This looks like an unzipping error? no issue when I run it using 1.39.5
mothur > make.contigs(file=project.file, processors=32)
Using 32 processors.
>>>>> Processing file pair fastq/11033CLWHITE.Remiszewski111033CLWHITE_S98_L001_R1_001.fastq.gz - fastq/11033CLWHITE.Remiszewski111033CLWHITE_S98_L001_R2_001.fastq.gz (files 1 of 25) <<<<<
Making contigs...
[WARNING]: reading ^_<8B>^H^D^@^@^@^@^@ expected a name with @ as a leading character, ignoring read.
[WARNING]: reading ^W9<B1>V^D@P<96><AA><E8><EE><AE><EA><CC>NE:E^P^@/2~G^D<EE><FD> expected a name with + as a leading character, ignoring.[WARNING]: names do not match. read ^_<8B>^H^D^@^@^@^@^@ for fasta and ^W9<B1>V^D@P<96><AA><E8><EE><AE><EA><CC>NE:E^P^@/2~G^D<EE><FD> for quality, ignoring.[WARNING]: Lengths do not match for sequence ^_<8B>^H^D^@^@^@^@^@. Read 38 characters for fasta and 13 characters for quality scores, ignoring read.[ERROR]: finding negative quality scores, do you have the right format selected? http://en.wikipedia.org/wiki/FASTQ_format#Encoding
[WARNING]: reading ^_<8B>^H^D^@^@^@^@^@ expected a name with @ as a leading character, ignoring read.
[WARNING]: reading F<CE>z<BF>%<B0>#*<A2><DA>Y<9D><DD>]<95>^U<8A><B0>-<B0>><AF>^?-<F5> expected a name with + as a leading character, ignoring.[WARNING]: names do not match. read ^_<8B>^H^D^@^@^@^@^@ for fasta and F<CE>z<BF>%<B0>#*<A2><DA>Y<9D><DD>]<95>^U<8A><B0>-<B0>><AF>^?-
<F5> for quality, ignoring.[WARNING]: Lengths do not match for sequence ^_<8B>^H^D^@^@^@^@^@. Read 37 characters for fasta and 12 characters for quality scores, ignoring read.[ERROR]: finding negative quality scores, do you have the right format selected? http://en.wikipedia.org/wiki/FASTQ_format#Encoding
^E2Tk@<B3><CC><CC>Z$<BE><99><E7>He^O<8E> is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
^R<E7>-ESC<CF>O;gL<BD><AA>M=S<C2>h<FB>fQN_<B3><D4>,j<AC>d##<C8>^S^V8<E8><B4>j<A3>^]^A<C5>nФXxCA<AE><F4>-<B8>X<95><F9><EE><88>B"<86><A4><C8>^_gc<AD><B9>0(-<EF><E6>P<B2><F0>^_2<D0>V^F
<80>fv<D4>@<F5>\<BB>0^OG5<D0><E5>t!^C]<BA><AF>^Ee<9F>^@<C8>{^B<C8>;<FC>^H_<E4><ED>n<A4><A3>
<F3><AA>{Z<B7><C1>kg<99><BD>(a<F1>l<9A><B0>M is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
^Z! is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
^]^F;<95>'^@^Y^E^B<88>c<CB>_ѓ<8F><B6>^R@̅>^_ is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.
6<A7>?^D@^@·^@<C2>s<DF>^G<90><BC>^_.Ө<E9>0<E3>^N^W<CA><D0>^Aa3<A7>fq<92>2<U+D7F1><BE>\
<U+0519><9E>^N<84>׀<95>50<BE>G<ED><97>^YȻYU*M)TY5)0I}t<93>^B<88> is in your forward fastq file and not in your reverse file, please remove it using the remove.seqs command before proceeding.