/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTTTGGTTAATAACCGCAGCAATTTACGTTACCCGCAGAAGATGCACCGGCTACCTCCGTGCCAGCAGCCGCGTTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGTGCGTAACGCGCTCGCAGTCGTTCTGTCAAGTCGGTTGTTAAATCCCCGGGCTCAACCTGGGAACTGCATTCTAA
    -+
    -6ABCCGGGFEGGGGGFGGGGGGFGFDGGGGFGGGGGGGGGGGDEGGGF8F9E@CC<8F,@F+@:F@@,CC,,,,,9CDCEDE7C+CFCFC,,,C,9CFFE,,,4++>++>+,,+:,CF,B8+BD<,@,,38+:++6,,::,,3+@B,3:,*3***,,,,7,,7<F**B7,3:><*@***,,*,4<<:8**4**4,7=8****;*;+++**;C**<<**/*;@+3<+++0*2*/**2*****)*.*02***2+<+*023***)1*9*:+700<C5***)/*++2;:5**))09*))2:6**/
    [email protected] M03099:23:000000000-APTLR:1:1101:23102:1978/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCCCCGGATAAGATAATGACGTTATCCGTAGAAGAAGCCCCTGCTAACTTCGTGCCAGCATCCGCGGTAATACGACTGGCGCTAGCGTTGTTCGGTATTACTGGTCGTAAAGCTCACGTAGGCTGATCGATCAGTCATGGGTGCAATCCCATGTCTCACCCCTGGCTCTGCCTTTCATACTTTCCCTCTGGATTATGTCAGAG
    -+
    -CCCCCGGGGDGGGGGFGGGGGGGGGFGGGGGGGGGGGGGGGGG>CFGG8FEFFFEF8E,CFBGEGG,,E,C<,9,,CEE=C8=@,CC@FF9,9CCFFFE,,54+7++4,C,E,,9,,9+++,:5<++,++,,,,,33A:+8=,,,,75C+B+:=<,+,,@@+@+@@**@,,*****,,*1>*5>:14*=B>6**26F9BF:,,5*1*+*2?+4<3*<*2*++**5;*110*<<+<+3+*3**+*3<:+++*+3377*/*11****37+9*3+:++3+2330+++-7A+)***/.)2*)**/
    [email protected] M03099:23:000000000-APTLR:1:1101:22637:2119/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCTGGGCTCAACCTGGGATGGTCATTTAGA
    -+
    -88BCCGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEFCFGGGGGGGGFFFGGGGGGGFFFFFGGGGGGGGGGGGGGFGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGG@FFFFGGGGGGGGFFGGGGGGGGFGGEGGFGGGGGGGGGGGGGGGGGGEGGGGGGGGFGCFGGGGGGGGGGGGGGGGGGGGGGGGGGGGDEGG>FGGGGGGGGC>CEEGEEGGGGGGGGF?ECGGGGCFDFGGFG>FCFGDFGGG(.::>4>F9:<7729F:
    [email protected] M03099:23:000000000-APTLR:1:1101:18265:2244/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA
    -+
    -68ACCGGGFGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGBFFFFFFFEFFGGFFEFGGEGFGGFFGGGGGGGGGGGGGGGGGEGGFGGGGFDFGGGGGFGDEGFGGGGGGGGGCGGGGGGGGGFFGGGGGGGGGGGGGGFFGGGGGGGGEGGDFGGGFGFE8EFGEEGGGGGGGGGGEEGGGGFEE8EGFGGGGGGF?@FGCG*:CGCFFFGGG5EGGBGGEGEEE@CEDGGFGGGGCG6CFGGGFFG=CEGGEEGGGG:>FGFFF?F?BC>AF@>
    [email protected] M03099:23:000000000-APTLR:1:1101:12491:2265/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCCGGCTAATACCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGAA
    ********
    *SNIP *
    ********
    -CCCCCGEGGGGGGGFGFFGGFGGEGFFFDA9CCFAD9CFGGGCFFFGGGGGGGGGGGGFGGGGGGGG@FEC,C<<FFF<FFFFGCGGGGFFFEEFG@FG9FFFG8=@,4DGDFFF<FEFGGDEGGGG,FFCFGGGGGGGFGGGGGGGGGGGFCFFGGGGGGGGGDGGFGGFFGFGGGGGGGFGGFGCFFGGGGGGGGDDGGCFFGGGFGGGGEGBECEGDC?9+CFFFCE/?*;:@*;CG5*5*8<CFEGE>;C7<FCCC7:CF6*<CCFC>CGGGGC*1<FEGCCF5FCGF**-+*28CD
    [email protected] M03099:22:000000000-APTMA:1:2119:14312:24605/1
    -CCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATACCTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGGAATACGTAGGGTGCAGGCGTTTACCGGATTTCTTGGGCGAAAGGCGTGCGCAGGCGGTTTGGCAGTCCGATGGTGAAGGCCCCGGCCCCAACCTGGGAACGGCATTGGAG
    -+
    -CCCCCGGG@GGEBCFGGFFGGGEFGGGGGGFGDFGGGGGGGGGGGGGGE<9EFFGGFFGGGGGGGGEFGGGCDFGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGCEFGGGGFGDGFEDEGGGGGGGGGGGGGGGGGCFCFGEFDFGGGFGCFC@DFGCGFCGGGGGGGDCGCFCFGGGCCFFFGFGEGC*:E6@@C:CFCC::8::*/*;**/++;*?*/+++2AF8;:*:C8*/://*2*/:**:CEGE*/6C5*+*1**/*2+<90+8EG5EG*)**;*;:6E=/>+*.*0(:*<:60
    [email protected] M03099:22:000000000-APTMA:1:2119:20365:24795/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT
    -+
    -CCCCCGGGGGGGGGGGGGGGGGGCEGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC<FFGGFGGGDGGGGGFGGDGGGDDGFGFFDAFGGGGGGGGGGGGGGGGGGFEFF7CFGGGGGGFGFCFFDGGGGGGGFGFGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGG?CFGGGGGGGGGGECEFFFGGG*:EEG@C?EGGGGGG>GGGGGG*8FGF99C7AC:FDFFD7CFGGGGCE5CEGGFGGGGFGGGFF4*)<>77DF
    [email protected] M03099:22:000000000-APTMA:1:2119:9975:24853/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA
    -+
    -CCCCCGG7C@CFGGGGGFGDGGCEFGGGG9FFGGGD9FFGGGGGGGGGCEFGGGGGDGGGGGGGGGGGGGGCFGFFGCEFFGGDGGFFEFFFAFGGEDGGC<BE@,>BF+?FFCFGFEF<@<EF9FGGGF,B,AAFGGGGGGGG3DF@FFFBF8DGFDFFFFFFCDGGGGFGGFFGGGCD7*@:@FC:><FC7FFF7CFGGGGECFG<F71=F>FFGBF<CFCEGFC@8BC>8C+CEEGGGGGGDGFFGGGGGFF*29:@FFF8CFG60<C:C7:?:5EG6CCCGG==FCCFG=:C6=>7*
    [email protected] M03099:22:000000000-APTMA:1:2119:11950:24861/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA
    -+
    -CCCCCDGGGGGGGGGGGFGGGGEGGGGGG<CFGGGGGGGGGGGGGGGGFGDFDGG,FG9FAFGGFGG,CFGFFGCFGFGFE9CGEGGGGFEFGFGGGFGGGF94C+C:FCGGF7+3BF7+BFGGGGGG<FF+++@+,<FFGGG>C*FGG8:::FGGGGGGG7EGGGEGGGGGGGGGGGGGFGGGGFEGGGGGGGGFGGGGGGEGGGGGGDEG?CGGGGGEGGGGGGGGGGGGGGGGGGCEGDGGGGGGG>EGF+7<AGGCGDGEGGGGGFCCFGGGGG*@CEGGGG=FFGFFFFFGG??FC
    [email protected] M03099:22:000000000-APTMA:1:2119:9959:24862/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA
    -+
    -ACCCCGCE;FEG,CFEFGCGGGFGGFAFGF9EF<FFCEFFECFCFFGGGCFGFF@CEDGF@C@ECFGGGGGFDEEFGG<CEGGFGGGFFFFGFECEDFGGGGFFFGG<FCCCFGGGGGGGGGCFFGFGFGCFFGGGGGGGGDFFFGGEFCGGCFDGGCFGGGG,FFGDGCGFFFEFGG>FFFGGFGGGGCFECCDFGGGGEGCFEFGGGGG:<CGDFGE<;FGC9A:<5CEGD>CF5CE5C*:8ECGCEF<CGGG;CC:98F6=EFGEG7@6@=GGG<EFFF8*9=D7<FGFFFB6F274:
    [email protected] M03099:22:000000000-APTMA:1:2119:17520:25205/1
    -CCTCCGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGGGCAACCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGCTGGGAAGATAATGACGGTACCAGCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTCGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACCGTAAAGTTGGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCTTCAAAACTATCGGTCTGGATTTCGAGAGAG
    -+
    -BCC-8@7:+6@CFDFGGDFGGG77EEFGGF<FFFFF-CFFECFCGGGD,@FFF9EEFFEC6CEGECE@GGGEE<CAFFE?FGGFCFFGGFEFGGG?BBFFFGGDGFD<FF8F?FFGAEGGGGGGFFC<A<EEE8EEFGGE7@G:=FGEFGGGGGDFGGGGFEGGDF*CF=CGG@:FGGGE7*=CGFDGGC9CC7*=:CFFC68CECECCCFGCEGGCFGGECGGGEG:*:/<F9+<5EGECC9<CC+AEEGDGC3:9EFC>95C=88<EEE7C6<++9<@CFCEGGGGG:+9CF?C*2>C<
    
    

  • Output aligned_reverse:  different than expected, difference (using diff):
    ( /tmp/tmp6a032gtwtest3_aligned_reverse.fastq v. /tmp/tmpwtm0jqdbtest3_aligned_reverse.fastq )
    --- local_file
    +++ history_data
    @@ -1,3812 +0,0 @@
    [email protected] M03099:23:000000000-APTLR:1:1101:19252:1849/2
    -CACTACCCGGTTTTCTTATCCTCTTTTCTCCCCCCCCTTTCCCCCCTCCTTCTCCGTTTTTTTCCCTTTCCTCCCCTTCCCCTCTTTTTTTCCTTCCTCTTTCTTCCCCTTTCCCCTCTTCCCCCCTTTTTCCCCCCTCCTCTTCCTTTCTCCTCCTCTCCCCTTTTCTTTTTCCTTTCCTTTTTTCTCCCCCTTCTTTCCCCTCCTCCTTTCTCTCCCCCCTTCCTTCCCTTTTCTCCCCGTTCTTCCCTTCCCCCCCTTCCCCCCTCTTTTTTCCCCCCCTTCTCTCCCCCTTTTTCC
    -+
    ---86,C,@+8+@,6,6,,;6C,,;C<-<;,;66+8+@+6<,,;,+8+,,,6,96,+9,66,+86:,,,,,,6,,,8,9,,:9,4,:,,::+,:,9949,,,,,,,5,,,,47,,84,4,,,,,,+++,,,6,7,33+++6,,2+,3,,,3++,,*,,,,*,,*43,/,3+,,,,*22+5,,,,22*,+13,*)*,2,2<+223),**(.*2.4+++*/*//4*(00)..).)0)).*))0*(0)((.)1())))(((((-,,0*2/),/,-)-0((.,((--((()).,.,****0+0()
    [email protected] M03099:23:000000000-APTLR:1:1101:15851:1971/2
    -CACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCTCCTGAGCGTCAGTCTTTGTCCAGTGGGCCGCCTTCGCCACCGGTTTTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGTATTCTCCCCCCCTCTACACTACTCAATCCTGCCAGTTTCGAATGCAGTTCCCAGGTTTAGCCCGTGGATTTCACATCCTACTTGCCATACCGCCTGCGTGCGCTTTACTCCCCGTAATTCCGATTTACGCTTGCCCCCTCCGTATTACCTCCGCTGCTGTCCCCTTCTTAGC
    -+
    --8AACFDEFGGF,CCE,CCCFC9CFC-EFEF66,@F@CCDE@C,C@E<,,,+8@66C,F<F<FAE<,,,,,,9++@=?=,BB,?,6+>+?C,5E@E8,,:499A,?<44@CFA,CB+6>@>,AEE8,,,9@=A,C?80=BEEG+=,,,,6==@,+6,7=8>,@D=D;+++859,+7;BC?,,4@:,,+8,:**4*66?F+5B,=>:**10=**9++*0,*7B*2A5/(680,88)>+)/2*-.)((6)92(-5)).(2(4(-00777<7(:08F)64).((46(34).4:2****30*).
    [email protected] M03099:23:000000000-APTLR:1:1101:23102:1978/2
    -CACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATTGGACCAGTTCGCCGCCTTCGCCACTGGTTTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGTTATTCCACTCACCTCTTCCATACTCCAGTTCGCCAGTTTCATTCGCAGTTCCACGGTTCATCCCTCGGCTTTCACTCCTTACTTATCGCTCCGCCTACCTTCGCTTTACGCCCAGTACTTCCTCTCACCGCTCTCCCCCCTCCTTTTTCGCCGCCTGCTTTCCCCTCTTTATC
    -+
    -9BCCCG<BEG>F7<CC,6ECED9CFC-CECEC@CCCFC:DE@FECFCAC,6+8@,:C,,9,,,:EC,C,9,+B+=:C@A<FE,8=,::54=9E=,4+++8+4A@,C+++8?AF,@<4>9,A,,,:+4++46,A,C,@+@DCDEFGA,6,@==,,*,333+>+3@,34,,+,,+++5;9;,,3*55*,+474,****1>F9+=,;>D+A9:4//B)))/1*9<*8F*79=.(,15)7)((**(2:7<?461))8*)((,(((.0:37)(1(.).7)2(((((,,((,))-).****20*-6
    [email protected] M03099:23:000000000-APTLR:1:1101:22637:2119/2
    -GACTACTAGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTACATGACCATCCCAGGTTGAGCCCAGGGCTTTCACACCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATCAACGATCGTCCCCTCCGTCTTACCGCGGCTGCTGGCACGGGGTTAGC
    -+
    -CCCCCEGGGGGGGGGGGGGGGDGFFGGGGGGGGGGGGGCFGGGGGDGFFFGGGGGGEFGGGGGGGGGGGFFFFGGGGGGGGGDGGGFGGGGGGGGGGGGGGGGGGFCEGDFGGFFGGDEGEEFGGF<EFFGGGGGGFGGE8EGFGGD8FGGG83BDADFGGGFFB;9E,?FFFFGGGFGD?EFD==EGFD7CFGG:@8FCCAC*:603ADEAABAF;CFGDGC7AD=(66>@DFEEFF@>*/86))9<6(6;)268((,/((/:97*(2-4(80)).46;6>7>0:??:025C*7?5*.6
    [email protected] M03099:23:000000000-APTLR:1:1101:18265:2244/2
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGATTGCACCCCCCGTATTACCGCGGCTGCTGGCACGGAGTTAGC
    -+
    -CCCCCDFGGGGGGGGGGGGGGGFFFGGGGGGGGGFEGGGGGEFGGGFGGGGGGGGECFGGGGGGGGGGGGGCGGFGFGGGGGGGGGGFDFGGGGGGGGGGGGGGFFFECEGFGGGGGGGEGGGGGGGGGGDFGGDCFG>EEGFFGGF?EGDCCGFGFGGGGGGFFGFGGGGFFFD<@FGGGGGFGGGGFEGGGGGDCC@FGFGF@GG7597@EAFFF@:78:56>C??BDB9D:AFB(7:/./8)).)64<:::2>62(332:9CD)4C>814FFFF6114029?4:?BFFGG59*2*.:
    [email protected] M03099:23:000000000-APTLR:1:1101:12491:2265/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCCACGCACGCCTTACGCCCAGTAAATCCGAGTACCGCTTGCACCCCTGCAACTTCCGCGGCCGCTGGCCCGAAGGAACC
    ********
    *SNIP *
    ********
    -CCCCCFEGGG:+@6ECC@E,@6EFFFGGC<@@C<6++8BCFFGDEDFFCEFE<CFGGFCG?<FCF<EFEFGG<@DFGD?DBFE,5:,:CFF@<FGFG:7FE<;FFFGE@8B,,AA@,CEFDFGGGD@7F,,@A:CGGG8E9?DDFEGG8EFGGFFGCGCEEC5@C=DDFGGFGGB=9DFF,69,4,@C?FCGG6EGFFFC@EFFFG5CB::/*:997<C4CFA(()55>?62(3))77)==@;47C3?<;6(//)97;1((,39)0(,C04(.(5<F0>9(3426:72137?07(106))
    [email protected] M03099:22:000000000-APTMA:1:2119:14312:24605/2
    -GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGACTTGCCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCACCGATTCCTCCGGCCTCCTGGCACGGCGTTTCC
    -+
    -C<BB8FG7FGGG7EEFCDGFFFFEEEFGGGGGGGEFGEFGGGGFGG9BFGACGCCCGGGGAGFGGEFFGGGGGGGCGGGECFGGGCEEAFFGGFGCGDEGECFGFGDGGGGAFGGDFEAEF9?:7CGGGDGEGGGFGGGECEGFCDED6>CF7>87;CFGFFAFFGE9D6;,,?4?D58E9B>C902*;?E*:EDD<>C:+7+6;A*7;;>/7(//61;/7C)(8)149D>4-4<A616CC6(*).5<28:3:14>(16:?FC05)(-*(((4)))0.(,((((4(.,((.,(((**())
    [email protected] M03099:22:000000000-APTMA:1:2119:20365:24795/2
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTCATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG
    -+
    -CCCCCGFDFGGGFGGGFGGCGGGGGGGGGGFEGFFGGGGGGEGGGGGGGDDFGCGGGGGGGGFGEGGG@7CGGGGGGGFGFFGGGGDGDGGGGDFGGGFGGGFG;F@FCEFDGGGGGGGGGFGFGGGGGGGFF=FAD=+>E6F5ED88CCFGGFAF6CFGGGFG,;A@@BFGGEFGGCGFCFGFF,8DFFEE<EG):8FGF?ACAGG3;EEEEEE618C85FD;?FB0<39>F06<:<9>C??*4:<<A0(341<B?F:(((+18)4:9(4(4.4:C,2,190(44?(3(5(((4=:)6
    [email protected] M03099:22:000000000-APTMA:1:2119:9975:24853/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGCGCCCGGGGATTTCTCCTCCAACTTCCTGACCCACCTACGCGCGCTTTACGCCCCGTAATTCCGATTACCGCTGTCACCCTTCGTATCACCGCGGCTGCTGCTACGACGTTAGC
    -+
    -CCCCCG8FFGGGDGGFGGGGFGAFGFGFFG@FGGGGGGDFFD;@FFFCFGGGFGC:FEEFDACF@FB@:87FF@FD9,CDFGEGGG8FFGG?9,CFFGDFGGEGFGD@F74?C<EFFGEEFDGF@ECEA<AEGGGGGF+@DDF5=AEGGF9DDDFGG8DFGG?F,@9>76,8>8:C+7D93,1,@,3@C7:**;C>D>BB+:,*A68235<*.4*+(02*:<8@E87(:.6,(349(4(:*(-),44<2((-34)-19>(-4097.,8F:<0(()-2-21(-,40::))-62:9(2/2(.
    [email protected] M03099:22:000000000-APTMA:1:2119:11950:24861/2
    -GGCTACTAGGGGTACTAATTCTCGTTTGTCCCCACGGTTTCGCACCTTCACGGTAGTCTTTATTCCGGCGACTCCCCTCGCCACCTGTAGTCCTCCAGGACTCTACGCAATTCACCGCCTCACCTGGAAATCTACCCCCCCCTTCCAGCATTCTACCTGCCCAGTTCCAATTCAGTTTCCCGGTTTAACCCCGGGGCTTCCACATCGACTTTACAGACCGCCCTCCTAGGCCTTACGCCCATTACATCCGATTAACGCCTTCACCCTCCGTATTCCCGCCTGCTCTGGCACCGTCTTAGG
    -+
    -B-<,66;,;CF7,,6C,C,,;C68FF,,;;FGGCC@+:CF@,,,8FD@,,;6B6,,66;@F,,,C,,@+8+6+,,B,A,47C,4A,CCC?F,E,,9,9,+4,,,,4++++8C,C9C++614?EF,4B,4,93,4,E1=+8++4*532,,,++,++,32,,@,*,6<;9,@,,,,+7+*>D,*:*4*,++?C*8EG)):F**)+()3*(,(;).7//;(=))2)(()()))(,.),4-(4C*,)0))641(((-().(,(4()+9=F((1(,,,4)40((((((())))).)(,,,*2)-)
    [email protected] M03099:22:000000000-APTMA:1:2119:9959:24862/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCACCTACGCGCGCCTTACGACCAGTAATTCCGATTAACGCTTGCACCCTTCGTATTACCGCGGCAGCTGCTACTCTGTTAGC
    -+
    -CCCCCFFGCFGGGFFE9<FFGGGEDEFFFGEFGCFGGG@FGGGGGFFFEECGEE:FFGGADFFF,CFGCF7FFG:AA?FG,BBFF?CF=EEG,F9F:CFECAACFGF@FGG9FAFF@EGCGFG@@C8E<FEGEFG8AFC=D?DFGGGGGGFFFFFFGC==F;D63E2@EDFD>C5F8EE>A64CFGFFGF@5*547CFE25:;=A;C@055*98>F3;F4C<6(5>69;:0(/()((,,2*.6:6)-)-5?13(6:03:02439772:C:?12.)6749909(-80(()--))).:<)-5
    [email protected] M03099:22:000000000-APTMA:1:2119:17520:25205/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATCTCACCTCTACACTCGGACTTCCACTCACCTCTCTCGAACTCCCGACCGATAGTTTTGACGGCAGTTCCGGGGTTGAGCCCCGGGATTTCACCCCCAACTTTACGGTCCGCCTACGTGCGCTTTACGCCCGGTCCTTCCGATCACCGCTATCCCCCTCCGTACTACCGTGTCTGCTGGCCCGTACGTCGC
    -+
    ---8ABFGE<@7<<FCFGGGF,CCCFA<FGG8DCECC+CCCEGGGDFF@FFFCFCC7EFGDC,,BFCF@D<,F8@4@FCGCEF7BEG,CEEGGGGEGF+,@@FGFGG?:,@+C;FFEC@DEGCG,B<:C6@C@FFFFFFC8FEDDGGG,@FGG,+:CGGGC7F*@=E*>B,+*@>5@;CGG>5C@CE74C<C*7=E3<5?FFC>8:731;8C3563)61:)7;7(.58:?342(:A<8?>G*-3)(6<4211(4-(419B0(.<?F7,39(38((.)2((((.)).60((((--((*0((4
    
