# Error message on make.contigs in 1.43.0

**URL:** <https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235>\
**Category:** mothur bugs\
**Created:** [November 26, 2019, 9:48pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235 "2019-11-26T21:48:49Z")\
**Posts on this page:** 10\
**Page:** 1

<div class="post-metadata">

**Author:** ![Kendra](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/kendra/32/112_2.png) [@Kendra](https://forum.mothur.org/u/Kendra)\
**Post date:** [November 26, 2019, 9:48pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/1 "2019-11-26T21:48:49Z")

</div>

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.
```

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<div class="post-metadata">

**Author:** ![Kendra](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/kendra/32/112_2.png) [@Kendra](https://forum.mothur.org/u/Kendra)\
**Post date:** [December 4, 2019, 7:12pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/2 "2019-12-04T19:12:50Z")

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Pat or Sarah? Ideas on what might be broken in make.contigs on .gz files with 1.43.0? I’m running this on a cluster, do I need to ask for something other than mothur to be updated to run 1.43.0?

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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:** [December 5, 2019, 1:23pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/3 "2019-12-05T13:23:10Z")

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I am not seeing that issue with our test files. Could you send the file pair and your logfile to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) so I can take a closer look?

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<div class="post-metadata">

**Author:** ![Kendra](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/kendra/32/112_2.png) [@Kendra](https://forum.mothur.org/u/Kendra)\
**Post date:** [December 5, 2019, 4:13pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/4 "2019-12-05T16:13:30Z")

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file pair? I’ll send those fastq and the logs.

Someone else working on the same server is having the same problem, so it’s completely possible it has to do with how our server is set up.

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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:** [December 6, 2019, 4:21pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/5 "2019-12-06T16:21:25Z")

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Hi Kendra,

Thanks for sending your files. I ran them with our prebuilt version without issue. I noticed in your logfile of 1.43.0 that mothur did not indicate the boost library was compiled with your mothur executable. We added this output in 1.43.0, and it should look like:

…

**Using ReadLine,Boost,HDF5,GSL**

mothur v.1.43.0

Last updated: 12/06/2019

by

Patrick D. Schloss

…

Your logfile indicates mothur was only built with the readline library and not the boost library which is used to read the gz files.

**Using ReadLine**

mothur v.1.43.0

Last updated: 12/05/2019

by

Patrick D. Schloss

I suspect that there is something not quite right with the makefile options when you built. Is USEBOOST ?= yes set?

Kind regards,

Sarah

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<div class="post-metadata">

**Author:** ![Kendra](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/kendra/32/112_2.png) [@Kendra](https://forum.mothur.org/u/Kendra)\
**Post date:** [December 6, 2019, 10:00pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/6 "2019-12-06T22:00:58Z")

</div>

Thanks Sarah, that fixed the problem.

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<div class="post-metadata">

**Author:** ![Kendra](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/kendra/32/112_2.png) [@Kendra](https://forum.mothur.org/u/Kendra)\
**Post date:** [December 6, 2019, 10:02pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/7 "2019-12-06T22:02:40Z")

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Mine says

```
Linux version

Using ReadLine,Boost
mothur v.1.43.0
Last updated: 12/06/2019
by
Patrick D. Schloss

```

What won’t work if HDF5 and GSL aren’t turned on?

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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:** [December 9, 2019, 1:03pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/8 "2019-12-09T13:03:35Z")

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The HDF5 library is used by the biom.info command to read biom files in HDF5 format.

The GSL library is used by the estimator.single command, [https://mothur.org/wiki/Estimator.single](https://mothur.org/wiki/Estimator.single).

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<div class="post-metadata">

**Author:** ![Kendra](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/kendra/32/112_2.png) [@Kendra](https://forum.mothur.org/u/Kendra)\
**Post date:** [December 11, 2019, 7:25pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/9 "2019-12-11T19:25:51Z")

</div>

thanks! I don’t use those, but I’ll try to tuck this in the back of my mind if someone asks me about them

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<div class="post-metadata">

**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [December 21, 2019, 7:30pm UTC](https://forum.mothur.org/t/error-message-on-make-contigs-in-1-43-0/20235/10 "2019-12-21T19:30:15Z")

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