make.contigs problem

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.

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,,225***<::2;,***++30:7C)2;<6++,2:32/000++292:5)+2+0.*+(/02*+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<>164/,4,4,<<9@8++212+<3:00+++9752+2+3+2+.+.++2+20*2180A+2*)17***:slight_smile://)/*(+.))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,+,+,333**,))))/)(0;**,()110()1*,8,-5:8)))).2/14().-()((.202/2((.-((-))0–((-408:(((((-((,2*******/11/2155*/,((,(,(,((((-
@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:/+/222/21/1-((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.

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.

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?

many thanks it worked perfectly.

OA