# make.contigs problem

**URL:** <https://forum.mothur.org/t/make-contigs-problem/2333>\
**Category:** Commands in mothur\
**Created:** [March 30, 2015, 4:48pm UTC](https://forum.mothur.org/t/make-contigs-problem/2333 "2015-03-30T16:48:48Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![oalzahal](https://avatars.discourse-cdn.com/v4/letter/o/e9bcb4/32.png) [@oalzahal](https://forum.mothur.org/u/oalzahal)\
**Post date:** [March 30, 2015, 4:48pm UTC](https://forum.mothur.org/t/make-contigs-problem/2333/1 "2015-03-30T16:48:48Z")

</div>

Hi all, i did MiSeq sequeincing (v13 2x300) of 16s rDNA and i received a forward and a reverse file per sample. I got problems with the first step, make.contigs. i can’t find any posting re this problem.  
i run:  
make.contigs(file=stability.files, processors=8)  
i get:

> > > > > Processing file pair E17\_S93\_L001\_R1\_001.fastq.gz - E17\_S93\_L001\_R2\_001.fastq.gz (files 1 of 96) \<\<\<\<\<  
> > > > > o��d� is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > V����5��{f��f�$\<\>���1e�(0�� is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ����C�[^���J4��i��z~l������Ī[��ng�[������1�"�%Y��3\_��l��Cn"\<@���}��’��\<�Y#��%���ߋ�$��e.��|r�M���O�B�ld��l�ݺD�+�N��b� is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > ?���r���u��vˬ��Hʞ���SŇ�T�7䞂3A�b��Js��aY� is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > C���Dn��!�&z���;q�)@c�f�l�˭� is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > Oa��4Q�5�\*,�sb���,�Qư��SnI����a’� is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > u\_��f,�\*��N����� is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.  
> > > > > Making contigs…  
> > > > > Segmentation fault

my question: is the problem really caused my missing sequences form forward or the reverse file? if so, how do i remove them? since mothur terminated and i don’t have a record of those missing sequences to remove?

many thanks for any help

O. A.

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<div class="post-metadata">

**Author:** ![oalzahal](https://avatars.discourse-cdn.com/v4/letter/o/e9bcb4/32.png) [@oalzahal](https://forum.mothur.org/u/oalzahal)\
**Post date:** [March 30, 2015, 5:09pm UTC](https://forum.mothur.org/t/make-contigs-problem/2333/2 "2015-03-30T17:09:54Z")

</div>

here is what my forward looks like  
@M00307:33:000000000-A78Y7:1:1101:15919:1934 1:N:0:82  
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATCCATGTCGAACGCTGAATCCCAGCTTGCTTCTCGGGTTTCCAGTCGCCCTCGTGTGCGTAACATATCGCAACGTCCCCCCTCGTCGCCCATAACTGATCGACAGTTCCCCTAATACCGCATCCGTCTTGCGTTAGAAAGCAGGGGACCTTCCTCCCCTCCCCTCTTCCACCGCCCCCTATCCGCTTTTCCCGTTCGTGGGGTAAAGCCCTACCCCGCCCCCCCTCCCTCCCCGGTCTTAGAGGTTCACCCC  
+  
CCCCBEFCGGGGDFFFFFGGGGGGGGGGGGGCGGGGEGCGFGGGECECE,C\<,\<\<C,CCC@:@,+,6,9,6=?,99B?,C,+:,9,:,+8+++:++,:4,+8++4,\<++++6+8+8\>,++3++6+++++38,88,3\*\*\*\*\*,4,_,22_5\*\*\*\<_::2;,\*\*\ ***++30:7C** )2;\<6++,2:32_/**000+_+29_2:_5)_+2+_0.\*+(/0_2**\*+2++;C)_15_\*/_:)/:1)2,))_(()0)1())))+)_0_)25\<5  
@M00307:33:000000000-A78Y7:1:1101:15922:1953 1:N:0:82  
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCTTAACACATGCAACTCGAACGCTGAAGCCCATCTTGCTTCTCCGGTGTCTCGTTGCGCCCCGGTGATTAACCTATCGCAACGTCCCGCTTCTTCGTTCATCACTGATCGAACCCTCACCTAATACCGCCTACGTCTTGTCTCATCAAGCCGCTTACCTTCCCCCCTTTCCCTCTTCCACCGGCCCATCTCTGCCTACCTCTTTTCTTCGTTAAAGCCCTACCCCGCCCCCCCTCACTACCATCTCCTCTCCACTGCCCCC  
+  
CCCCCGGGGGFFGFFFEGGFFGGGGGGEFGE:@FFGGGDGFGGGGAEFF,E,6,6C,CFF@:86+,:6C,:A?,99?5,C,++8++4,9+,8+++++++6++,\<,:,8,8=+++86+6+8\>+++8+,7,+,7,@,8,=@**,36,6,2\<_\>16_4/,4,4,\<_\<9@8++212+\<3:00+++9752+2+3_+2+_._+.++2+20\*2180A+2\*)_17_\*\*\*🙂_/_/)/\*(**+.)_)3).()(\*\*0+,(1_  
@M00307:33:000000000-A78Y7:1:1101:13705:1954 1:N:0:82  
AGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGATGACGCTTCTATCTTTCTAGAGTTCTTCTTAGTTGCTCACGGGTTAGTAACGCATAGGTTATCTGCCTCTTCTTTTGGTATAGCCATTCGAAACGTTCATTAATACCCGATACTCCCTACCGTGGAAAGATTTATCGCTAACCCATCAGCCCATGTCCTATCACCTTCTTGGTAAGTTAATGTCTTCCCACGGCCCTGACGCACCTCCCCCCCTCGACTGTCTACGTCCCCCCTCCCA  
+  
CCCCCGGGGGGGGDFGFGGGGGGEEGGGGCCEGGGGD@@CFGGF\<EFGF6F\<CE9E7FFFC,:6?,88B7???,95,\<\<,:\<,:,95,\<,:,?,9,++++9,:,+@7=+A8\>?E,\<,A=,A,A,57,@,C9\<F@FE\<\<,6,3\>+,7,9,CD,++@@E9C\<\>6,5,@_6C9:,8,5=:7D\*2_\*,4,4,_,2;5,2,=;7:,+,+245,3+;9:@+.3+5+2++3:++12C_:\*\*210\*2)\*_2/;11/()8((1+.4(.(02\>,_(\*0  
@M00307:33:000000000-A78Y7:1:1101:17074:2021 1:N:0:82  
AGAGTTTGATCCTGGCTCAGAGTGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGATGAAGCTTCTAGCTTGCTAGAGTGCTGATTAGTGGCGCCCGGGTGAGTAACGCATAGGTTATGTGCCTCTTCCTTTGGTATAGCCATTGGCAACGCTGTTTAATCCCCGATAATCCCTACTGCGGAAAGATTTATCGCTACGCCATACGCCTATGTCCTATCAGCTTGTAGGTAAGGTAATGCCTTACAAAGGCTATGACGGACAACCGGCCCTAGAGAGGGAACGTACACCCTCAAC  
+