    

  • Output unaligned_forward:  different than expected, difference (using diff):
    ( /tmp/tmpzgucbj4gtest3_unaligned_forward.fastq v. /tmp/tmp3tcrsl1_test3_unaligned_forward.fastq )
    --- local_file
    +++ history_data
    @@ -1,188 +0,0 @@
    [email protected] M03099:22:000000000-APTMA:1:2119:6395:7637/1
    -AGCCCACGAGACCGTGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCAATCCCACGCGACCAAGCCAACGAGAGCCTGCCAGCGACCCCCCACCGACTACTTCCTGACGACGGTTCCTTTCCCTCTACTAAATCTCATCCCCTGCTCACTGCGTCCAAGCGTCACCGGAAATACACATACCTACATCTCTAGTCGTCCTTACTTGTCTTTACTCGTGTCCATACTGTTCTTTTAGTCAACTGTAACATGCCATTTTTCTATGTTGTTCTATCCTTTGTT
    -+
    -ACCCCGGECG@@6@,;FEF<FE:FE7<@+@CFGGGG:@:+D:@FG:CEC++8@B7F7+@@7<BF+C=++,:,,B,B=++@++@+,,++,,33++++:,3,3,B,:83++8@@***8***5*,,,,,,8,8*::<*8**,<,,,,,,+,,,,22,,,,8?FC,*4+<@,,,777</;**2+0***2*20***/*0++3++2++02+0++030+++2</2C**+++++0+303<+++<C****2<<+*++03++2+*+0+*29>?+<++++++0++3++*++0++02+3**0+*0*(3*+/2*
    [email protected] M03099:22:000000000-APTMA:1:2119:14420:7911/1
    -ACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGCGACGAGCCCACGTGACGATCCCACGAGACAAGCCCCCCCGACGCGCCCACGAGACGAGCCCCCGCTACGAACCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACAAAACACGCCCTCAGCCCGTACTCCGTCGACTTGCTCAAACAAACAAACCAAACATCGCAATTCACTTGCTCAATGCCTCCACATAAAACTTACTCCGACACCACTGTCGAATCACTTCTAT
    -+
    -CC<@@:FFGEGGD+@FFC@6DEGFGC@@7+@FFFA@@@CF7,67@CFCF:+@+C>+4CFF,8=+9,A+B:EC?,<+4++@,,B,DD+@+6@+6@++5CC+3*5**5****1:+1****1**,4<FC71<*<*+**4CE5:8:2::/:*:CEE5**/*:**/**AC***2/:AE**:*;5***;****:8****++****/1*<8//*2**2*3+0++2AF885:**22*****2++*****0++3+++++++++*++0***0++3+03<+3+3++221**12**9+2+/1*)1*(+*+*20
    [email protected] M03099:22:000000000-APTMA:1:2119:16611:8029/1
    -AGCCCACGAGACCGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGAGCCCACGAGACGGACCCACGCCGCGAGTCCACTAGTCGACCTCACGTGCCGAGCCCCCCCCCGCGCCCCCCGACATACCCCCCCCTACCGACCCCACCCACCCCGTCTCACTACCTAGCCGCCGCCTCCCCCCGCCATCGTCACAACCCACCCAACAGAGAGCTCCAAGTCCACCCGCTCTCAGCATACACACTCCGTCCATCACCACATCCTCCCTCCCACCTCTTGCACTGCCCTTCACCCTCAC
    -+
    -CCCCCDFGGGGE@CCEGGFFGGEDCF;CE7@FFCG@+6CFG7FDFFGGC:+@,F@FFD8F=++@C::=7FE<+++++844>4:?<<,,,,<>3+++3,BB,,+:++8FF<+@********4<F:F1**4*0,002::E5*/*0**:**2****1**/:*1*;;+3+++03++2**/*/********2*/:**+222**+0*288**/******+**2<+3+++++33<*/***:13+0++39C03+*****/***+332*058++*+0*;*8*C**22*++0+323+0C*<)*1)+/1)66
    [email protected] M03099:22:000000000-APTMA:1:2119:19507:8186/1
    -AGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACTAGACCCAGCCCACGAGACCGCGCCCACGAGACCCAACCCACTAGACCGTTCCCACCATCCCGAGCCCACCATACCTAGCCCACTACACACCGCCCACGCCACCCCACCCACCACACCGCACCCCCATGATCTATCACACCTGAACCAGCACACGAGACCCACACCACGACTGACGGTCACACTCCACCGCATCCA
    -+
    -CCCCCGGGGGGGGGEGGGGGGEGE@FGGGGGGGGGGCFDGFEGGGGGGGEG+C@F:7FFGGGGF:>CGGE@EGGGGGD7+:FGB+@CFCDFGE:3CC+@FFECEF,@@DEC,8>CFEDC5**1*=*4=<4<CFC:*<CC*8*877<:,2,3A6*1*0,A+**/+01:**:*:F*;*;3+2;++6C*2***+3+;+***1:*8C5***/;8**/*1:******/*/*/*1****00++++3++30<**+*+3;A55******)*/**/;*/*2/**:*)+3***/*2?6***/*0(*)*008
    [email protected] M03099:22:000000000-APTMA:1:2119:13480:8544/1
    -AGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGTGCCCACCAGACCGAGCCCACGAAACCGAGCCCACCAGCCCGATCCCACGAGACCGCGACCACGAGACCGAGCCCAAGATACCGTGCCCACGAGCCCGACTCCCACGTCCCCAACCATCTTCACCTGATAAAACCACATTCGACTCAACGTGTCTACACCTCCACAGCTACCGAACCTATCCTCCCCCACGATCTACCTCCCG
    -+
    -CCCCCGGGGGGGGGGGGGGGGGGGGGGGGDEGGGDE>@:FGCC7CFGGGG@:CGFC+@FCF8FFCCCFF@C+@CFFG7>@FF7@>=FC=FGGCF+:+C+3C<FCC+,8,@DC7*:>8D7<7*=1F77*=*8C7*****=***1<87+*2*1*/****/**/*1*2:8*:*::****22<C?****2;+1***1*//2/*/2**0**/***2*1/*+++000+3++*++++++2***++0+2;*/+0*//*+2++*0:**2/7*+**32<*8*****+00+++*****2)*/)*/)+*+.*-
    [email protected] M03099:22:000000000-APTMA:1:2119:11271:8937/1
    -AGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGTGCCCACGAGACCGAGCCCACGAAACCGAGCCCACTAGACCGTGCCGACGAGATCGAGCCCACGTGAATGAGTCCAAGAGACCGAGCTCACAAGACAGATGCAACCGGGACCCGCCCACGATAGCTATCCCACGTGCGTCATCTCAATAATCCCTCGCAAGTGCACTCACCCCAATAACACGTGACACTACCATTGCGACAGT
    ********
    *SNIP *
    ********
    -CCCCCDFGGGCFFGGG+CF<FFGGGC@FFG7FDFE:CC+6,+@:FF@,C:+@FFCE+7=FDCF+@>FCC=++:C<F,+,,:D,,,:=,=,BCF:+3B+3,+@,3,3*3@EC**11>****3,8<8C:,**41+,8,<88,8,<2,,28,,<,?,8,*,5:*,?,4,,302++3++**188*2*2329+03+++03+*+++2<C8++++30**2**++30,3++++++22++2+2*;@8+2++<@9+00<+2+<+:+++220::+*****/*+0A++30+<C<<+29+0*22)*))3*0**-
    [email protected] M03099:22:000000000-APTMA:1:2119:19368:19712/1
    -AGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCTAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACTAGACCGAGCCCACGAGACAGAGCCCACGACAACGAGCCCACGAGACCGAGCCCACCAGACTCGTTGCAATAACGTGTGCCCACTTCCACTTCACAAAAAACCACGTCTATACTACTCTACTCTGACTTCATAGCTCACCTTACGGCTCACGACTACTGAAGCTTTCAGGCCTCAGCGATAA
    -+
    -CCCCCGGGGGGGGGGEGGDGGGGEEGGDCGFGFFGGFFGBFE7FCGGGGGGEGGDCCC:FFEE@:>CCFC8+@FGGGEEDF:F,=F8=DFGCFFGG3@::7FBFD+**@CEC7B@FGGG,,3?,8<7*<::FCFE@<*2,,,,8*4<F>***1*1**/2***/::*2**:*2/2;*2/;*+<*;***+33++3:**32+<;AE>C+++<++++++0/;*1**/***/2*+20++<++0+++2+++++++3<+++*+++*+3*0**:**2+2*2**<+*<++++02+00***)2/(3)*)--
    [email protected] M03099:22:000000000-APTMA:1:2119:18423:20592/1
    -ACGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGCCCCCACGACACCTATCCCCCGCGCCCAGCCCCCCGAACCCCAGCCCACCACCCCTACCCCCCTAGACCCACCCCACAAGACCCAGCCCACGCGACCAAACCAACCACCCCCCCCACACACACCCCACACCACCCAACCCAACCAACCGAACCCAACCCACACGACCCAAACCACGCCACCCAGACCCCACCACACACCCCCCACCCCCCCCAACACTCCCCCCCCACGACCAGCCCAACACCTCCACACCCGACC
    -+
    -CCCC@CGGGGFGECFCC@FGFG8C:6++@CCE+@6C-@+C+8CDF7+@:F++@B++@C,C,,C,++++++8@+,,BF+8+++3+@FE++D<F,3+3++@++:,@3D*5**,,88,,**8*8*1,,38,,8,,8********<****=88******1**1::C8C85:*2*2***/*;/**1*2*2**/***2;***2?C5**/*:8*****2/*/*8;*;***********2*****;;/**:******/****)2*****1+*2*2/****2***/9****1//*:****)2)(*)*)1-
    [email protected] M03099:22:000000000-APTMA:1:2119:24030:22105/1
    -ACGGGCGTCGGAAGCATCAGGGCCCGACAGTGCCAGTCCTGCCATGGGATGGGCGGCAACGAACCGCGCCCTGCCGGGATGGTTCTCAATGCTGCGGCAAACGGCGTCTTTTACCGAACCGGCATCTATCACCACGGTCTGATCTCCGGTGCGGTCAAGAATACCGGGAAGAATAGCGATGGTGGTATCGACCGGGACGGTGATCAGGACCAGCGAGGCATCACTGAGTGAGTTCTCCAGTGAGGTGCTCCTGTCAACCCGTCCCCTTGAAAGCGCCTGCTGCAAATGGCCGGCATTTGTT
    -+
    -CCCBCGGGGGGGGGGGGGFGGGGGGGGGFEGFGGGGGGGGGGG@FEGGFGGDFGDFGGGGGGGGG@FCEGGCEFGFEF>:FGFEFGGGFGGGFFGGGGGGGGCFGGGGGGGG<FEGCGGGG:FGGGDGFGFFGGG@CCFCF9,FFFG7FGCCFGGGFGGGGGC:FE:CEEEG8CDGGDGGGCFGGGGGGEGGEEGGEGGGC>EEFGGGGGGF/@CE8CEGFGC9<<FGFGGGGGGGGG?FGGCCDFCDCFGGGGG9C?F*:>GEGGG>*<8<EGEGEGFG?FCCF7C?=CC5DB>E*+/:*
    [email protected] M03099:22:000000000-APTMA:1:2119:7498:23338/1
    -ACGGGCGGTGGCGATCTCGTGGACGATGACGTTGATCCTCGTCTCCCCGGATACGGGGATGAAGCTGCAGCCGGTGCCGTCTCTGACCAGCTGGGCCTCCAGCTGCCTGCCCGCAAAGCCGGCGATGAAGCCGCGGGCCCGGTTCTCGGCGCCGAGGGCGGTCAGGACCTTCGATACGTCGATCCCCTTCCCTCCGGCGTAGCTCTCCTCCCGGATTATCCTGTTGGGGACGTCCTCCCTCATCACGTCGATGAGGAGGGTCCGATCGAGGGCTGGGTTGATGGTTATGGTGTAAATCATC
    -+
    -CCCCCFFGGGGGG+FFFFGGGGGGGGGGGGGGGGFFGGGFDEFEFGFGFFGGGGGGEGGGGGGGGEGGFGGGGGGGGGG?FGGGGGGGGGGE8FC=FGGG@CGGCCFAFGGGGGC7:FFFEEGGCFGAFFGGD*3:F:C<:7<FGGGCFGCGGD<?8>EGG>CGG8<CFFFGF8CFG5EF5CGGGGGGGGGGGGGGEGGGG*@?@?CCFFFGE>EG>CCCFFC?@+*:8:CEE:EEFGGFG=7@9920;E>89<DGG?D*ACFGEEECG;C*86:;ECEG++<CFC+<C+3/>74+*2*2A
    [email protected] M03099:22:000000000-APTMA:1:2119:22063:24539/1
    -ACGGGCGGTGTGTACACATCTCCGAGCCCACGAGACAGCCCACGAGACATCCTACGAGACCGCCCGCAAGAAAGCCCCCGAGACATCCCACCCTCCGGCCCTCCAAGAGAACGACCACGCGGCCCACGTGCCCCGACACCTAAGCGGGTCCTAGAAGGCGCAAGCACGACTCCCTCCGTGCTAGGGTCAGCCCTCATACGACGGAAACCCGCGATCTTCTTAATCAACGTTCGCTAGAACACCCTAGGCTGACTCCGACGAACAGACTGCAGGACCGACGCTCGACCCCGCAACCACCACG
    -+
    -CCCCCD@CFG@BE,CF<,CCFGGDE:@FCA@@@@:@<F,,@@6+++++C,,,,9:,6,7@6:CCC+4+@>F,,,:,+4@++4++4,:,B,A+8=+++3++@+=+:,,:<,,,63+++++++3*******,**3*4**4**,,,,,******8><,,8*<<5**2**0*****+/02**1;;*+0**22*;+*2***+2<0;**//**0*;*1**::*<+,+3333<+**1*;***2*++3**:*8?00*+**0+*+*/)**)2/0;*+3;++**//2)****/*)2**/22)1.,*9*)/-
    [email protected] M03099:22:000000000-APTMA:1:2119:14880:24914/1
    -ACGGGCGGTAAGTAGAGCCGATTCGTTGACAAGGTTGGCAAGGTCAGCACCGGTAAACCCGGGAGTACCCCTTGCTATCACTTTGAGATCTACCTCCCGGGATAGAGGTATCTTCCCCGAGTGAACAGCACGTATCTTCTCCCTTCCCTTAACATCAGGAACATCAGCAATGACCTGCCGGTCGAATCTACCAGGCCTTAAAAGAGCCGGATACAGAACATCAGGCCTGTTTGTGGCAGCTATGATTATCAAACCCTCAGTGGTTTCAAAACCGTCCATCTCAACAAGAAGCTTGTTGAGA
    -+
    -CC8B@:FEFGCFF<FGGFGEFFEGGFF@@FFCFDFFGGGGGC,66,CFCFCFGGGGG@@F:B@=>6C,,6DFF8<<CFCFGGCGCEFGFFDFG<F54+8CE:><=FGGGGGFCF,CF<FFGFCFCFCFF@,@>3?FCFF<D9BFG8D8FFGG9DGFGGGG7BDACF,,@<BGCFCGDFCFG@CFCFCGG,DCG,<FC:FCGGG91FFCEGG@*?915?B:@FGCE78<*5?B+2*88*:5CC9E:CD7+A7+3995>84+<*;F7*A?<EC@C*A;83?+2:9C<+:676+)0*.:>6?**
    
