# make.contigs error
**URL:** https://forum.mothur.org/t/make-contigs-error/1221
**Category:** mothur bugs
**Created:** [February 6, 2013, 7:35pm UTC](https://forum.mothur.org/t/make-contigs-error/1221 "2013-02-06T19:35:29Z")
**Posts on this page:** 9
**Page:** 1
### Author:  [@acait](https://forum.mothur.org/u/acait)
#### Post date: [February 6, 2013, 7:35pm UTC](https://forum.mothur.org/t/make-contigs-error/1221/1 "2013-02-06T19:35:29Z")
I am unable to use the make.contigs command with my files.
mothur \> make.contigs(ffastq=CD34\_5\_1.fastq, rfastq=CD34\_5\_2.fastq)
Using 1 processors. Reading fastq data... [ERROR]: read HWI-ST1207:222:C166PACXX:5:1101:4344:2181 1:N:0:ACTT from CD34\_5\_1.fastq, but read HWI-ST1207:222:C166PACXX:5:1101:4344:2181 2:N:0:ACTT from CD34\_5\_2.fastq. Done.
mothur \> make.contigs(ffastq=CD34\_5\_1.fastq, rfastq=CD34\_5\_2.fastq, format=illumina)
format is not a valid parameter.
The valid parameters are: ffastq, rfastq, align, match, mismatch, gapopen, gapextend, threshold, processors, inputdir, and outputdir.
Using 1 processors.
[ERROR]: did not complete make.contigs.
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [February 6, 2013, 9:28pm UTC](https://forum.mothur.org/t/make-contigs-error/1221/2 "2013-02-06T21:28:00Z")
What version of mothur are you using?
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### Author:  [@acait](https://forum.mothur.org/u/acait)
#### Post date: [February 6, 2013, 10:46pm UTC](https://forum.mothur.org/t/make-contigs-error/1221/3 "2013-02-06T22:46:11Z")
The same error occurs with v.1.27.0 and v.1.29.1
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [February 8, 2013, 2:15pm UTC](https://forum.mothur.org/t/make-contigs-error/1221/4 "2013-02-08T14:15:10Z")
Could you send your fastq files to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com)?
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### Author:  [@poroyko](https://forum.mothur.org/u/poroyko)
#### Post date: [March 30, 2013, 4:29am UTC](https://forum.mothur.org/t/make-contigs-error/1221/5 "2013-03-30T04:29:28Z")
I have almost similar problem with make.contigs
I am running v.1.29.2 on Win7 64 bit machine. Problem appears with MiSeq SOP data set.
This is the start:
mothur \> make.contigs(file=stability.files1.txt, processors=8)
Using 8 processors.
Reading fastq data…
[WARNING]: can’t find F3D0, ignoring pair.
[WARNING]: can’t find F3D141, ignoring pair.
…
Here it continues:
[WARNING]: For sequence M00967:43:000000000-A3JHG:1:1101:11786:2744 I read a sequence of length 251 from F3D141\_S207\_L001\_R1\_001.fastq, but read a sequence of length 250 from F3D141\_S207\_L001\_R2\_001.fastq, ignoring.
[WARNING]: For sequence M00967:43:000000000-A3JHG:1:1101:11786:2744 I read 251 quality scores from F3D141\_S207\_L001\_R1\_001.fastq, but read 250 quality scores from F3D141\_S207\_L001\_R2\_001.fastq, ignoring.
…
At the end of run program created no “group” output.
Program has processed only 10 out of 21 files from the SOP data set. Program uses only each first file and skips second file and so on. Please see log file record:
…
It took 113 secs to process 52299 sequences.