  
  
  
and reverse

@M00307:33:000000000-A78Y7:1:1101:15919:1934 2:N:0:82  
GTATTACCGCGGCGGCTTGCACGTAGTTAGCCGGTCCTTATTCTTCATTTACCGTCATCACCCCCTCTTATTTCCACCTCCCTTTTCTCCCCTTCCAATTTTCCTCTCCACCCCCATGCCCTTCTTCCCCCCCCCTCCTTTCCTCCTTCCCCCTTCCCCCCCTTCTCCACCATTCCCCCCCCCCCCCCCCCCTCCCACTCCCTCCCTCCCCCCCTTCCCCCCTCCCCCTCCCCTCCCCCCCACCCCCCCCACACTCCTCCCCTCCCCTCCCCCTCCCCTCCCCCCCCCCCCACTCCCCTC  
+  
A66A,6CC,+++86+@C++:,C6C,68;\<@BC6+8+@CF,69C\<CC,9,CC,AC,B\<,:6+@+,5,9,96,95,94,9A?,4,44,9,46\>++,4@14,++,),_+3+5+3++,5,+,+,33_3\*\*,)_)))_/)(_0;\*\*,(_)110()1\*,**8,-5:8))_)_**)._2/14().-()((.20__2/2((.-((-))0–((-408:(((((-((,2_\*\*\*\*\*\*\*/1_ **1/2** 155_\*/_,((,(,(,((((-  
 @M00307:33:000000000-A78Y7:1:1101:15922:1953 2:N:0:82  
GTATTACCGCGGCTGCTTGCACGTAGTTAGCCGTTCCTTATTCTTCAGGTCCCGTCATCAGCCCCCCTTATTATCAACACCCTTTTCTTCCCTTCCCAATTTCCTCTCCCACCCCAATCCCTTCTCCCCCCCCCCCGCCTGCCCTGTCTCCCCCTCCTCCCACTCTCCCACTTTCCCCCCCCCCCCCCCCCCCACGCCTCCCCCCCGGTCCCCTTTCCCCCCTTCCCCCCCCCCCCCCCCACACCCCCTCCCCCCCCCCCCCCTTCATCCCCTCTCCCCCCCCCCCTCACCCCCTCCTCA  
+  
-66A6\<C\<8+48@+86\<,6\<CD;@6@CEFEE+,CEC66AEAFE9,;,;C+AFB\<\<\<,59,8+++,9665,9,6+44,99,AE\<,4,9,4,9,9+6+++4,9,9,+04)+0+++3+00+1_,_,33,_+_,__))0;,3))/(_,(+_0,008((1(()1)1))).**)(()-))(.)()1229/2((),((,.)0,((((43828((((,(,-/21:/**+/2__22/21_/_1-((4(–(((((.  
 @M00307:33:000000000-A78Y7:1:1101:13705:1954 2:N:0:82  
GAATTACCGCGGCTGCTGGCACGGAGTTAGCCGGTGCTTATTCGTTATATACCGTCATTATCTTCCCTAACAAAATGAGTTTACAATCCTAAAACCTTCATCCTCCACGCGGCGTTGCTGCTTCACGCTTTCCCCCCTTGACCACTATTCCCTCCTTCTCCCTCCCGTATGACTCTCGACCCTGCCTCACCTCCACTCTCTCCCTTCACCCCCCCCCCTCCTCTCCCCCTCACACCCTTCCTCCCCCTATCCCCTCCCCACCATCCACCTGCCCACCCACCCATCCCCTTCACCTACATC  
+  
8-AB,\<C@@:@+@+\>@F,;@AEFF:+8E@FEEC+8+@FFFDFG8;C7,:,C:FE,4\<\<BA6,?,4C,C@,A,:,C;E9,\>\>E\<E,\<9@F\<BE,D===EC4B=\>+@:+4++46,6,@,+,)+36@8@C+06,+,339,224\>@3+15323,3=))3),+30,/35)-2,186,2/2,4,1)420,)5/84(.).()))120022_((02(.(585(,.))((1\*\*())()(,(/2/0/_++ **32+/1/10** -(((.)-)((().  
 @M00307:33:000000000-A78Y7:1:1101:17074:2021 2:N:0:82  
GTATTACCGCGGCGGCTGGCACGGAGTTAGCCGGTGCTTATTCGTTAGATACCGTCATTATCTTCTCTAACAATAGCAGTTTACAATCCTAAAACCTTCATCCTCCACGCGGCGTCGCTGCTTCAGCGTTTCCCCCATTGCGCCATATTCCCCACTGCTGCCTCCCGTAGGCTTCTGGCCCGTGTCTCACTTCCACCGTGCCCGTTCACCCTCCCCGGCCCGCCACCCGCACTCCCCTTTGTTAGCCCATACCCTCCCACCTCACACCTCAGACCTAACCACACCCCTATACCATCACT  