    

  • Output unaligned_reverse:  different than expected, difference (using diff):
    ( /tmp/tmpanf_89ratest3_unaligned_reverse.fastq v. /tmp/tmp0_b_ir7ktest3_unaligned_reverse.fastq )
    --- local_file
    +++ history_data
    @@ -1,188 +0,0 @@
    [email protected] M03099:22:000000000-APTMA:1:2119:6395:7637/2
    -CCCTCCTCTCATATTATTTGATCCCTGCTCTCTACTTGCTCGTTCATGCGCACCTCTTCAGTACAATTGTTTTGCCTCCGTAGTCTTTGGTCCTACGCATAACTACGCATTTCACTGTTCAATGCTAATTGCCATTCCTCTCTCTCTTAATCATTCGAGCGTTCCACCACTCCAAGTCCATCTCGTGTCCTGTGTCTTTCAACTCTTTCTTACCTCTGTGTCTGATCCTGTGTTCCGTCCGTTCATTCTCATTTATCATAGCTCCCTGTTATGTATCCATTCTTCGCGTTCTGTATGGG
    -+
    --6,,6@FE,,,,,<9,,,<,,=,6-C<E,;@,,,,,,,6C,,@,C6;E;+,++7;,,,;,,6,6,,,,,6,,;@<,,59:@,889,,,,,:?BF9=,@F7,99E,,,+4,,:,9E,9,4,,,,99A,,,,,9:9,,,+94;=,+99,,3,+?,3+,,,,+++31:,16@+,,@,*6+*,,,,,,,+,66,3,6,,+269++*,*+@+;3*,*;)*5*)52+,+**+0***0)*5**))0**0)3)**/2**2*/*/***1*7,+**))0*****/9+**11*0**-(,((/6..)4+((
    [email protected] M03099:22:000000000-APTMA:1:2119:14420:7911/2
    -CCGGTCTGTGTGTGCCCTATCGCCTCTATCGTCCCGCCATTTCCTTCCAGTCTTTGTCTTCTATACCCATCTTACGCTTCTGACGCTCCCCACTGTTGCCATGCTGTCTCTCGCTCTTCAATTCTTAGCATTCAACATGCCACGCTGCTCATGCCGCGCTTTCTTCCCTACTCCACTTGTTAGATTGATTATCTCTGTGTGTGCGCATGATTGCTATCGTCTTGTCATGTAGCTCTATGACTATCCACAATGTGGCACTCTCTTCTGCTGTGTGCAGTTCTCTCGAAACTGTTGACATATT
    -+
    -8A,6,@,;,<C,C,,,,;,BC,,,-;6<,,,,;8@:7F68;,C,<EE@CCE,,,<C<FF9,C,C,,<,,C,C@,E,=@,8E,5C,,8,8:,,+9,C,,,,,,,,,9:,,9C=@,,,9,,,,:,<,,,,9?A8A9,,,+,,,,23++++,4+3,+*+++6+36+,,3*,,,6,2,*,+3,7,,,,@8@++,,,2,7+++85+04****0)*,*313+*)*0/8*1/***/4***:**/**,,*11*(*((-.****(0*(./)231:.)1/)(/())+)))/1741)(((.))/).++))))
    [email protected] M03099:22:000000000-APTMA:1:2119:16611:8029/2
    -ACTACTCTATCCTCTCCCCCCCCCCTACATTCGCTGTTTCTTACCTCCTTCTTCCTTCTTAATTCCCTCCCCCCCATTTCTTTCTTCATCATTTATCGAATCTCATCTCTGCCCCGCTATTCCGTCTGCCCCCGCCTCACCCTGTCACCTCGTTTTGCTCCTCATCCTCTCCACTTCCTCTGTTCCATATCCTATTCTCTCCACCTACTCGAATGTCTCCCGTCGCATACTTTCCTCCTCATCCACTCCTATCGTCCCTTCCGCTTCCGTCTTGTCCCTTCTGACTCGACTATATCTTT
    -+
    -,,8;,,,,6,;C;CCC<,,776+8@+,,6,,CE,8,,6<,9C,,,,,9,6C<,C,6B,,,,,9,<6,,6,6,7+++95B,@55,,,,<C?5,95:,,++,>+@>,,9,559,,4++++++9,,,8,,+,66A++1+=+,,13+32,,,+5:+3++@,,,7*,,,0,,,,,1,B?81,,,,,,,5,++,,65@C1+47448,0+0*(05,6(((//)2:+8)(,2,,..676)))/9)83()0.9).5((.))5-,((())2)..((/)-.(((-*).))6(4).)).(.((()+0))).
    [email protected] M03099:22:000000000-APTMA:1:2119:19507:8186/2
    -CTGGCATTTCATCTCCTTCAGCTCCACTTGTTGTTTACCGGGTTTTCTTTGTACTTCTACTCACCACTCCTAGTTAGCTCTGTACTGTGGGCTACTCCGGGACCCGATGCAGCCTGCTCTGCGTCACTCGATTGCTGGTCAGCTCAGCCCATACTCTTGCTTTGACCTTGGATCGTGTTCGCCACACTGTCCTTTAGGTCCTGATCATGTGTATGATCTCGCCACCTTGCTCGACTTCGTCGCCACCATTCACCCTCGTGATTCTTACGACGCGTGAGTACGCATTATGTTATGGTAG
    -+
    -6,8,,6,,,,,,,,;,,,,,,,,;6,=<,;;66C,6,;C,++6,,:@E6,,;,,,,<C,6C,,,,6,,6;6,,,<,,,,,,::,,,,<,B,,:,,,,:,++++6,@@+,89,9,,,,,,9,,+8+++,9=@<9+,,+,,,9@538,,,4++,+366,,,6,+3,,0,6,7,6,*+6),,3+6+++,0=,,,+,,+2+,++*,*17+*3*7****+**,+2,30)*)-)+0/*/)/)(**0((/-((/-/)9)1)((/1(((*+3+))3(((((-()-()).((((().).))5)++))
    [email protected] M03099:22:000000000-APTMA:1:2119:13480:8544/2
    -ACTCACACCGTCTATAATTCTCTCCGCCCCCCCTGCCTTTGTCCCTCAGCTTCTGTCAGTTCTCTGCATCTGGCCTTATCTCCTGGCGTTATCCCCTAGACTTCTGGTGTTTACGCCTACCTCTGCAATTTCATCTTACCCATCACTCTGTCAGTTTCACTGTTTCCGTCACCTTTCCAATTTTGACTCCTGGGTTTTTCGCCGTTACTAATGTTCTCGCCATTCACGCTCTCCCGCCCACCTCATCAGACATCTGCTGTCTCCTTCACAGTTACAGTGTATGTCTGTAGTTACATCGTA
    -+
    --8,,66C,,7,,,,,,,,,<,,6-;CE,++8@++,6,,,,;,C,,@,6,,,CF,,,,6,9,,,,,,6,,,,6,A,5A,,,,,,,,,6+8+4B,,5,,,94,,94,,,,9,=,,5+6+,6,,,,,9,,,,93AE,4=+,,49,5,,67,7++4=;3,,,,C,+,:@*3+,6+1,+,+1,,63,,7@+2+3,,+6>7+33+01:0*4*))3,****+2*6*/5*)*+*1))-((*((-/(4*/(*((1).)))()/))).).)4+*;))*)))))))*))).).)--))))))..4+<)(-(
    [email protected] M03099:22:000000000-APTMA:1:2119:11271:8937/2
    -ACCTGCTGTTTCATCTATCCCTTCTTTTTAGTTTCCCGTCAGTTCCTTTGCTTTTCTTTCTCTTATCCACATCTGATTCTTCATCCTCTTACTGTATTATATCTCTCCGTGTCCTCGCTAGATTTCACCTACTACCGACTTAACTTGTGCTCACGACTGACAATATCTCGTACAATGACTGATTTCGTTGTGTGTCTCTCACTGCTGGCTAACTATATAGCTTACATGCTCTTACTACACGATGATCGCTCACTGCGTGAGTGCCATCGGTACAGCAGAATATGTGTCCTCGTCTTTAGTA
    ********
    *SNIP *
    ********
    -8A6,8@,C,C6EC,C,C,;,;C86-,;,;+,,@::+@+,C,,6,<,,<@6C6,6,;,<E,<;C@C66,:<,C,5<=BFBBCE,+=F,@E<,,:,5,CA?4,,,,,,,4,B,,,94,,4@F,4CF5,,,942A9,4,0,94,,4,9E,,,=+,+*,,939,C+,,,1@E,@,3@;,?9@,3,,6,6,++,,36++++2,++*,*3,+))0,)***1**,5+8*)1*)**4*3*).*2*/,,))*))))(-(**0((((0/3),/28))2((//(,)2)((((((((.)-((-(,)0+),(
    [email protected] M03099:22:000000000-APTMA:1:2119:19368:19712/2
    -TTAGCCACACGCTACAGAGCAGAGACAGAGTTCATTCACGTGACTGGAGTGCGCACAGGCGTAAGGACTCGTAGAAGAGCGATTATTGTGATCCTCTCTGCCTAGCCCGACGGGGGCCTCCACGCTTCACCGTGCCTTTATGCAAAGGACGTCGCTGACACCGTCAGCGCCGCGCGTGTGGGCACCCCAACCTCTACACGCCCGACTGCCGTGTTCTTGATGTAACATGTCTGTCGATTGCGCCTTATGACCTGTCACAACTGCACACACATACCTCAGCCTTCACGGGTTTGTACACG
    -+
    -,,,,,,6,=,++,,+,,,66,6-C,,,;,,,,6,,6,6,,,,,,,,,,,,,66@@+@;,6C6+,6,99CC<,,,8,,BB,+44,,,,,,5,5,5,6,,9,,,,,4,,,44@+C7:>+++,33,>++8+,,,8,@D6,,,,,5E,,3@87+53<+4:9*3,3*34/1*,4**4)=D1*3:1*//**5**43**+*2*3**-/()1)-((*((-()()+0*,0-)*)))*()6<>).((*33)*-((-)))))()()))-).1)/6)(*((,(.).*.)(()((-)).(-(((((*+)-)(
    [email protected] M03099:22:000000000-APTMA:1:2119:18423:20592/2
    -CGGGCGGTGTGTGCTGATACTATGCTTGGCCGCCAATTCCTTTAAGTTT
    -+
    -8,,,@F@+6,,;,CECEGCFGGCC-C,C@EFCF+++C<<EECC,6@,CC
    [email protected] M03099:22:000000000-APTMA:1:2119:24030:22105/2
    -ACGGCCGATTTGTGCATGGCACGGCAATATATTCCCCCCCTCATATATGGGCCGCGAGCACTACCCATTCCGTCTTCATCGGGTCGGGGGGCACATCCCACACTCAACGTCCCACACGCTTTTGCGCTGCCCACTCGATCACGTGATCGACTCGCTCCTTAGTGGGCATTTTAGCACTTGTCTCCCCATGGCGGCTAGGCTGTAGGTGAGCCGAGTGCGGACTCATCTTTCACCGACTTGCGCAGCGAGTACTCGTAGCAGACCCGGCGCTGACCACCAGCCACTGCAGTGTACGACCGT
    -+
    ---,,,6+686,66;<F,,,;,;8++66,,,;6B,,,,+6++8C9,,55,,,6,66@+++8:CE,6,,9,9C=,B,,<,,59?+A48+4++*1162,,,6,2*1,,,,5***1=,4=7*8**42,8******1+**0***;*2*0***+1*1*2/75**+2+0*+**-:2++2<C7+*)++09:++2*9***21**)1*2**(*)*+2.-(+(,(()()*)/*),)*)))*..).(((((,+(()(((((,()))-,4(()),*.).-(),((((()*((,((((5)))(.())--**((,
    [email protected] M03099:22:000000000-APTMA:1:2119:7498:23338/2
    -GCCCAGTCCCCCCCTACTGCCAGCTGCGCCGTTAAGTCAGGCGGGCCAGCTCCGAATCTAGAGGATAACGACTACAACAGAAATAAGCAGAATGATTAAAGCCCCACATCACGGCGGCTAACCTGCATGCACACTACTCTCGTCTAAACCCATGGCCGACACGTTCCAATGACCTCACCAGCTGCCCACCATTAATAACTGCCTCGATCTCATGTGCTAGCCTCGAGCTCCTCACACACTTCAGCGTAACGCCGCCTCACCCACCCACCACATACCTTCAACATCCTGTGCTTCTTCTA
    -+
    --A<@,,,,,,6++7+:,,;,66,--,6++,++68,,,,6,,C++++8,,,9,6,+,4,<,,,,4,,5:C=F4B+4,,4,44<<9,B,,,,9,A,5,,,,8,4A+++++,,,,3+3+++4+:,,:5@<B9:,3,,,4*3,@<*0*,1,,,*/***1D,*4:4)*60(*++++4+)+*(/*+=*3++*1;7**01+++1,**.+3*<<((.24)-)1.)020,7).),(())(((),,((**))2-)(((((,((((4(((((1)))(,1(.(..))2)).)))..)())..)).-++)))
    [email protected] M03099:22:000000000-APTMA:1:2119:22063:24539/2
    -CGCTACTGGCGTACCTAATCCCGTTCCCTACCCTCCCCTGCGTACCTACCCGCGATTAAGTGTGCTGCAGGCTTCATTCACCATAGGTCTTGCCCTCAATCCCAACGAATTTCACTGCTACAGCCATAGTTTAACCTGGCTCTCCATACCCCATGTCTACCATTCATTGCAGCCTTTGTCTATCTGCACTCTTGAATTGCAACATTAATTCACCTCATCCCCACCTTACTCTTTGTTCTCTACGTCAGTACCCACATCTGTCACCACTCGCTATGTACCACGCTCTCTCACCACTTCAGG
    -+
    -6,8,7+,,=,+87+,,<,,;C<,;-,,,6;,6C,,86B,,C+B6@,;,,;CF++@7CF,,6,<,,,,::,CFC,<,A4,<,,,9,6,<B,,,:,,4E,9,,,9,,B:,+,+4,,5CC,,,,,,,49E?<,,,4CEDD,9@,,3,,,,3,0+++*,@D,633*7,7*,,6,,63*,+*,7,,8,,,3++,8=+,7++2,+5*,)*,+*0*7*5:**1),<+<9)1<:56@?/*1**/01,5**2>5((/*0****((0.**/,+1*)(2,(.,((/3))//6(1((()/./)(.,<2))))
    [email protected] M03099:22:000000000-APTMA:1:2119:14880:24914/2
    -GCGACGGGTACGAGAGAGATCAGTGGGAATAGAAATGAAAGGAGGCGGAAGTAAGAACACAAACGAGTCGGTGTAATCTAAATGGAGAGGAGGACTAAGGTGCTGAATACGGCTGGAGCTAGGGGGGTGGCACATGGTCGATACTGACTGATCAACTGTGATGTCGCTCTTAGTAGTGGTGGAACAGGACTGGATATGGCTATTAGGACTGGGTATCATAAACATGCTACTATGGGTAACTTACTACGACAACACTTGGAGGCTAACATCACTATGTAACTATCGAAAGTGAGATTACGAT
    -+
    ---8,86+86+,8,68+:B8,;6CC--,,,,;6,,;,,,,,,,,,,8+8+6+,<<,,,,:,,9,:,6+8,68+86,,,,4,,,:,:,,,8,,+88+,9B<,9A,9@;A==9+++88+,,,,,,84++***4+*,++7*21****)++++++*331)*+++++39:+*(/**23+3*+*(2C***+0*2***+*1*+**039>)0)/0:248*(..)).)3*00*-.)).)*,).).(4)(,0--2)))(-(((((()-).).(*0)),4:7)).-))2))))--)-((-,))))))30),(-
    
