# make.contigs error
**URL:** https://forum.mothur.org/t/make-contigs-error/2111
**Category:** Commands in mothur
**Created:** [November 4, 2014, 1:19am UTC](https://forum.mothur.org/t/make-contigs-error/2111 "2014-11-04T01:19:46Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@Locon833](https://forum.mothur.org/u/Locon833)
#### Post date: [November 4, 2014, 1:19am UTC](https://forum.mothur.org/t/make-contigs-error/2111/1 "2014-11-04T01:19:46Z")
Hi all,
I’m relatively new to working with sequence data generated from Illumina’s MiSeq. I have previously worked with the QIIME pipeline and wanted to try mothur.
I made a 3 column mapping file with the first column being the sample name, the second column being the forward fastq file name, and the third column being the reverse fastq file name.
I was working through the MiSeq SOP with mothur trying to join my paired end reads but am getting this error:
mothur \> make.contigs(file=/Users/laurenoconnell/Desktop/Thesis\_Data/mothur/stability.files^T)
Using 1 processors. Reading fastq data... [WARNING]: can't find PE12\_S1\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE12\_S1\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE15\_S2\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE15\_S2\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE17\_S3\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE17\_S3\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE12\_S4\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE18\_S4\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE20\_S5\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE20\_S5\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE21\_S6\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE21\_S6\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE23\_S7\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE23\_S7\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE26\_S8\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE26\_S8\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE27\_S9\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE27\_S9\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE92\_S10\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE29\_S10\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE30\_S11\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE30\_S11\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE32\_S12\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE32\_S12\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE33\_S13\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE33\_S13\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE35\_S14\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE35\_S14\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE36\_S15\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE36\_S15\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE38\_S16\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE38\_S16\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE39\_S17\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE39\_S17\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE41\_S18\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE41\_S18\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE42\_S19\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE42\_S19\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE44\_S20\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE44\_S20\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE45\_S21\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE45\_S21\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE47\_S22\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE47\_S22\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE48\_S23\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE48\_S23\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE50\_S24\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE50\_S24\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE51\_S25\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE51\_S25\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE52\_S26\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE52\_S26\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE55\_S27\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE55\_S27\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE56\_S28\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE56\_S28\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE61\_S29\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE61\_S29\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE62\_S30\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE62\_S30\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE64\_S31\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE64\_S31\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE66\_S32\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE66\_S32\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE67\_S33\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE67\_S33\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE68\_S34\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE68\_S34\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE71\_S35\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE71\_S35\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE73\_S36\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE73\_S36\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE74\_S37\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE74\_S37\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE79\_S38\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE79\_S38\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE82\_S39\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE82\_S39\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE83\_S40\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE83\_S40\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE85\_S41\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE85\_S41\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE86\_S42\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE86\_S42\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE87\_S43\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE87\_S43\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE89\_S44\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE89\_S44\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE90\_S45\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE90\_S45\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE92\_S46\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE92\_S46\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE93\_S47\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE93\_S47\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE95\_S48\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE95\_S48\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE96\_S49\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE96\_S49\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE98\_S50\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE98\_S50\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE99\_S51\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE99\_S51\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE101\_S52\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE101\_S52\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE102\_S53\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE102\_S53\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE104\_S54\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE104\_S54\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE105\_S55\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE105\_S55\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE107\_S56\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE107\_S56\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE108\_S57\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE108\_S57\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE110\_S58\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE110\_S58\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE111\_S59\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE111\_S59\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE113\_S60\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE113\_S60\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE114\_S61\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE114\_S61\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE119\_S62\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE119\_S62\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE120\_S63\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE120\_S63\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE122\_S64\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE122\_S64\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE123\_S65\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE123\_S65\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE125\_S66\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE125\_S66\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE126\_S67\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE126\_S67\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE128\_S68\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE128\_S68\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE129\_S69\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE129\_S69\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE131\_S70\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE131\_S70\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE132\_S71\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE132\_S71\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE134\_S72\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE134\_S72\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE136\_S73\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE136\_S73\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE138\_S74\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE138\_S74\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE140\_S75\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE140\_S75\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE141\_S76\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE141\_S76\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE143\_S77\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE143\_S77\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE144\_S78\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE144\_S78\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE146\_S79\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE146\_S79\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE147\_S80\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE147\_S80\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE149\_S81\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE149\_S81\_L001\_R2\_001.fastq, ignoring pair. [WARNING]: can't find PE150\_S82\_L001\_R1\_001.fastq, ignoring pair. [WARNING]: can't find PE150\_S82\_L001\_R2\_001.fastq, ignoring pair. Done. It took 0 secs to process 0 sequences.
The data that I am using is already demultiplexed and the adapters/barcodes have been trimmed off.
I was able to generate the fasta files doing each sample individually, but I wasn’t able to get them to work in a batch so that the fasta file was only 1 large combined file of all my samples, rather than individual files per sample.
If anyone has any suggestions on what I might be doing wrong and how to fix it I would greatly appreciate it!
Thanks,
Lauren
---
### Author:  [@qqcumber](https://forum.mothur.org/u/qqcumber)
#### Post date: [November 4, 2014, 1:52am UTC](https://forum.mothur.org/t/make-contigs-error/2111/2 "2014-11-04T01:52:55Z")
stability.files
---
### Author:  [@Locon833](https://forum.mothur.org/u/Locon833)
#### Post date: [November 4, 2014, 2:37am UTC](https://forum.mothur.org/t/make-contigs-error/2111/3 "2014-11-04T02:37:15Z")
That’s just what I named my mapping file.
---
### Author:  [@qqcumber](https://forum.mothur.org/u/qqcumber)
#### Post date: [November 4, 2014, 7:27am UTC](https://forum.mothur.org/t/make-contigs-error/2111/4 "2014-11-04T07:27:49Z")
oh sorry… I am newbie hehe
I tried make.contigs with the full directory to the stability file like you did and it didn’t work for me either.
But it worked for me when I set.dir first to the folder location where I keep the stability file and fastq files.
set.dir(input=, output=)
make.contigs(file=stability.files^T)
---
### Author:  [@Locon833](https://forum.mothur.org/u/Locon833)
#### Post date: [November 4, 2014, 7:59pm UTC](https://forum.mothur.org/t/make-contigs-error/2111/5 "2014-11-04T19:59:14Z")
Thanks for the suggestion. I changed my directory and was able to get everything to work properly!