+  
A-A@6CFFEC+6C+\>\>CFCECFGFFEFEGGFGCE@:FFGGAFF8FDC,6C\<DFGGGDEB,5CE9F,C?CCABF,5\>,C,:CAEGG9BEFGFGF\<,BC9E,\>==,\<,B=B8=C+6++3+686@D,2++18?CG+\>B0AC+696:8EA/=9D,6\<,)3\>);D,9B2()0=)00,)41:=03).1+1+8?F+4))1)(,.9718)(,))19/**2?@(()(-((.80,)))(.)0+0(.(((()(/,**/3\*+2__2000+1+++_\*+/_1_/:(,)).-))…))  
@M00307:33:000000000-A78Y7:1:1101:18534:2095 2:N:0:82  
GCATCACTGCGGCGCCTGGCACGGAGTAAGCCGGCGATTATTAGTTAGTTACCGTAATTAACTTCACGAAAAAAAGGAGATTACAATCCTAAAAACTTCATTTTCCACGCGACGTAGCTGCATCAGTGTTTCCACCATGGAGAAATATACCCTACTGCTGCCACTAGTAGAAGTCTGTACGTTGTGTCACTTCCAGAGAGCAAGGTGCAACGACAAGGCCAGAAACCAGTCAATACCTTGGTACGCCAGTACACGACAAGAAACAAAAGAAAAACTAGACAGAAAGCGGACGCAAAAAAAA  
+

  
again many thanks

O. A.

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<div class="post-metadata">

**Author:** ![oalzahal](https://avatars.discourse-cdn.com/v4/letter/o/e9bcb4/32.png) [@oalzahal](https://forum.mothur.org/u/oalzahal)\
**Post date:** [March 30, 2015, 6:05pm UTC](https://forum.mothur.org/t/make-contigs-problem/2333/3 "2015-03-30T18:05:28Z")

</div>

Just to add more information. I overlooked something very important: this MiSeq run included both 16s and ITS for the same barcode. So basically i need to separate 16s and ITS within each file before proceeding. Does that mean i need to classify my files using a SILVA and the dumped sequences will be the ITS?

again thanks  
O. A.

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [March 30, 2015, 6:06pm UTC](https://forum.mothur.org/t/make-contigs-problem/2333/4 "2015-03-30T18:06:20Z")

</div>

E17\_S93\_L001\_R1\_001.fastq.gz - E17\_S93\_L001\_R2\_001.fastq.gz look like they are compressed. Mothur can’t read compressed files yet. It’s on our “todo” list, :). Can you try running the command with the E17\_S93\_L001\_R1\_001.fastq and E17\_S93\_L001\_R2\_001.fastq files?

---

<div class="post-metadata">

**Author:** ![oalzahal](https://avatars.discourse-cdn.com/v4/letter/o/e9bcb4/32.png) [@oalzahal](https://forum.mothur.org/u/oalzahal)\
**Post date:** [March 31, 2015, 2:58am UTC](https://forum.mothur.org/t/make-contigs-problem/2333/5 "2015-03-31T02:58:41Z")

</div>

many thanks it worked perfectly.

OA