    

  • Output output_bam:  different than expected, difference (using sim_size):
    ( /tmp/tmpyp8pv00dtest3_bam.bam v. /tmp/tmps_1ekcqutest3_bam.bam )
    Files /tmp/tmpyp8pv00dtest3_bam.bam=353441b but /tmp/tmps_1ekcqutest3_bam.bam=92b - compare by size (delta=200) failed
    

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/bin/merge-paired-reads.sh: line 54: perl: command not found
    /usr/local/bin/merge-paired-reads.sh: line 56: perl: command not found
    /usr/local/bin/merge-paired-reads.sh: line 58: paste: command not found
      The input reads file or reference file is empty, or the reads file is not in FASTA or FASTQ format, no analysis could be made.
    /usr/local/bin/unmerge-paired-reads.sh: line 49: perl: command not found
    /usr/local/bin/unmerge-paired-reads.sh: line 51: perl: command not found
    /usr/local/bin/unmerge-paired-reads.sh: line 49: perl: command not found
    /usr/local/bin/unmerge-paired-reads.sh: line 51: perl: command not found
    

  Standard Output:

  •    Processing /corral4/main/objects/f/7/0/dataset_f7067834-638c-4fee-b63d-3162833e7a7e.dat ..
       Processing /corral4/main/objects/d/8/c/dataset_d8c485de-6e89-4b47-ac7c-0733f1a94aa7.dat ..
       Interleaving /corral4/main/objects/f/7/0/dataset_f7067834-638c-4fee-b63d-3162833e7a7e.dat and /corral4/main/objects/d/8/c/dataset_d8c485de-6e89-4b47-ac7c-0733f1a94aa7.dat ..
       Done.
    
       Processing /corral4/main/jobs/048/221/48221881/outputs/galaxy_dataset_cd31b39f-fa99-42b5-8585-ca4584b8d5aa.dat ..
       Processing /corral4/main/jobs/048/221/48221881/outputs/galaxy_dataset_e5457e53-0484-4a1a-bc71-3deed540e0df.dat ..
       Done.
       Processing /corral4/main/jobs/048/221/48221881/outputs/galaxy_dataset_e8d13603-218c-42e3-9552-46c061729eea.dat ..
       Processing /corral4/main/jobs/048/221/48221881/outputs/galaxy_dataset_b424256b-a054-4d31-aa0a-c7d405a17df3.dat ..
       Done.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    sequencing_type	{"__current_case__": 1, "forward_reads": {"values": [{"id": 107953031, "src": "hda"}]}, "paired_type": "--paired_in", "reverse_reads": {"values": [{"id": 107953037, "src": "hda"}]}, "sequencing_type_selector": "paired"}
    strand_search	""
    databases_type	{"__current_case__": 2, "database_name": {"values": [{"id": 107953040, "src": "hda"}]}, "databases_selector": "history", "max_pos": "100000", "seed_length": "18"}
    aligned_fastx	{"__current_case__": 0, "aligned_fastx_selector": "--fastx", "other": true}
    log	false
    report	{"__current_case__": 1, "blast": {"__current_case__": 1, "blast_output": "False"}, "otu": {"__current_case__": 1, "otu_map": "False"}, "print_all_reads": false, "report_best": {"__current_case__": 0, "report_best_min_lis": "2", "report_best_type": "1"}, "report_type": "best"}
    e_value	"1.0"
    match	"2"
    mismatch	"-3"
    gap_open	"5"
    gap_ext	"2"
    ambiguous_letter	"-3"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fastqsanger"

• ❌ toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

  Problems:

  • Output aligned_paired:  different than expected, difference (using diff):
    ( /tmp/tmpqtj1k7cbtest5_aligned.fasta v. /tmp/tmpjohju3hstest5_aligned.fasta )
    --- local_file
    +++ history_data
    @@ -1,3732 +0,0 @@
    ->ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATTCCCCGTGTGTGCTGCTTGCCTTCGGTTTGTATATCACTTTCTTTTTTGACGACTCTCTTTTTTTTATTACCTTTCTTTTTTTACTTTACCTACATTTTCTGCTCCGTCTTTCTTCTTTCCTTCTTCCTCTCTCATCCGTATGTTGCAACCTTTTTTCTTTTTTCCTTTTCTTTTATCTCTCTTTTTTGTTTCTTCACGTTTTCTTTTACCTCCCCTTTCTCTTCCTGTTAACTTCCTCCTAT
    ->ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTTTGGTTAATAACCGCAGCAATTTACGTTACCCGCAGAAGATGCACCGGCTACCTCCGTGCCAGCAGCCGCGTTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGTGCGTAACGCGCTCGCAGTCGTTCTGTCAAGTCGGTTGTTAAATCCCCGGGCTCAACCTGGGAACTGCATTCTAA
    ->ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/2
    -CACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCTCCTGAGCGTCAGTCTTTGTCCAGTGGGCCGCCTTCGCCACCGGTTTTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGTATTCTCCCCCCCTCTACACTACTCAATCCTGCCAGTTTCGAATGCAGTTCCCAGGTTTAGCCCGTGGATTTCACATCCTACTTGCCATACCGCCTGCGTGCGCTTTACTCCCCGTAATTCCGATTTACGCTTGCCCCCTCCGTATTACCTCCGCTGCTGTCCCCTTCTTAGC
    ->ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCCCCGGATAAGATAATGACGTTATCCGTAGAAGAAGCCCCTGCTAACTTCGTGCCAGCATCCGCGGTAATACGACTGGCGCTAGCGTTGTTCGGTATTACTGGTCGTAAAGCTCACGTAGGCTGATCGATCAGTCATGGGTGCAATCCCATGTCTCACCCCTGGCTCTGCCTTTCATACTTTCCCTCTGGATTATGTCAGAG
    ->ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCTGGGCTCAACCTGGGATGGTCATTTAGA
    ->ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/2
    -CACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATTGGACCAGTTCGCCGCCTTCGCCACTGGTTTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGTTATTCCACTCACCTCTTCCATACTCCAGTTCGCCAGTTTCATTCGCAGTTCCACGGTTCATCCCTCGGCTTTCACTCCTTACTTATCGCTCCGCCTACCTTCGCTTTACGCCCAGTACTTCCTCTCACCGCTCTCCCCCCTCCTTTTTCGCCGCCTGCTTTCCCCTCTTTATC
    ->ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/2
    -GACTACTAGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTACATGACCATCCCAGGTTGAGCCCAGGGCTTTCACACCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATCAACGATCGTCCCCTCCGTCTTACCGCGGCTGCTGGCACGGGGTTAGC
    ->ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA
    ->ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCCGGCTAATACCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGAA
    ->ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/2
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGATTGCACCCCCCGTATTACCGCGGCTGCTGGCACGGAGTTAGC
    ->ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCCACGCACGCCTTACGCCCAGTAAATCCGAGTACCGCTTGCACCCCTGCAACTTCCGCGGCCGCTGGCCCGAAGGAACC
    ********
    *SNIP *
    ********
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGATGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGACAGAAATCCAGCCGGCTAATCCCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTTAAAGCCCTGGGCTCAACCTGGGAACTGCAGGGGAA
    ->ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/1
    -CCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATACCTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGGAATACGTAGGGTGCAGGCGTTTACCGGATTTCTTGGGCGAAAGGCGTGCGCAGGCGGTTTGGCAGTCCGATGGTGAAGGCCCCGGCCCCAACCTGGGAACGGCATTGGAG
    ->ERR1877483.32950 M03099:22:000000000-APTMA:1:2119:8336:24549/2
    -GACTACCGGGGTATCTAATGCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCTCCGCACGCTTTAAGCACAGTCATTCCGAGTAACGCTTGCACCCTTCGTATTACCGCGGCTGCTGGCACGAAGTTACC
    ->ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/2
    -GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGACTTGCCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCACCGATTCCTCCGGCCTCCTGGCACGGCGTTTCC
    ->ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT
    ->ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA
    ->ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/2
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTCATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG
    ->ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGCGCCCGGGGATTTCTCCTCCAACTTCCTGACCCACCTACGCGCGCTTTACGCCCCGTAATTCCGATTACCGCTGTCACCCTTCGTATCACCGCGGCTGCTGCTACGACGTTAGC
    ->ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA
    ->ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA
    ->ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCACCTACGCGCGCCTTACGACCAGTAATTCCGATTAACGCTTGCACCCTTCGTATTACCGCGGCAGCTGCTACTCTGTTAGC
    ->ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/1
    -CCTCCGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGGGCAACCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGCTGGGAAGATAATGACGGTACCAGCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTCGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACCGTAAAGTTGGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCTTCAAAACTATCGGTCTGGATTTCGAGAGAG
    ->ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATCTCACCTCTACACTCGGACTTCCACTCACCTCTCTCGAACTCCCGACCGATAGTTTTGACGGCAGTTCCGGGGTTGAGCCCCGGGATTTCACCCCCAACTTTACGGTCCGCCTACGTGCGCTTTACGCCCGGTCCTTCCGATCACCGCTATCCCCCTCCGTACTACCGTGTCTGCTGGCCCGTACGTCGC
    
    