Output File Names:
stability.files1.trim.contigs.fasta
stability.files1.trim.contigs.qual
stability.files1.contigs.mismatch
stability.files1.scrap.contigs.fasta
stability.files1.scrap.contigs.qual
F3D141\_S207\_L001\_R1\_001.trim.contigs.fasta
F3D141\_S207\_L001\_R1\_001.scrap.contigs.fasta
F3D141\_S207\_L001\_R1\_001.trim.contigs.qual
F3D141\_S207\_L001\_R1\_001.scrap.contigs.qual
F3D141\_S207\_L001\_R1\_001.contigs.mismatch
F3D143\_S209\_L001\_R1\_001.trim.contigs.fasta
F3D143\_S209\_L001\_R1\_001.scrap.contigs.fasta
F3D143\_S209\_L001\_R1\_001.trim.contigs.qual
F3D143\_S209\_L001\_R1\_001.scrap.contigs.qual
F3D143\_S209\_L001\_R1\_001.contigs.mismatch
F3D145\_S211\_L001\_R1\_001.trim.contigs.fasta
F3D145\_S211\_L001\_R1\_001.scrap.contigs.fasta
F3D145\_S211\_L001\_R1\_001.trim.contigs.qual
F3D145\_S211\_L001\_R1\_001.scrap.contigs.qual
F3D145\_S211\_L001\_R1\_001.contigs.mismatch
F3D147\_S213\_L001\_R1\_001.trim.contigs.fasta
F3D147\_S213\_L001\_R1\_001.scrap.contigs.fasta
F3D147\_S213\_L001\_R1\_001.trim.contigs.qual
F3D147\_S213\_L001\_R1\_001.scrap.contigs.qual
F3D147\_S213\_L001\_R1\_001.contigs.mismatch
F3D149\_S215\_L001\_R1\_001.trim.contigs.fasta
F3D149\_S215\_L001\_R1\_001.scrap.contigs.fasta
F3D149\_S215\_L001\_R1\_001.trim.contigs.qual
F3D149\_S215\_L001\_R1\_001.scrap.contigs.qual
F3D149\_S215\_L001\_R1\_001.contigs.mismatch
F3D1\_S189\_L001\_R1\_001.trim.contigs.fasta
F3D1\_S189\_L001\_R1\_001.scrap.contigs.fasta
F3D1\_S189\_L001\_R1\_001.trim.contigs.qual
F3D1\_S189\_L001\_R1\_001.scrap.contigs.qual
F3D1\_S189\_L001\_R1\_001.contigs.mismatch
F3D3\_S191\_L001\_R1\_001.trim.contigs.fasta
F3D3\_S191\_L001\_R1\_001.scrap.contigs.fasta
F3D3\_S191\_L001\_R1\_001.trim.contigs.qual
F3D3\_S191\_L001\_R1\_001.scrap.contigs.qual
F3D3\_S191\_L001\_R1\_001.contigs.mismatch
F3D6\_S194\_L001\_R1\_001.trim.contigs.fasta
F3D6\_S194\_L001\_R1\_001.scrap.contigs.fasta
F3D6\_S194\_L001\_R1\_001.trim.contigs.qual
F3D6\_S194\_L001\_R1\_001.scrap.contigs.qual
F3D6\_S194\_L001\_R1\_001.contigs.mismatch
F3D8\_S196\_L001\_R1\_001.trim.contigs.fasta
F3D8\_S196\_L001\_R1\_001.scrap.contigs.fasta
F3D8\_S196\_L001\_R1\_001.trim.contigs.qual
F3D8\_S196\_L001\_R1\_001.scrap.contigs.qual
F3D8\_S196\_L001\_R1\_001.contigs.mismatch
Mock\_S280\_L001\_R1\_001.trim.contigs.fasta
Mock\_S280\_L001\_R1\_001.scrap.contigs.fasta
Mock\_S280\_L001\_R1\_001.trim.contigs.qual
Mock\_S280\_L001\_R1\_001.scrap.contigs.qual
Mock\_S280\_L001\_R1\_001.contigs.mismatch
The “real MiSeq files” were behaving in the similar way. Program ignores grouping information and uses only half of the files.
Sincerely yours,
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### Author:  [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [March 30, 2013, 11:37am UTC](https://forum.mothur.org/t/make-contigs-error/1221/6 "2013-03-30T11:37:03Z")
Ahem… You aren’t supposed to know about the MiSeq\_SOP page yet! This will only work with the version that we will release on Monday.
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### Author:  [@poroyko](https://forum.mothur.org/u/poroyko)
#### Post date: [March 30, 2013, 9:58pm UTC](https://forum.mothur.org/t/make-contigs-error/1221/7 "2013-03-30T21:58:23Z")
Ups… Until Monday then. I am looking forward to see the release.
---
### Author:  [@bletzmc](https://forum.mothur.org/u/bletzmc)
#### Post date: [January 26, 2015, 3:53pm UTC](https://forum.mothur.org/t/make-contigs-error/1221/8 "2015-01-26T15:53:30Z")
I am having a problem with the make.contigs command in mothur. I am a newbie to using this pipeline so it is likely something simple but I just have no clue 🙂
When I run the command:
mothur \> make.contigs(file=/Users/Molly-Mac/Desktop/Next\_gen\_data\_analysis/Test\_Germany/amphibian\_Test.files)
I get the following:
Using 2 processors. Reading fastq data... [WARNING]: can't find AltB2\_S407\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find AltB2\_S407\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find AltB3\_S408\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find AltB3\_S408\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find AltB4\_S409\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find AltB4\_S409\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find AltB5\_S410\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find AltB5\_S410\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find AltB6\_S411\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find AltB6\_S411\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find AltB7\_S412\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find AltB7\_S412\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find AltB8\_S413\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find AltB8\_S413\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find AltB9\_S414\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find AltB9\_S414\_L001\_R2\_001.fastq, ignoring pair. Done. It took 0 secs to process 0 sequences.
## Output File Names:
The files are housed in the same folder as the inputed file. I have also tried running this with the example data set form the Wiki page, using the stability.files as the input and I get the same error.
Can anyone direct me on how to solve this and get it to “find” the files?
Thanks!
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### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [January 27, 2015, 3:33pm UTC](https://forum.mothur.org/t/make-contigs-error/1221/9 "2015-01-27T15:33:03Z")
[http://www.mothur.org/wiki/Frequently\_asked\_questions#Mothur\_can.27t\_find\_my\_input\_files](http://www.mothur.org/wiki/Frequently_asked_questions#Mothur_can.27t_find_my_input_files)