MiSeq SOP make.contigs w/ group count

Commands in mothur
1

Hi,

I’m new to mothur and trying to become familiar with analyzing data. I recently downloaded the latest version (v.1.33.2). With the test data on the Miseq SOP wiki website, I am able download (wget), combine (make.contigs), and summarize (summary.seqs) my data. It’s wasn’t until I got to the screen.seqs step

(screen.seqs(fasta=stability.trim.contigs.fasta, group=stability.contigs.groups, maxambig=0, maxlength=275)

that I realized that I my make.contigs output does not contain a “stability.contigs.groups” file. Was this file suppose to be part of my make.contigs output? Or was I suppose to make this file?

Not having the stability.contigs.groups file is preventing me from proceeding with the tutorial and later opening my own Miseq data set. I’ve extensively searched the forum and online and haven’t been able to solve this problem. Any help would be greatly appreciated!

Currently, my make.contigs(file=stability.files, processors=1) output is:
stability.trim.contigs.fasta
stability.trim.contigs.qual
stability.contigs.mismatch
stability.scrap.contigs.fasta
stability.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

2

Hmmm, looks weird. Can you possibly start over and see what the files look like after make.contigs? When I do this my directory looks like… The ones with “****” were generated by make.contigs

F3D0_S188_L001_R1_001.fastq
F3D0_S188_L001_R2_001.fastq
F3D141_S207_L001_R1_001.fastq
F3D141_S207_L001_R2_001.fastq
F3D142_S208_L001_R1_001.fastq
F3D142_S208_L001_R2_001.fastq
F3D143_S209_L001_R1_001.fastq
F3D143_S209_L001_R2_001.fastq
F3D144_S210_L001_R1_001.fastq
F3D144_S210_L001_R2_001.fastq
F3D145_S211_L001_R1_001.fastq
F3D145_S211_L001_R2_001.fastq
F3D146_S212_L001_R1_001.fastq
F3D146_S212_L001_R2_001.fastq
F3D147_S213_L001_R1_001.fastq
F3D147_S213_L001_R2_001.fastq
F3D148_S214_L001_R1_001.fastq
F3D148_S214_L001_R2_001.fastq
F3D149_S215_L001_R1_001.fastq
F3D149_S215_L001_R2_001.fastq
F3D150_S216_L001_R1_001.fastq
F3D150_S216_L001_R2_001.fastq
F3D1_S189_L001_R1_001.fastq
F3D1_S189_L001_R2_001.fastq
F3D2_S190_L001_R1_001.fastq
F3D2_S190_L001_R2_001.fastq
F3D3_S191_L001_R1_001.fastq
F3D3_S191_L001_R2_001.fastq
F3D5_S193_L001_R1_001.fastq
F3D5_S193_L001_R2_001.fastq
F3D6_S194_L001_R1_001.fastq
F3D6_S194_L001_R2_001.fastq
F3D7_S195_L001_R1_001.fastq
F3D7_S195_L001_R2_001.fastq
F3D8_S196_L001_R1_001.fastq
F3D8_S196_L001_R2_001.fastq
F3D9_S197_L001_R1_001.fastq
F3D9_S197_L001_R2_001.fastq
HMP_MOCK.v35.fasta
Mock_S280_L001_R1_001.fastq
Mock_S280_L001_R2_001.fastq
mothur.1394625707.logfile
mothur.1394626270.logfile
stability.batch
stability.contigs.groups ***
stability.contigs.report ***
stability.files
stability.scrap.contigs.fasta ***
stability.trim.contigs.fasta ***
3

Thanks Pat! It worked!

I got the correct results once I downloaded the latest version of mothur (v. 1.33.2) and started over. Initially, I stated that I was using the latest version but I soon realized that I was using an older version (v. 1.29.1). Maybe that was the problem.

Either way, I was able to successfully complete the Miseq SOP analysis!