  • Output unaligned_paired:  different than expected, difference (using diff):
    ( /tmp/tmpslfy4l9vtest5_unaligned.fasta v. /tmp/tmpv004wn8jtest5_unaligned.fasta )
    --- local_file
    +++ history_data
    @@ -1,268 +0,0 @@
    ->ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/2
    -CACTACCCGGTTTTCTTATCCTCTTTTCTCCCCCCCCTTTCCCCCCTCCTTCTCCGTTTTTTTCCCTTTCCTCCCCTTCCCCTCTTTTTTTCCTTCCTCTTTCTTCCCCTTTCCCCTCTTCCCCCCTTTTTCCCCCCTCCTCTTCCTTTCTCCTCCTCTCCCCTTTTCTTTTTCCTTTCCTTTTTTCTCCCCCTTCTTTCCCCTCCTCCTTTCTCTCCCCCCTTCCTTCCCTTTTCTCCCCGTTCTTCCCTTCCCCCCCTTCCCCCCTCTTTTTTCCCCCCCTTCTCTCCCCCTTTTTCC
    ->ERR1877483.46 M03099:23:000000000-APTLR:1:1101:21301:4734/2
    -GATACACGGGGATCTCTAACCGTTTGCGCCCCACGCGTTCGCTCCTCACCGCCAGATACAGGCCAGAGAAACGCCTTCGCCACAGGGGTTCCCCCACAGCTATACACATATCACCCCGACACGCCGGATTCCACACTCCACTCCTGCACTCACGATCCCCCGATTCCAATGAGCATTCCCGTGTGAGCCGGGAGCGTATACACAAACCATAGACACACCCCGCCACGCCCTCTGTGCCCCAAAGAACTGTAAAAGACGTTCCACCCCCGAGTAAACCCGCGTCTTCTAGCGCGGGGGTCGG
    ->ERR1877483.70 M03099:23:000000000-APTLR:1:1101:20716:6121/1
    -ACTACGGGAGGCAGCAGCGGGGAATCTTGGACAATGGGCGAAAGCCTGATCCAGCCAACCCGCGTGTGTGAAGAAGGCCTTCGGTTTGTAAACCACTTTAAGGTGGGAGGAAGGGCAGTAAGTTAATACCTTGATGGTTTGACGCTACCAACAGAATAAGCACCGGCGAACTTCGTGGCAGCAGCCGCGGGAAAACGGAGGGTGCCAGGGTTAATCGGAAGTAATGGGCGTAAAGCGCGAGTTGGGGGGTCAGCAAGTTGGAGGTGAAAGCCCCGGGCGCAGACGGGGAACAGCCGCCAAA
    ->ERR1877483.76 M03099:23:000000000-APTLR:1:1101:25401:6445/2
    -GCGCAGGGGGCTCACCGGGTTGCAGAAGAGAGACCGCACTACCAGGTAATATACTACTCGTTTGTCCCCCCGACTTTGTCACTCCACATCCACCCTACTCCCCCCCGCCCCCCTTGCCCCCCGCGCCCCCCCCCCCCCTTACGACTTGTCCCCCCCCAACCCGCCCTTTTCCTGCCCCTTCCCTCCCCCACCCTACCACACGCGCGCACACTGTCCTCCCCTGCCCTCCCCGCTTTCCGTACTACGTGTACTCCCACACCTCTCCCCTCTTCATCCCTCATTGACGCTATATTCCTCCCC
    ->ERR1877483.95 M03099:23:000000000-APTLR:1:1101:10309:7883/2
    -GACTACATGGGTTTTTAAATCCGGTTCCCTCCCCACGCTTTCCTCCTTAGCCGTCAGAATTAACCCATGAGCCTCCTTCCCCTTTTGTTGTTCCCCTACTTTCCAACAGTTTCTCCTCTTACATGCAAATTTCCGCCAACCCTTCCTTATCTCTAGTTTAACTGATCAAAGTACATTACTAGGGTTGCGCCGTAGCTTTCACCATTTGACTTTTTATCCACCCACCTGCCGCTTTACTCCCATATATCCCATCACCCTCTTCCCCCCTCCTCTTTCCACCGGCTGCGGCCACACACTTAT
    ->ERR1877483.107 M03099:23:000000000-APTLR:1:1101:20082:8248/2
    -GACTACTGGGGTATCTAATCCTGTTCGCTACCCAAACTTTCCCACATTATCGTCCGCTTATGGCCAGGGCGTCGCCTTCGCCACTGATTTTCCTCCACGTATCTACCCATTTCACCTCTCCCCCTGGCAATCCCCCCCCCTCTCCACGCCTCCAGTCTGCCTTTTCTAAATTACCATTCCCGGTTCCCCCCGGGGCCTTCACCTCTCGCTTAACCAACCTCCCCCACGTGCTTTTCCTCCCATACTTCCGCTTAACCCTCCTCCCCCCCGTCATACCCCGGCCTCGCGCCCCGCCTTGTC
    ->ERR1877483.116 M03099:23:000000000-APTLR:1:1101:28087:8411/2
    -GACCACAAGGGTATCCAAATCCTTTCGGCTCCCACCCCTTTGGCCCCCAACCTCAGTTACAGATCAGGCGGTCCGCCTCCCCACCTGTGTTCCCCCCCGACACTTCCCATTTCACCCCCACACCCGGGACTCCCCCCTCCTCCTCCGCACCTCACGCCCCCAGTTTTCAATTACACTCCCCGGTTTGCCCCCGGGCCTTTCCCTCCCACTTTACAACACGCCCTCCAGCCCCTTTACCCCAACTATTCCCGCCACCCGTTCGCACCCACCGTGTTCCTCGTACTCTGCGCCGTAGTTAGC
    ->ERR1877483.127 M03099:23:000000000-APTLR:1:1101:12005:9181/2
    -GCCTACTGGGGTATCTTATACACATCTGACGTTGCCGACGACTTAATAGGTGTAGGATTCCGAGGGAGCCGAACTACTAAAATTAGGATTGAAGACTCAGATCCGAACTGAGACCTACTTTGTAGATTTGCATCCTGTCACCAGGTAGCTGCCCTCTGTATCGGCCCTTGTAGCACGTTTGTAGCCCTTGACGTACGGGCCCTTCTGAGTTTACGTCCTCCCTGCCTTCCTCACTTCTTTCGTCGGCAGTCCCTTTAGAGTCCCCAGCTTAACCTGCTGTCAACTACAGGCAAGCGTTTC
    ->ERR1877483.149 M03099:23:000000000-APTLR:1:1101:6596:10202/1
    -ACTACGGGAGGCAGCAGCTAGGAATCTTCCGCAATGGGCGCAAGCCTGACGGAGCGACGCCGACTGGAGGAAGAAGACCTTCGGGGTGTAAACTCCTGAACCCGGGACGAAACCACCGAGGCGGGGACGGACGGTACCGGGGCAATCGCGCCGGCCAACGCCGAGCCAGCAGGCGCGGTTATACGGAGGGCGCGAGCGTCACCCGGATTAACTGGGTGTAAAGGGCGCGAAGGCGTCCTGGGCCGTACCACGTGGAAGACCACGGGTCAACCGTGGAGGAGCGGGGGATAAGCTCAGGCAA
    ->ERR1877483.167 M03099:23:000000000-APTLR:1:1101:22979:11600/2
    -GACCACTAGGGTTTCTAATCCCGTTTGCTCCCCACCCTTTCCCGTCTTAGTCTCAATTCCGTCCCCGCGAGCCGCCCTCGCCATCGGTTGTCCCCCTCGTTTCTGCGCATTTCCCCCCTTCACCCGGAATTCCCCCCTCCCCTTCCGGCCTCCAGCCAGACCGTTTCCACCGGCATTTCATGGTTGGGGCCCGGGCTTTCCACACGGACCTAGCGAGCCCCCCCAACGCCGCTTAACCCCCATTCATCCCGACCAACGCTTCCCCCCACCTATGTCCCCCGCCTCCTGCCCGCACTTTAC
    ->ERR1877483.183 M03099:23:000000000-APTLR:1:1101:27013:12199/2
    -GACTACAGGGTATCTATTACTGTTTGCGCCCCACACGTTCGCAACTGAGCGTCAGTCTTTGTGCAGGGGGCCGCCCTCTCCACCGGTATGCCCCCCGCTCTCTACGCATTTCACCCCTACACCCGGAATTCTACCCCCCTCTACCAGACTCAATCCTGCCCGTTTCGCAGGCAGTTCCCAGGTTTTGGCCGCTGACTTTTCATCCCCGTTTACCTACCCCCCCCGCGCGCGCTACGCCCCGCAATTCCCATCACCGCTTGTGCCCCCCGCCTTTCCCCCGCTGCGCGCCCCGGGTTTACG
    ********
    *SNIP *
    ********
    -ACGAGCCCACGAGACCGAGCCCACGAGACCGAGCCCACGAGACCGCCCCCACGACACCTATCCCCCGCGCCCAGCCCCCCGAACCCCAGCCCACCACCCCTACCCCCCTAGACCCACCCCACAAGACCCAGCCCACGCGACCAAACCAACCACCCCCCCCACACACACCCCACACCACCCAACCCAACCAACCGAACCCAACCCACACGACCCAAACCACGCCACCCAGACCCCACCACACACCCCCCACCCCCCCCAACACTCCCCCCCCACGACCAGCCCAACACCTCCACACCCGACC
    ->ERR1877483.32864 M03099:22:000000000-APTMA:1:2119:18423:20592/2
    -CGGGCGGTGTGTGCTGATACTATGCTTGGCCGCCAATTCCTTTAAGTTT
    ->ERR1877483.32872 M03099:22:000000000-APTMA:1:2119:13774:21033/2
    -GACCCTCTGAGTAACCAGTCCCGGTTGCTTACCACACGTGCCAACCCGAGCGGATCAACCAAGCCAGTGCGCCCACTCCCACACCGCATCCCCTCCGAAATTCCAACACTCACACCTCCACTCTCATGATTCCCGCCTCCTACCTCTGTCTCCACTCGACCCGCACACACGGAACCGAGTCGATCCATCCCCGTCATACCACTTATACCTCAATGATCCACCTAAGTTCCCCTGATTCCCCGTCCTAGCGATCATCTCACTGCCCCTCCCGTACCTCATGTCTCCACTTCCCAGCATAGA
    ->ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/1
    -ACGGGCGTCGGAAGCATCAGGGCCCGACAGTGCCAGTCCTGCCATGGGATGGGCGGCAACGAACCGCGCCCTGCCGGGATGGTTCTCAATGCTGCGGCAAACGGCGTCTTTTACCGAACCGGCATCTATCACCACGGTCTGATCTCCGGTGCGGTCAAGAATACCGGGAAGAATAGCGATGGTGGTATCGACCGGGACGGTGATCAGGACCAGCGAGGCATCACTGAGTGAGTTCTCCAGTGAGGTGCTCCTGTCAACCCGTCCCCTTGAAAGCGCCTGCTGCAAATGGCCGGCATTTGTT
    ->ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/2
    -ACGGCCGATTTGTGCATGGCACGGCAATATATTCCCCCCCTCATATATGGGCCGCGAGCACTACCCATTCCGTCTTCATCGGGTCGGGGGGCACATCCCACACTCAACGTCCCACACGCTTTTGCGCTGCCCACTCGATCACGTGATCGACTCGCTCCTTAGTGGGCATTTTAGCACTTGTCTCCCCATGGCGGCTAGGCTGTAGGTGAGCCGAGTGCGGACTCATCTTTCACCGACTTGCGCAGCGAGTACTCGTAGCAGACCCGGCGCTGACCACCAGCCACTGCAGTGTACGACCGT
    ->ERR1877483.32900 M03099:22:000000000-APTMA:1:2119:9095:22203/2
    -GACTACTGGGGTATCTAATACTGTTTTCTCCCCCCGGTTTCGCACCTTAGTGGTAGTTTAAGTCCCGGAGGTCGGCCTCGCCACCTGTTTTTCTTCCTATTTTCTCGCATTTTACCGCCTAACAAGACATTCCACCACTCTCTACCGTACCTTAATCAGGCAGGTATGGGTGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCTTCCTACCATACCACCTTCGCGAGCGTTACGACCAGCAACTGCCTATAACACTTGCACCCTTTGTAATACCGCTGACGTTGGCACGTAGTTAGT
    ->ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/1
    -ACGGGCGGTGGCGATCTCGTGGACGATGACGTTGATCCTCGTCTCCCCGGATACGGGGATGAAGCTGCAGCCGGTGCCGTCTCTGACCAGCTGGGCCTCCAGCTGCCTGCCCGCAAAGCCGGCGATGAAGCCGCGGGCCCGGTTCTCGGCGCCGAGGGCGGTCAGGACCTTCGATACGTCGATCCCCTTCCCTCCGGCGTAGCTCTCCTCCCGGATTATCCTGTTGGGGACGTCCTCCCTCATCACGTCGATGAGGAGGGTCCGATCGAGGGCTGGGTTGATGGTTATGGTGTAAATCATC
    ->ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/2
    -GCCCAGTCCCCCCCTACTGCCAGCTGCGCCGTTAAGTCAGGCGGGCCAGCTCCGAATCTAGAGGATAACGACTACAACAGAAATAAGCAGAATGATTAAAGCCCCACATCACGGCGGCTAACCTGCATGCACACTACTCTCGTCTAAACCCATGGCCGACACGTTCCAATGACCTCACCAGCTGCCCACCATTAATAACTGCCTCGATCTCATGTGCTAGCCTCGAGCTCCTCACACACTTCAGCGTAACGCCGCCTCACCCACCCACCACATACCTTCAACATCCTGTGCTTCTTCTA
    ->ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/1
    -ACGGGCGGTGTGTACACATCTCCGAGCCCACGAGACAGCCCACGAGACATCCTACGAGACCGCCCGCAAGAAAGCCCCCGAGACATCCCACCCTCCGGCCCTCCAAGAGAACGACCACGCGGCCCACGTGCCCCGACACCTAAGCGGGTCCTAGAAGGCGCAAGCACGACTCCCTCCGTGCTAGGGTCAGCCCTCATACGACGGAAACCCGCGATCTTCTTAATCAACGTTCGCTAGAACACCCTAGGCTGACTCCGACGAACAGACTGCAGGACCGACGCTCGACCCCGCAACCACCACG
    ->ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/2
    -CGCTACTGGCGTACCTAATCCCGTTCCCTACCCTCCCCTGCGTACCTACCCGCGATTAAGTGTGCTGCAGGCTTCATTCACCATAGGTCTTGCCCTCAATCCCAACGAATTTCACTGCTACAGCCATAGTTTAACCTGGCTCTCCATACCCCATGTCTACCATTCATTGCAGCCTTTGTCTATCTGCACTCTTGAATTGCAACATTAATTCACCTCATCCCCACCTTACTCTTTGTTCTCTACGTCAGTACCCACATCTGTCACCACTCGCTATGTACCACGCTCTCTCACCACTTCAGG
    ->ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/2
    -GGCTACTAGGGGTACTAATTCTCGTTTGTCCCCACGGTTTCGCACCTTCACGGTAGTCTTTATTCCGGCGACTCCCCTCGCCACCTGTAGTCCTCCAGGACTCTACGCAATTCACCGCCTCACCTGGAAATCTACCCCCCCCTTCCAGCATTCTACCTGCCCAGTTCCAATTCAGTTTCCCGGTTTAACCCCGGGGCTTCCACATCGACTTTACAGACCGCCCTCCTAGGCCTTACGCCCATTACATCCGATTAACGCCTTCACCCTCCGTATTCCCGCCTGCTCTGGCACCGTCTTAGG
    ->ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/1
    -ACGGGCGGTAAGTAGAGCCGATTCGTTGACAAGGTTGGCAAGGTCAGCACCGGTAAACCCGGGAGTACCCCTTGCTATCACTTTGAGATCTACCTCCCGGGATAGAGGTATCTTCCCCGAGTGAACAGCACGTATCTTCTCCCTTCCCTTAACATCAGGAACATCAGCAATGACCTGCCGGTCGAATCTACCAGGCCTTAAAAGAGCCGGATACAGAACATCAGGCCTGTTTGTGGCAGCTATGATTATCAAACCCTCAGTGGTTTCAAAACCGTCCATCTCAACAAGAAGCTTGTTGAGA
    ->ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/2
    -GCGACGGGTACGAGAGAGATCAGTGGGAATAGAAATGAAAGGAGGCGGAAGTAAGAACACAAACGAGTCGGTGTAATCTAAATGGAGAGGAGGACTAAGGTGCTGAATACGGCTGGAGCTAGGGGGGTGGCACATGGTCGATACTGACTGATCAACTGTGATGTCGCTCTTAGTAGTGGTGGAACAGGACTGGATATGGCTATTAGGACTGGGTATCATAAACATGCTACTATGGGTAACTTACTACGACAACACTTGGAGGCTAACATCACTATGTAACTATCGAAAGTGAGATTACGAT
    
    

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/bin/merge-paired-reads.sh: line 54: perl: command not found
    /usr/local/bin/merge-paired-reads.sh: line 56: perl: command not found
    /usr/local/bin/merge-paired-reads.sh: line 58: paste: command not found
      The input reads file or reference file is empty, or the reads file is not in FASTA or FASTQ format, no analysis could be made.
    

  Standard Output:

  •    Warning: /corral4/main/objects/7/0/c/dataset_70c25aa4-5d74-45ed-854c-7741cd2a2422.dat seems to be in fasta format (this script is for fastq reads only)
       Warning: /corral4/main/objects/0/8/a/dataset_08af56ba-c35b-4c54-8992-15794abc8084.dat seems to be in fasta format (this script is for fastq reads only)
       Processing /corral4/main/objects/7/0/c/dataset_70c25aa4-5d74-45ed-854c-7741cd2a2422.dat ..
       Processing /corral4/main/objects/0/8/a/dataset_08af56ba-c35b-4c54-8992-15794abc8084.dat ..
       Interleaving /corral4/main/objects/7/0/c/dataset_70c25aa4-5d74-45ed-854c-7741cd2a2422.dat and /corral4/main/objects/0/8/a/dataset_08af56ba-c35b-4c54-8992-15794abc8084.dat ..
       Done.
    
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    sequencing_type	{"__current_case__": 1, "forward_reads": {"values": [{"id": 107953030, "src": "hda"}]}, "paired_type": "", "reverse_reads": {"values": [{"id": 107953036, "src": "hda"}]}, "sequencing_type_selector": "paired"}
    strand_search	""
    databases_type	{"__current_case__": 2, "database_name": {"values": [{"id": 107953040, "src": "hda"}]}, "databases_selector": "history", "max_pos": "100000", "seed_length": "18"}
    aligned_fastx	{"__current_case__": 0, "aligned_fastx_selector": "--fastx", "other": true}
    log	false
    report	{"__current_case__": 1, "blast": {"__current_case__": 1, "blast_output": "False"}, "otu": {"__current_case__": 1, "otu_map": "False"}, "print_all_reads": false, "report_best": {"__current_case__": 0, "report_best_min_lis": "2", "report_best_type": "1"}, "report_type": "best"}
    e_value	"1.0"
    match	"2"
    mismatch	"-3"
    gap_open	"5"
    gap_ext	"2"
    ambiguous_letter	"-3"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fasta"

• ❌ toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna (Test Test trinotate 3.2.2+galaxy0 #6)

  Problems:

  • Output aligned_forward:  different than expected, difference (using diff):
    ( /tmp/tmpo9b6duyotest6_aligned_forward.fasta v. /tmp/tmpim34sv54test6_aligned_forward.fasta )
    --- local_file
    +++ history_data
    @@ -1,1740 +0,0 @@
    ->ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATTCCCCGTGTGTGCTGCTTGCCTTCGGTTTGTATATCACTTTCTTTTTTGACGACTCTCTTTTTTTTATTACCTTTCTTTTTTTACTTTACCTACATTTTCTGCTCCGTCTTTCTTCTTTCCTTCTTCCTCTCTCATCCGTATGTTGCAACCTTTTTTCTTTTTTCCTTTTCTTTTATCTCTCTTTTTTGTTTCTTCACGTTTTCTTTTACCTCCCCTTTCTCTTCCTGTTAACTTCCTCCTAT
    ->ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTTTGGTTAATAACCGCAGCAATTTACGTTACCCGCAGAAGATGCACCGGCTACCTCCGTGCCAGCAGCCGCGTTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGTGCGTAACGCGCTCGCAGTCGTTCTGTCAAGTCGGTTGTTAAATCCCCGGGCTCAACCTGGGAACTGCATTCTAA
    ->ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/2
    -CACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATTGGACCAGTTCGCCGCCTTCGCCACTGGTTTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGTTATTCCACTCACCTCTTCCATACTCCAGTTCGCCAGTTTCATTCGCAGTTCCACGGTTCATCCCTCGGCTTTCACTCCTTACTTATCGCTCCGCCTACCTTCGCTTTACGCCCAGTACTTCCTCTCACCGCTCTCCCCCCTCCTTTTTCGCCGCCTGCTTTCCCCTCTTTATC
    ->ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/2
    -GACTACTAGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTACATGACCATCCCAGGTTGAGCCCAGGGCTTTCACACCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATCAACGATCGTCCCCTCCGTCTTACCGCGGCTGCTGGCACGGGGTTAGC
    ->ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/2
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGATTGCACCCCCCGTATTACCGCGGCTGCTGGCACGGAGTTAGC
    ->ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCCACGCACGCCTTACGCCCAGTAAATCCGAGTACCGCTTGCACCCCTGCAACTTCCGCGGCCGCTGGCCCGAAGGAACC
    ->ERR1877483.7 M03099:23:000000000-APTLR:1:1101:8123:2395/2
    -GACTACACGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCACTCTGACGCACTCTAGTCTTGCCGTCTCCACTGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGCCTTGCACACACGCCTGCGCAAGCATCACGCCCAGTAATTCCGACTAACGCTTGCACCCTACGTATTTCATCCGCTGCTGGCCCGGCTTTAGCA
    ->ERR1877483.8 M03099:23:000000000-APTLR:1:1101:19895:2425/2
    -GACTACTCGGGTATCTAATCCTGTTCGCTACCCACACTTTCGCACATGAGCGTCAGTCTTTGGCCAGGGAGTCGCCTTCGCCACTGATGTTCCTCCAGATATCTACGCATTTCACCGCTACACCTGGAATTCCACTCCCCTCTCCAAGACTCTAGTCTGCCAGTTCTAAATGACCATCCCAGGTTGAGCCCGGGGCTTTCACATCTAGCTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTCGCACCCTCCGTGTTACCGCGGCTGCGGGCCCGGAGAGAGC
    ->ERR1877483.9 M03099:23:000000000-APTLR:1:1101:24195:2452/2
    -GACTACTGGGGTATCCAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACTATCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGAAGTTACCAGGTTGAGCCCGGGAATTTCACATCTAACTTAACAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGAATAACGCTTGCCCTCTACGTATTACCGCGGCTGCTGGCACAGAGTTAGC
    ->ERR1877483.10 M03099:23:000000000-APTLR:1:1101:8960:2646/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCAAGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCACTACGCAATTCACTGCTACAACGGGAATTCCGCTACCCTCTACCACCCTCTAGTTGTCCAGTTTTCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCAAAACAGACTTAAACAACCACCTACGCACGCATTACGCTCAGCACATCCGAGTAACGCTTGCACACCTCGTCTTACACGCGCTGCTGCCCCGGAGGTACC
    ->ERR1877483.11 M03099:23:000000000-APTLR:1:1101:17700:2703/2
    -GACTACAAGGGTATCTAATCCTGTTCGCTCCCCATGCTTTCGCTCCTCAGCGTCAGGTAATTCCCAGAGAACCGCCTTCGCCACCAGTGTTCCTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCGTTCTCCCCTGAATACCTCTAGTCTGCCCGTATCGGAAGCACGCTCAGGGTTGAGCCCTGAGTTTTCACTCCCGACGCGACAAACCGCCTACGAGCCCTTTACGTCCAATAATTCGGGACAACGCTCGGACCCTACGTATTACAGCGGCGCCTAGCACGGAGGTGGC
    ********
    *SNIP *
    ********
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCAACTTAACAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCTGTATCACCGCGACTGCTGGCACAGAGTTCGCG
    ->ERR1877483.32940 M03099:22:000000000-APTMA:1:2119:22034:23939/2
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTAATGGACCAGTAAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGCATTTCACCTCTACACTCGGAATTCCACTTACCTCTTCCATACTCCTGATTCCCAGTATCAAATGCAGTCTCGCAGTTGAGCTGCGGGATTTCACCCTTGACTTAAATATCCGCCTACGTGCGCTTTACGCCCAGTAATTCCGAACAACGCTAGACCCCTTCGTATTACCGCTGCTGCTGGCACGACGTTAGC
    ->ERR1877483.32941 M03099:22:000000000-APTMA:1:2119:21316:24023/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTAATGGACCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATTTCACCTCTACACTCGGAATTCCACTCACCTCTTCCATACTCCAGATCGACAGTATCAAAGGCAGTTCCAGGGTTGAGCCCTGGGATTTCACCCCTGACTGATCGATCCGCCTACGTGCGCTTTACGCCCAGTAATTCCGTACAACGCTCGCCCCCTTCGTATTACCGCGTCTGCTGGCACGTATTTAGC
    ->ERR1877483.32942 M03099:22:000000000-APTMA:1:2119:22743:24096/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACATCAGTGTCAGTATTAGTCCAGTAGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCCCCGCTCCACAGGAAATTCCACCCCCCTCTACCATACTCTCGCCCAGTAGTTTTGGAGGAAGTCTCCAGGTTTAGCCCCGTGATTTCCCCTCCCACTTGCTGAACCACCTACGCCCCCTTTACGCCCAGTCATTCCGCTTAACGCTTGCACCCTTCGTATTACCGCGGCGTGTGCCACGACGTTACC
    ->ERR1877483.32943 M03099:22:000000000-APTMA:1:2119:20410:24202/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTCTATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCGTACTCTAGTCAGGCAGTTATGGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCATCTTACCAAACCACCTACGCGCGCTTTACGCCCATTACTTCCGCTTAACGCTTGCACCCTTCGTATTACCACGGCTGCTTGCACGAACTTAGCG
    ->ERR1877483.32944 M03099:22:000000000-APTMA:1:2119:18061:24218/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCTATTAACGCTTGCACCCTCCGTATTACCGCTGCTACTGGCACGGATTTAGC
    ->ERR1877483.32945 M03099:22:000000000-APTMA:1:2119:18837:24311/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCAACTTAACAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCTGTATTACCGCGGCTGCTGGCACAGAGTTAGC
    ->ERR1877483.32946 M03099:22:000000000-APTMA:1:2119:18816:24311/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCATCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGCATTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTAACAAACCACCTACGCCCCCTTTACCCCCAGTAATTCCGATTCACGCTTTCACCCTCTGTATTACCTCGGCTGCTAGCACAGCCATAGC
    ->ERR1877483.32947 M03099:22:000000000-APTMA:1:2119:7531:24361/2
    -GACTACTAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCGTACTCTAGTCAGGCAGTTATGGATGCAATTCCCCGGTTTAGCCCGGGGATTTCACTCCCCTCTTACCCAACCACCTACGCGCCCTTTACGCCCAGTACTTCCGATTACCGCTTGCCCCCTTCGTATTACCGCGACTGCTGGCACGAAGTTAGC
    ->ERR1877483.32950 M03099:22:000000000-APTMA:1:2119:8336:24549/2
    -GACTACCGGGGTATCTAATGCTGTTTGCTCCCCACGCTTTCGTGCCTCAGTGTCAGTGTTGGTCCAGGTAGCTGCCTTCGCCATGGATGTTCCTCCCGATCTCTACGCATTTCACTGCTACACCGGGAATTCCGCTACCCTCTACCACACTCTAGTTGTCCAGTTTCCACTGCAGTTCCCAGGTTGAGCCCAGGGCTTTCACAACAGACTTAAACAACCACCTCCGCACGCTTTAAGCACAGTCATTCCGAGTAACGCTTGCACCCTTCGTATTACCGCGGCTGCTGGCACGAAGTTACC
    ->ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/2
    -GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCCCATCAGACTTGCCAAACCGCCTGCGCACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCACCGATTCCTCCGGCCTCCTGGCACGGCGTTTCC
    ->ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/2
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTCATTCCGATTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTGGCACGGAGTTAG
    ->ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGCGCCCGGGGATTTCTCCTCCAACTTCCTGACCCACCTACGCGCGCTTTACGCCCCGTAATTCCGATTACCGCTGTCACCCTTCGTATCACCGCGGCTGCTGCTACGACGTTAGC
    
    

  • Output aligned_reverse:  different than expected, difference (using diff):
    ( /tmp/tmpb6reqslrtest6_aligned_reverse.fasta v. /tmp/tmp72jd91zvtest6_aligned_reverse.fasta )
    --- local_file
    +++ history_data
    @@ -1,1740 +0,0 @@
    ->ERR1877483.3 M03099:23:000000000-APTLR:1:1101:23102:1978/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCCCCGGATAAGATAATGACGTTATCCGTAGAAGAAGCCCCTGCTAACTTCGTGCCAGCATCCGCGGTAATACGACTGGCGCTAGCGTTGTTCGGTATTACTGGTCGTAAAGCTCACGTAGGCTGATCGATCAGTCATGGGTGCAATCCCATGTCTCACCCCTGGCTCTGCCTTTCATACTTTCCCTCTGGATTATGTCAGAG
    ->ERR1877483.4 M03099:23:000000000-APTLR:1:1101:22637:2119/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCTGGGCTCAACCTGGGATGGTCATTTAGA
    ->ERR1877483.5 M03099:23:000000000-APTLR:1:1101:18265:2244/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA
    ->ERR1877483.6 M03099:23:000000000-APTLR:1:1101:12491:2265/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGAAGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGAAAGAAATCCAGCCGGCTAATACCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCAGTGGAA
    ->ERR1877483.7 M03099:23:000000000-APTLR:1:1101:8123:2395/1
    -ACTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATAACTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGAAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGCAAGTCTGATGTGAAAGCCCCGGGCTCAACCTGGGAACGGCATTGGCG
    ->ERR1877483.8 M03099:23:000000000-APTLR:1:1101:19895:2425/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTTGTGAGGAAAAGTTAGTAGTTAATACCTGCTAGCCGTGACGTTAACAACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGCTAGATGTGAAAGCCCCGGGCTCAACCTGGGATGGTCATTTAGA
    ->ERR1877483.9 M03099:23:000000000-APTLR:1:1101:24195:2452/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGTATTAATCTAATAAGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAACCGCGGTAATAAAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGTAGGTGGTTTGTTAAGTTGGGTTTGAAATTTACGGGGTTAACCTGGGAACTGTATTCTAA
    ->ERR1877483.10 M03099:23:000000000-APTLR:1:1101:8960:2646/1
    -CCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAAAAAGTACCGTTCGAATAGGGCGGTACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGGTTAAGTCTGTTGTGAAAGCCCTGGGCTCAACCTGGGAACTGCCGTGGA
    ->ERR1877483.11 M03099:23:000000000-APTLR:1:1101:17700:2703/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCAACGCCGCGTGAGGGATGACGGCCTTCGGGTTGTAAACCTCTTTCAGCAGGGACGAAGCGAGAGTGACGGTACCTGCAGAAGAAGGACCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGTAGGCGGTTTGTCGCGTCGGGAGTGAAAACTCAGGGCTCAACCCTGAGCGTGCTTCGGATACGGGCAGACTAGAGGTATT
    ->ERR1877483.12 M03099:23:000000000-APTLR:1:1101:9100:2742/1
    -ACTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGAGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGCTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGGCTGTCAAGTCGGATGTGAAATCCACGGGCTCAACCTGGGCACTGCATTCGAA
    ->ERR1877483.13 M03099:23:000000000-APTLR:1:1101:15854:2768/1
    -CCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGA
    ********
    *SNIP *
    ********
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCACCGGAGAAGATAATGACGGTATCCGGAGAAGAAGCCCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGATCGATCAGTCAGGGGTGAAATCCCAGGGCTCAACCCTGGAACTGCCTTTGATACTGTCGATCTGGAGTATGGAAGAG
    ->ERR1877483.32942 M03099:22:000000000-APTMA:1:2119:22743:24096/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA
    ->ERR1877483.32943 M03099:22:000000000-APTMA:1:2119:20410:24202/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGGTACGATGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCATA
    ->ERR1877483.32944 M03099:22:000000000-APTMA:1:2119:18061:24218/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGTAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT
    ->ERR1877483.32945 M03099:22:000000000-APTMA:1:2119:18837:24311/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCATTAACCTAATACGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAA
    ->ERR1877483.32946 M03099:22:000000000-APTMA:1:2119:18816:24311/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCATTAACCTAATACGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAA
    ->ERR1877483.32947 M03099:22:000000000-APTMA:1:2119:7531:24361/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGGTAAGATGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCATA
    ->ERR1877483.32950 M03099:22:000000000-APTMA:1:2119:8336:24549/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTGATCCAGCCATACCGCGTGGGTGATGAAGGCCTTCGGGTTGTAAAGCCCTTTTGTTGGGACAGAAATCCAGCCGGCTAATCCCTGGTTGGGATGACGGTACCCAAAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTACTCGGAATTACTGGGCGTAAAGCGTGCGTAGGTGGTTGTTTAAGTCTGTTGTTAAAGCCCTGGGCTCAACCTGGGAACTGCAGGGGAA
    ->ERR1877483.32951 M03099:22:000000000-APTMA:1:2119:14312:24605/1
    -CCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATACCTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGGAATACGTAGGGTGCAGGCGTTTACCGGATTTCTTGGGCGAAAGGCGTGCGCAGGCGGTTTGGCAGTCCGATGGTGAAGGCCCCGGCCCCAACCTGGGAACGGCATTGGAG
    ->ERR1877483.32952 M03099:22:000000000-APTMA:1:2119:20365:24795/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGAT
    ->ERR1877483.32953 M03099:22:000000000-APTMA:1:2119:9975:24853/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA
    ->ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGGTTGTGGTTAATAACCGCAGCAATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAA
    ->ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCAACCTGGGAACTGCCTCCAAA
    
    

  • Output unaligned_forward:  different than expected, difference (using diff):
    ( /tmp/tmp8oc74nsztest6_unaligned_forward.fasta v. /tmp/tmps1bhb8yutest6_unaligned_forward.fasta )
    --- local_file
    +++ history_data
    @@ -1,260 +0,0 @@
    ->ERR1877483.1 M03099:23:000000000-APTLR:1:1101:19252:1849/2
    -CACTACCCGGTTTTCTTATCCTCTTTTCTCCCCCCCCTTTCCCCCCTCCTTCTCCGTTTTTTTCCCTTTCCTCCCCTTCCCCTCTTTTTTTCCTTCCTCTTTCTTCCCCTTTCCCCTCTTCCCCCCTTTTTCCCCCCTCCTCTTCCTTTCTCCTCCTCTCCCCTTTTCTTTTTCCTTTCCTTTTTTCTCCCCCTTCTTTCCCCTCCTCCTTTCTCTCCCCCCTTCCTTCCCTTTTCTCCCCGTTCTTCCCTTCCCCCCCTTCCCCCCTCTTTTTTCCCCCCCTTCTCTCCCCCTTTTTCC
    ->ERR1877483.2 M03099:23:000000000-APTLR:1:1101:15851:1971/2
    -CACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCTCCTGAGCGTCAGTCTTTGTCCAGTGGGCCGCCTTCGCCACCGGTTTTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGTATTCTCCCCCCCTCTACACTACTCAATCCTGCCAGTTTCGAATGCAGTTCCCAGGTTTAGCCCGTGGATTTCACATCCTACTTGCCATACCGCCTGCGTGCGCTTTACTCCCCGTAATTCCGATTTACGCTTGCCCCCTCCGTATTACCTCCGCTGCTGTCCCCTTCTTAGC
    ->ERR1877483.69 M03099:23:000000000-APTLR:1:1101:26536:6120/1
    -CCTACGGGAGGCAGCAGCGGGGAATATTGCACAATGGGCGAAAGCCTGATCCAGCCATACCGCGTGCGTGATGACGGCCTTAGGGTTGTAAACCGCTTTCAGTTGGGAAGAAGATCACTATCCTTCCAGAAGAGTCTTCGGCCGTCTCCGTGCCAGCAGCCGCGGTCATACGTAGGGAGCACACGTTGTCCGGCATTGTTGGGCGTAACGTGCTCGTAGGCGACTGAGCAAGTCGGGCGTGAAAGTCTGGGGCTCAACCCCAGGAAGACGCTCGAGGCTGTTTTCGCTAACGTCAGTTAAA
    ->ERR1877483.70 M03099:23:000000000-APTLR:1:1101:20716:6121/1
    -ACTACGGGAGGCAGCAGCGGGGAATCTTGGACAATGGGCGAAAGCCTGATCCAGCCAACCCGCGTGTGTGAAGAAGGCCTTCGGTTTGTAAACCACTTTAAGGTGGGAGGAAGGGCAGTAAGTTAATACCTTGATGGTTTGACGCTACCAACAGAATAAGCACCGGCGAACTTCGTGGCAGCAGCCGCGGGAAAACGGAGGGTGCCAGGGTTAATCGGAAGTAATGGGCGTAAAGCGCGAGTTGGGGGGTCAGCAAGTTGGAGGTGAAAGCCCCGGGCGCAGACGGGGAACAGCCGCCAAA
    ->ERR1877483.95 M03099:23:000000000-APTLR:1:1101:10309:7883/2
    -GACTACATGGGTTTTTAAATCCGGTTCCCTCCCCACGCTTTCCTCCTTAGCCGTCAGAATTAACCCATGAGCCTCCTTCCCCTTTTGTTGTTCCCCTACTTTCCAACAGTTTCTCCTCTTACATGCAAATTTCCGCCAACCCTTCCTTATCTCTAGTTTAACTGATCAAAGTACATTACTAGGGTTGCGCCGTAGCTTTCACCATTTGACTTTTTATCCACCCACCTGCCGCTTTACTCCCATATATCCCATCACCCTCTTCCCCCCTCCTCTTTCCACCGGCTGCGGCCACACACTTAT
    ->ERR1877483.96 M03099:23:000000000-APTLR:1:1101:10292:7893/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTAATGGACCAGTGAGCCGCCTTCTCCACTGGTGTTCCTCCGAATATCTACGAATTTCACCTCTACACTCGGAATTCCACTCACCTCTTCCATACTCCAGATCGACAGTATCAAAGGCAGTTCCAGGTTTGAGCCCTGGGCTTTCACCCCTGACTGATCGATCCGCCTACGTGCGCTTTACGCCCAGTAATCCCGAAAAACGCTAGCCCCCTTCGTATTCCCGCGCCAGCTGGCCCGCAGGTGCC
    ->ERR1877483.115 M03099:23:000000000-APTLR:1:1101:28104:8405/2
    -GACTACAAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACAGACCAGAGAGTCGCCTTCGCCACTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGAATTCCACTCTCCTCTTCTGCACTCAAGTTCCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCCGCGAGCCCTTTACGCCCAATACTTCCGGACAACGCTTGCCCCCTCCGTCTTACCGCCGCTGCTGGCCCGTCGTTAGC
    ->ERR1877483.116 M03099:23:000000000-APTLR:1:1101:28087:8411/2
    -GACCACAAGGGTATCCAAATCCTTTCGGCTCCCACCCCTTTGGCCCCCAACCTCAGTTACAGATCAGGCGGTCCGCCTCCCCACCTGTGTTCCCCCCCGACACTTCCCATTTCACCCCCACACCCGGGACTCCCCCCTCCTCCTCCGCACCTCACGCCCCCAGTTTTCAATTACACTCCCCGGTTTGCCCCCGGGCCTTTCCCTCCCACTTTACAACACGCCCTCCAGCCCCTTTACCCCAACTATTCCCGCCACCCGTTCGCACCCACCGTGTTCCTCGTACTCTGCGCCGTAGTTAGC
    ->ERR1877483.149 M03099:23:000000000-APTLR:1:1101:6596:10202/1
    -ACTACGGGAGGCAGCAGCTAGGAATCTTCCGCAATGGGCGCAAGCCTGACGGAGCGACGCCGACTGGAGGAAGAAGACCTTCGGGGTGTAAACTCCTGAACCCGGGACGAAACCACCGAGGCGGGGACGGACGGTACCGGGGCAATCGCGCCGGCCAACGCCGAGCCAGCAGGCGCGGTTATACGGAGGGCGCGAGCGTCACCCGGATTAACTGGGTGTAAAGGGCGCGAAGGCGTCCTGGGCCGTACCACGTGGAAGACCACGGGTCAACCGTGGAGGAGCGGGGGATAAGCTCAGGCAA
    ->ERR1877483.150 M03099:23:000000000-APTLR:1:1101:18892:10219/1
    -CCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGCGCAAGCCTGATCCAGCCATGCCGCGTGTCTGAAGAAGGCCTTCGGGTTGTAAAGGACTTTTGTTCGGGAGGAAATCCCGCTGGTTAATACCTGGCGGGGATGACAGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGCAAGTCTGATGTGAAAGCCCCGGGCTCAACCTGGGAACGGCATTGGAG
    ->ERR1877483.183 M03099:23:000000000-APTLR:1:1101:27013:12199/2
    -GACTACAGGGTATCTATTACTGTTTGCGCCCCACACGTTCGCAACTGAGCGTCAGTCTTTGTGCAGGGGGCCGCCCTCTCCACCGGTATGCCCCCCGCTCTCTACGCATTTCACCCCTACACCCGGAATTCTACCCCCCTCTACCAGACTCAATCCTGCCCGTTTCGCAGGCAGTTCCCAGGTTTTGGCCGCTGACTTTTCATCCCCGTTTACCTACCCCCCCCGCGCGCGCTACGCCCCGCAATTCCCATCACCGCTTGTGCCCCCCGCCTTTCCCCCGCTGCGCGCCCCGGGTTTACG
    ********
    *SNIP *
    ********
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAACTCCCCGGGCTCAACCTGGGAACTGCCTCCAAA
    ->ERR1877483.32864 M03099:22:000000000-APTMA:1:2119:18423:20592/2
    -CGGGCGGTGTGTGCTGATACTATGCTTGGCCGCCAATTCCTTTAAGTTT
    ->ERR1877483.32865 M03099:22:000000000-APTMA:1:2119:16207:20617/2
    -GACTACAAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATCAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCGTACTCTAGTCAGGCAGTTATGGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCCATCTTACCAAACCACCTACGCGCGCTTTACGCCCAGTAATTCCGATTACCGCTTGCACCCTTCGTATCACCGCGTCGGCTGGCACGAACTTAGC
    ->ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/1
    -ACGGGCGTCGGAAGCATCAGGGCCCGACAGTGCCAGTCCTGCCATGGGATGGGCGGCAACGAACCGCGCCCTGCCGGGATGGTTCTCAATGCTGCGGCAAACGGCGTCTTTTACCGAACCGGCATCTATCACCACGGTCTGATCTCCGGTGCGGTCAAGAATACCGGGAAGAATAGCGATGGTGGTATCGACCGGGACGGTGATCAGGACCAGCGAGGCATCACTGAGTGAGTTCTCCAGTGAGGTGCTCCTGTCAACCCGTCCCCTTGAAAGCGCCTGCTGCAAATGGCCGGCATTTGTT
    ->ERR1877483.32899 M03099:22:000000000-APTMA:1:2119:20673:22173/1
    -CCTACGGGAGGCAGCAGCGGGGAATATTGGACAATGGGCGAAAGCCTGATACAGCCACGCCGCGTGGGTGAAGAAGGCCCTCGGATTGTAAAGCACTGTTAGGTGGGAGGAAGGGCAGTAAGTTAATAACTCGCTGTTTTCAGGTTATCCACAGAATTAGTACCCGCTAACTTTGTGCTAGCAGACGCGGTCATACAAAGGGTGCAAGCGTTTATCTGAGTTACTGGGAGGAAAGAGCGCGTAGGTGGGTTGGTAAGATGGATGTGAAATGTCCGGGCGCAACACGGGAACAGCATCCATA
    ->ERR1877483.32900 M03099:22:000000000-APTMA:1:2119:9095:22203/2
    -GACTACTGGGGTATCTAATACTGTTTTCTCCCCCCGGTTTCGCACCTTAGTGGTAGTTTAAGTCCCGGAGGTCGGCCTCGCCACCTGTTTTTCTTCCTATTTTCTCGCATTTTACCGCCTAACAAGACATTCCACCACTCTCTACCGTACCTTAATCAGGCAGGTATGGGTGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCTTCCTACCATACCACCTTCGCGAGCGTTACGACCAGCAACTGCCTATAACACTTGCACCCTTTGTAATACCGCTGACGTTGGCACGTAGTTAGT
    ->ERR1877483.32901 M03099:22:000000000-APTMA:1:2119:9107:22299/2
    -GCCTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATGTCACATCCGACTTGACAGACCGCCTGCGTGCGCTTTACTCCCAGTCATTCGGCTTAACGCTTGCACCCTCCGTATTACCGCGGCTGCTCGCACGGAGGTAGC
    ->ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/2
    -GCCCAGTCCCCCCCTACTGCCAGCTGCGCCGTTAAGTCAGGCGGGCCAGCTCCGAATCTAGAGGATAACGACTACAACAGAAATAAGCAGAATGATTAAAGCCCCACATCACGGCGGCTAACCTGCATGCACACTACTCTCGTCTAAACCCATGGCCGACACGTTCCAATGACCTCACCAGCTGCCCACCATTAATAACTGCCTCGATCTCATGTGCTAGCCTCGAGCTCCTCACACACTTCAGCGTAACGCCGCCTCACCCACCCACCACATACCTTCAACATCCTGTGCTTCTTCTA
    ->ERR1877483.32927 M03099:22:000000000-APTMA:1:2119:15956:23349/2
    -GACTACGCGGGGATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCAACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGTCAGTCAGTTTTGAATGCAGTTCCCAGGTTGAGCCCGTGGATTTCACATCAAACTTAACATACCACCTACGCGCGCTCTACGCCCATTAATCCCGACTAACGCATGCACCCTCTGTATTACCGCGGCTGCTGGGACAGAGTTAGC
    ->ERR1877483.32948 M03099:22:000000000-APTMA:1:2119:21559:24504/2
    -GACTACCGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAATTTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCCCCTACGCGCGCTATACGCCCAGTAATTCCGATTAACGCTTGCACCCTGCGTATTACCGCGGCTGCTGGCACGCAGTTAGC
    ->ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/2
    -CGCTACTGGCGTACCTAATCCCGTTCCCTACCCTCCCCTGCGTACCTACCCGCGATTAAGTGTGCTGCAGGCTTCATTCACCATAGGTCTTGCCCTCAATCCCAACGAATTTCACTGCTACAGCCATAGTTTAACCTGGCTCTCCATACCCCATGTCTACCATTCATTGCAGCCTTTGTCTATCTGCACTCTTGAATTGCAACATTAATTCACCTCATCCCCACCTTACTCTTTGTTCTCTACGTCAGTACCCACATCTGTCACCACTCGCTATGTACCACGCTCTCTCACCACTTCAGG
    ->ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/1
    -ACGGGCGGTAAGTAGAGCCGATTCGTTGACAAGGTTGGCAAGGTCAGCACCGGTAAACCCGGGAGTACCCCTTGCTATCACTTTGAGATCTACCTCCCGGGATAGAGGTATCTTCCCCGAGTGAACAGCACGTATCTTCTCCCTTCCCTTAACATCAGGAACATCAGCAATGACCTGCCGGTCGAATCTACCAGGCCTTAAAAGAGCCGGATACAGAACATCAGGCCTGTTTGTGGCAGCTATGATTATCAAACCCTCAGTGGTTTCAAAACCGTCCATCTCAACAAGAAGCTTGTTGAGA
    ->ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/1
    -CCTCCGGGAGGCAGCAGTGGGGAATCTTAGACAATGGGGGCAACCCTGATCTAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGCTGGGAAGATAATGACGGTACCAGCAGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGGGCTCGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGACCGTAAAGTTGGGGGTGAAATCCCGGGGCTCAACCCCGGAACTGCCTTCAAAACTATCGGTCTGGATTTCGAGAGAG
    
    

  • Output unaligned_reverse:  different than expected, difference (using diff):
    ( /tmp/tmpxbty7rgetest6_unaligned_reverse.fasta v. /tmp/tmpy0ao_usktest6_unaligned_reverse.fasta )
    --- local_file
    +++ history_data
    @@ -1,260 +0,0 @@
    ->ERR1877483.45 M03099:23:000000000-APTLR:1:1101:24920:4667/2
    -GACTACTCGGGTATCTAATCCTGTTTGCTCCCCAAGCTTTCGTGCATGAGCGTCAGTGTTATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATATCTACGCATTTCACTGCTACACGCGGAATTCTACTTCCCTCTGACGCACTCTAGTCTTGCAGTATCGAATGCCGTTTCCCGGTTGAGCCCGGGGATTTCACATCAGACTTACAAAACCGCCTGCACACGCTTTACGCCCAGTAATTCCGATTAACGCTTGCATCCTACGTATTACCGCGTCTGCTGTAACGTAGTTAGC
    ->ERR1877483.46 M03099:23:000000000-APTLR:1:1101:21301:4734/2
    -GATACACGGGGATCTCTAACCGTTTGCGCCCCACGCGTTCGCTCCTCACCGCCAGATACAGGCCAGAGAAACGCCTTCGCCACAGGGGTTCCCCCACAGCTATACACATATCACCCCGACACGCCGGATTCCACACTCCACTCCTGCACTCACGATCCCCCGATTCCAATGAGCATTCCCGTGTGAGCCGGGAGCGTATACACAAACCATAGACACACCCCGCCACGCCCTCTGTGCCCCAAAGAACTGTAAAAGACGTTCCACCCCCGAGTAAACCCGCGTCTTCTAGCGCGGGGGTCGG
    ->ERR1877483.75 M03099:23:000000000-APTLR:1:1101:20308:6281/2
    -GACACAAGGGTATCTCATCCTGTTTGCTCCCCACGCTTTCGCCCCCCAGTGCCAGTATTTGTCTAGTTGGTCGCCTTCTCCACTGTGTTACCTCCCTTTATCTACGCATTTCACCCCTCCACACCAAATTTCCCACTCCCCTACCCTACTCTATTCCTTCCCTTTTGCGAATGTTTCCCCCTTTTTGCCCCCGGTTCTTTCACCTCCCTTAAAAAACCCCCCCACCGCGCCTTTCACCCCTAAATTCCCATTAACCCTTTCACCCACTCTATTACCCCGGCTCTGCGCACATAGTTTTCT
    ->ERR1877483.76 M03099:23:000000000-APTLR:1:1101:25401:6445/2
    -GCGCAGGGGGCTCACCGGGTTGCAGAAGAGAGACCGCACTACCAGGTAATATACTACTCGTTTGTCCCCCCGACTTTGTCACTCCACATCCACCCTACTCCCCCCCGCCCCCCTTGCCCCCCGCGCCCCCCCCCCCCCTTACGACTTGTCCCCCCCCAACCCGCCCTTTTCCTGCCCCTTCCCTCCCCCACCCTACCACACGCGCGCACACTGTCCTCCCCTGCCCTCCCCGCTTTCCGTACTACGTGTACTCCCACACCTCTCCCCTCTTCATCCCTCATTGACGCTATATTCCTCCCC
    ->ERR1877483.107 M03099:23:000000000-APTLR:1:1101:20082:8248/2
    -GACTACTGGGGTATCTAATCCTGTTCGCTACCCAAACTTTCCCACATTATCGTCCGCTTATGGCCAGGGCGTCGCCTTCGCCACTGATTTTCCTCCACGTATCTACCCATTTCACCTCTCCCCCTGGCAATCCCCCCCCCTCTCCACGCCTCCAGTCTGCCTTTTCTAAATTACCATTCCCGGTTCCCCCCGGGGCCTTCACCTCTCGCTTAACCAACCTCCCCCACGTGCTTTTCCTCCCATACTTCCGCTTAACCCTCCTCCCCCCCGTCATACCCCGGCCTCGCGCCCCGCCTTGTC
    ->ERR1877483.108 M03099:23:000000000-APTLR:1:1101:28179:8259/2
    -GACTACTAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCATCGGTATTCCTCCGCATCTCTACGCATTTCACTGCTACACGCGGAATTCTACCCCCCTCTGACGCACTCTAGTCTTGCAGTCTCCAATGCCGTTCCCAGGTTGAGCCCGGGGCTTTCACATCAGACTTGCAAAACCGCCTGCGCCCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTACGTATTACCGCGCCTGCTGGCACGTAGTTAGC
    ->ERR1877483.127 M03099:23:000000000-APTLR:1:1101:12005:9181/2
    -GCCTACTGGGGTATCTTATACACATCTGACGTTGCCGACGACTTAATAGGTGTAGGATTCCGAGGGAGCCGAACTACTAAAATTAGGATTGAAGACTCAGATCCGAACTGAGACCTACTTTGTAGATTTGCATCCTGTCACCAGGTAGCTGCCCTCTGTATCGGCCCTTGTAGCACGTTTGTAGCCCTTGACGTACGGGCCCTTCTGAGTTTACGTCCTCCCTGCCTTCCTCACTTCTTTCGTCGGCAGTCCCTTTAGAGTCCCCAGCTTAACCTGCTGTCAACTACAGGCAAGCGTTTC
    ->ERR1877483.128 M03099:23:000000000-APTLR:1:1101:17447:9215/2
    -GACTACTCGGGTATCTAATCCTGTCTACTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTTGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACAAGACTCAAGCCTGCCAGTTTCGAATGCAGTTCCCAGGTTGAGCCCGGGGATTTCAAATCCGACTTGACAGACCGCCCGCGTGCGCCTTACGCCCAGTAATTCCGATTAACGCTTGCCCCCTCCGTATTACCCCGGCCTCTGGCCCGGGGTTAGC
    ->ERR1877483.167 M03099:23:000000000-APTLR:1:1101:22979:11600/2
    -GACCACTAGGGTTTCTAATCCCGTTTGCTCCCCACCCTTTCCCGTCTTAGTCTCAATTCCGTCCCCGCGAGCCGCCCTCGCCATCGGTTGTCCCCCTCGTTTCTGCGCATTTCCCCCCTTCACCCGGAATTCCCCCCTCCCCTTCCGGCCTCCAGCCAGACCGTTTCCACCGGCATTTCATGGTTGGGGCCCGGGCTTTCCACACGGACCTAGCGAGCCCCCCCAACGCCGCTTAACCCCCATTCATCCCGACCAACGCTTCCCCCCACCTATGTCCCCCGCCTCCTGCCCGCACTTTAC
    ->ERR1877483.168 M03099:23:000000000-APTLR:1:1101:26900:11613/2
    -GACTACAGGGGTATCTAATTCTGTTTGCTCCCCACGCTTTCGCACCTCAGTGTCAGTATTAGTCCAGGTGGTCGCCTTCGCCACTTGTGTTCCTTCCTATATCTACGCATTTCACCGCTACCCCGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTCGAGTCAGTTCCCAGGGTGAGCCCGGGGATTTCACCTCCCACTTGCTGAACCACCTACGCGCCCTTTACCACCAGTAATTCCCATTTACTATTGCACCCCTCGTATTATCGCGGCTGCGCGCACCCAGTTCGC
    ->ERR1877483.191 M03099:23:000000000-APTLR:1:1101:15859:12475/2
    -GACCACAAGGGTATCCAATCCTGTTCGCTCCCCACGCCTTCGCTCCTCAGCCTCAGTTACAGACCAGAGAGTCGCCTTCGCCCCTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGAATTCCACTCACCTCCTCTGCACCCAAGTTCCCCAGTTTCCAATGACCCTCCCCGGGTGAGCCGCGGGCCTTCCCCTCAGACTTAAGAAACCGCCTGCGCGCCCTTTACGCCCCATAAATCCGCACAACGCTTGCCCCCCACCTCTTACAGCGGCTGCCGGCACGGAGTTAGC
    ********
    *SNIP *
    ********
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGGTAAGATGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCCATA
    ->ERR1877483.32872 M03099:22:000000000-APTMA:1:2119:13774:21033/2
    -GACCCTCTGAGTAACCAGTCCCGGTTGCTTACCACACGTGCCAACCCGAGCGGATCAACCAAGCCAGTGCGCCCACTCCCACACCGCATCCCCTCCGAAATTCCAACACTCACACCTCCACTCTCATGATTCCCGCCTCCTACCTCTGTCTCCACTCGACCCGCACACACGGAACCGAGTCGATCCATCCCCGTCATACCACTTATACCTCAATGATCCACCTAAGTTCCCCTGATTCCCCGTCCTAGCGATCATCTCACTGCCCCTCCCGTACCTCATGTCTCCACTTCCCAGCATAGA
    ->ERR1877483.32873 M03099:22:000000000-APTMA:1:2119:20965:21047/2
    -ACTACAAGGGTATCTAATCCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTTACAGACCAGAGAGTCGCCTTCGCCACTGGTGTTCCTCCACATCTCTACGCATTTCACCGCTACACGTGGAATTCCACTCTCCTCTTCTGCACTCAAGTTCCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGCAACCGCCTGCGAGCCCTTTACGCCCAATCATTCCGTACAACGCTTGACACCTCCGTATTACCGCGCCTGCTGGCGCGTCGTTAGC
    ->ERR1877483.32898 M03099:22:000000000-APTMA:1:2119:24030:22105/2
    -ACGGCCGATTTGTGCATGGCACGGCAATATATTCCCCCCCTCATATATGGGCCGCGAGCACTACCCATTCCGTCTTCATCGGGTCGGGGGGCACATCCCACACTCAACGTCCCACACGCTTTTGCGCTGCCCACTCGATCACGTGATCGACTCGCTCCTTAGTGGGCATTTTAGCACTTGTCTCCCCATGGCGGCTAGGCTGTAGGTGAGCCGAGTGCGGACTCATCTTTCACCGACTTGCGCAGCGAGTACTCGTAGCAGACCCGGCGCTGACCACCAGCCACTGCAGTGTACGACCGT
    ->ERR1877483.32899 M03099:22:000000000-APTMA:1:2119:20673:22173/2
    -GACTACTAGGGTATCTAATCCTGGTTGCTCCCCACGCTTTAGCACCTCAGTGTCAGTAACAGGTCAGGTGGTCGCCTTCGCCACTGGTGTTCTTTCCCATATCGAACCAGTTCAGCGCTACACAGGAAATTCCACCACTCCCTGCTGGACTCTAGTTGGGCAGTTATGGTTGCAGTTCGTAGGTTCAGCCCGGTGATTTCACTTCCTATTTACCGACCCACCTACTCGCCTCATAATCCCCCACACTCGGTTTTACGCTGCCACCTGTCTTATAACCACGGTAGTGATGACAACGTTACGG
    ->ERR1877483.32926 M03099:22:000000000-APTMA:1:2119:7498:23338/1
    -ACGGGCGGTGGCGATCTCGTGGACGATGACGTTGATCCTCGTCTCCCCGGATACGGGGATGAAGCTGCAGCCGGTGCCGTCTCTGACCAGCTGGGCCTCCAGCTGCCTGCCCGCAAAGCCGGCGATGAAGCCGCGGGCCCGGTTCTCGGCGCCGAGGGCGGTCAGGACCTTCGATACGTCGATCCCCTTCCCTCCGGCGTAGCTCTCCTCCCGGATTATCCTGTTGGGGACGTCCTCCCTCATCACGTCGATGAGGAGGGTCCGATCGAGGGCTGGGTTGATGGTTATGGTGTAAATCATC
    ->ERR1877483.32927 M03099:22:000000000-APTMA:1:2119:15956:23349/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCATTAACCTAATACGTTAGTGTTTTGACGTTACCGACAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCAAGCGTTAATCGTAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTTGTTAAGTTGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCAAA
    ->ERR1877483.32948 M03099:22:000000000-APTMA:1:2119:21559:24504/1
    -CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGTCTTCGGATTGTAAAGCACTTTAAGTTGGGAGGAAGGGCAGTAAGTTAATACCTTGCTGTTTTGACGTTACCAACAGAATAAGCACCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGTTCAGCAAGTTGGAGGTGAAATCCCCGGGCTCACCCTGGGAACTGCCTCCAAA
    ->ERR1877483.32949 M03099:22:000000000-APTMA:1:2119:22063:24539/1
    -ACGGGCGGTGTGTACACATCTCCGAGCCCACGAGACAGCCCACGAGACATCCTACGAGACCGCCCGCAAGAAAGCCCCCGAGACATCCCACCCTCCGGCCCTCCAAGAGAACGACCACGCGGCCCACGTGCCCCGACACCTAAGCGGGTCCTAGAAGGCGCAAGCACGACTCCCTCCGTGCTAGGGTCAGCCCTCATACGACGGAAACCCGCGATCTTCTTAATCAACGTTCGCTAGAACACCCTAGGCTGACTCCGACGAACAGACTGCAGGACCGACGCTCGACCCCGCAACCACCACG
    ->ERR1877483.32954 M03099:22:000000000-APTMA:1:2119:11950:24861/2
    -GGCTACTAGGGGTACTAATTCTCGTTTGTCCCCACGGTTTCGCACCTTCACGGTAGTCTTTATTCCGGCGACTCCCCTCGCCACCTGTAGTCCTCCAGGACTCTACGCAATTCACCGCCTCACCTGGAAATCTACCCCCCCCTTCCAGCATTCTACCTGCCCAGTTCCAATTCAGTTTCCCGGTTTAACCCCGGGGCTTCCACATCGACTTTACAGACCGCCCTCCTAGGCCTTACGCCCATTACATCCGATTAACGCCTTCACCCTCCGTATTCCCGCCTGCTCTGGCACCGTCTTAGG
    ->ERR1877483.32955 M03099:22:000000000-APTMA:1:2119:9959:24862/2
    -GACTACAGGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGTGCATGAGCGTCAGTGTCATCCCAGGGGGCTGCCTTCGCCACTGGTGTTCCTTCCTATATCTACGCATTTCACCGCTACACAGGAAATTCCACCACCCTCTACCATACTCTAGCCCAGTAGTTTTGGAGGCAGTTCCCAGGTTGAGCCCGGGGATTTCACCTCCAACTTGCTGAACCACCTACGCGCGCCTTACGACCAGTAATTCCGATTAACGCTTGCACCCTTCGTATTACCGCGGCAGCTGCTACTCTGTTAGC
    ->ERR1877483.32956 M03099:22:000000000-APTMA:1:2119:14880:24914/2
    -GCGACGGGTACGAGAGAGATCAGTGGGAATAGAAATGAAAGGAGGCGGAAGTAAGAACACAAACGAGTCGGTGTAATCTAAATGGAGAGGAGGACTAAGGTGCTGAATACGGCTGGAGCTAGGGGGGTGGCACATGGTCGATACTGACTGATCAACTGTGATGTCGCTCTTAGTAGTGGTGGAACAGGACTGGATATGGCTATTAGGACTGGGTATCATAAACATGCTACTATGGGTAACTTACTACGACAACACTTGGAGGCTAACATCACTATGTAACTATCGAAAGTGAGATTACGAT
    ->ERR1877483.32957 M03099:22:000000000-APTMA:1:2119:17520:25205/2
    -GACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGCACCTCAGCGTCAGTATCGAGCCAGTGAGCCGCCTTCGCCACTGGTGTTCCTCCGAATATCTACGAATCTCACCTCTACACTCGGACTTCCACTCACCTCTCTCGAACTCCCGACCGATAGTTTTGACGGCAGTTCCGGGGTTGAGCCCCGGGATTTCACCCCCAACTTTACGGTCCGCCTACGTGCGCTTTACGCCCGGTCCTTCCGATCACCGCTATCCCCCTCCGTACTACCGTGTCTGCTGGCCCGTACGTCGC
    
    

  Command Line:

  Exit Code:

  • 0

  Standard Error:

  • /usr/local/bin/merge-paired-reads.sh: line 54: perl: command not found
    /usr/local/bin/merge-paired-reads.sh: line 56: perl: command not found
    /usr/local/bin/merge-paired-reads.sh: line 58: paste: command not found
      The input reads file or reference file is empty, or the reads file is not in FASTA or FASTQ format, no analysis could be made.
    /usr/local/bin/unmerge-paired-reads.sh: line 49: perl: command not found
    /usr/local/bin/unmerge-paired-reads.sh: line 51: perl: command not found
    /usr/local/bin/unmerge-paired-reads.sh: line 49: perl: command not found
    /usr/local/bin/unmerge-paired-reads.sh: line 51: perl: command not found
    

  Standard Output:

  •    Warning: /corral4/main/objects/7/0/c/dataset_70c25aa4-5d74-45ed-854c-7741cd2a2422.dat seems to be in fasta format (this script is for fastq reads only)
       Warning: /corral4/main/objects/0/8/a/dataset_08af56ba-c35b-4c54-8992-15794abc8084.dat seems to be in fasta format (this script is for fastq reads only)
       Processing /corral4/main/objects/7/0/c/dataset_70c25aa4-5d74-45ed-854c-7741cd2a2422.dat ..
       Processing /corral4/main/objects/0/8/a/dataset_08af56ba-c35b-4c54-8992-15794abc8084.dat ..
       Interleaving /corral4/main/objects/7/0/c/dataset_70c25aa4-5d74-45ed-854c-7741cd2a2422.dat and /corral4/main/objects/0/8/a/dataset_08af56ba-c35b-4c54-8992-15794abc8084.dat ..
       Done.
    
       Processing /corral4/main/jobs/048/221/48221739/outputs/galaxy_dataset_2f3140bb-ee47-4d06-8ce6-327fe99ff7d9.dat ..
       Processing /corral4/main/jobs/048/221/48221739/outputs/galaxy_dataset_1217a86e-7099-461b-97aa-86793c958097.dat ..
       Done.
       Processing /corral4/main/jobs/048/221/48221739/outputs/galaxy_dataset_90bccb74-bb70-4d31-9d57-5c2617915c23.dat ..
       Processing /corral4/main/jobs/048/221/48221739/outputs/galaxy_dataset_1f106479-ea22-4933-8212-880b88cffe9c.dat ..
       Done.
    

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    sequencing_type	{"__current_case__": 1, "forward_reads": {"values": [{"id": 107953030, "src": "hda"}]}, "paired_type": "--paired_out", "reverse_reads": {"values": [{"id": 107953036, "src": "hda"}]}, "sequencing_type_selector": "paired"}
    strand_search	""
    databases_type	{"__current_case__": 2, "database_name": {"values": [{"id": 107953040, "src": "hda"}]}, "databases_selector": "history", "max_pos": "100000", "seed_length": "18"}
    aligned_fastx	{"__current_case__": 0, "aligned_fastx_selector": "--fastx", "other": true}
    log	false
    report	{"__current_case__": 1, "blast": {"__current_case__": 1, "blast_output": "False"}, "otu": {"__current_case__": 1, "otu_map": "False"}, "print_all_reads": false, "report_best": {"__current_case__": 0, "report_best_min_lis": "2", "report_best_type": "1"}, "report_type": "best"}
    e_value	"1.0"
    match	"2"
    mismatch	"-3"
    gap_open	"5"
    gap_ext	"2"
    ambiguous_letter	"-3"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fasta"

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna (Test tool test #1)

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    sequencing_type	{"__current_case__": 0, "reads": {"values": [{"id": 107953026, "src": "hda"}]}, "sequencing_type_selector": "not_paired"}
    strand_search	""
    databases_type	{"__current_case__": 2, "database_name": {"values": [{"id": 107953040, "src": "hda"}]}, "databases_selector": "history", "max_pos": "10000", "seed_length": "18"}
    aligned_fastx	{"__current_case__": 0, "aligned_fastx_selector": "--fastx", "other": true}
    log	false
    report	{"__current_case__": 2, "blast": {"__current_case__": 0, "blast_format": "1 cigar qcov", "blast_output": "True"}, "print_all_reads": false, "report_num_alignments": {"__current_case__": 1, "report_num_alignments_type": "1"}, "report_type": "num_alignments"}
    e_value	"1.0"
    match	"2"
    mismatch	"-3"
    gap_open	"5"
    gap_ext	"2"
    ambiguous_letter	"-3"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fastqsanger"

• ✅ toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna (Test test against test.galaxyproject.org #2)

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    sequencing_type	{"__current_case__": 0, "reads": {"values": [{"id": 107953028, "src": "hda"}]}, "sequencing_type_selector": "not_paired"}
    strand_search	""
    databases_type	{"__current_case__": 2, "database_name": {"values": [{"id": 107953040, "src": "hda"}]}, "databases_selector": "history", "max_pos": "10000", "seed_length": "18"}
    aligned_fastx	{"__current_case__": 0, "aligned_fastx_selector": "--fastx", "other": false}
    log	true
    report	{"__current_case__": 0, "report_type": "None"}
    e_value	"1.0"
    match	"2"
    mismatch	"-3"
    gap_open	"5"
    gap_ext	"2"
    ambiguous_letter	"-3"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fasta"

• ✅ toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna (Test Test roary 3.13.0+galaxy2 #4)

  Command Line:

  Exit Code:

  • 0

  Traceback:

  Job Parameters:

  • Job parameter	Parameter value
    sequencing_type	{"__current_case__": 0, "reads": {"values": [{"id": 107953027, "src": "hda"}]}, "sequencing_type_selector": "not_paired"}
    strand_search	""
    databases_type	{"__current_case__": 2, "database_name": {"values": [{"id": 107953040, "src": "hda"}]}, "databases_selector": "history", "max_pos": "100000", "seed_length": "18"}
    aligned_fastx	{"__current_case__": 1, "aligned_fastx_selector": ""}
    log	false
    report	{"__current_case__": 1, "blast": {"__current_case__": 1, "blast_output": "False"}, "otu": {"__current_case__": 0, "coverage": "0.97", "de_novo_otu": true, "id": "0.97", "otu_map": "True"}, "print_all_reads": false, "report_best": {"__current_case__": 0, "report_best_min_lis": "2", "report_best_type": "1"}, "report_type": "best"}
    e_value	"1.0"
    match	"2"
    mismatch	"-3"
    gap_open	"5"
    gap_ext	"2"
    ambiguous_letter	"-3"
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fasta"

[jennaj]

Diff failed but result exists, considering done