Stability.contigs.count_table

1

hello
I am running mothur
But after running
mothur > summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table)
it is giving a error
Unable to open stability.contigs.count_table. Trying mothur’s executable directory stability.contigs.count_table.

There is no file named stability.contigs.count_table. Help me what I need to change.

2

Hi,

Can you post the previous commands you’ve run?

Thanks
Pat

3

Below was my previous step code-
#!/bin/bash
source /apps/profiles/modules_asax.sh.dyn
module load mothur/1.48.0
mothur “#make.contigs(file=stability.files, processors=16)”

5

So till now what I did
Step1-
#!/bin/bash
source /apps/profiles/modules_asax.sh.dyn
module load mothur/1.48.0
mothur “#make.file(inputdir=., type=fastq, prefix=stability)”

this created the file stability.files

Step2-
#!/bin/bash
source /apps/profiles/modules_asax.sh.dyn
module load mothur/1.48.0
mothur “#make.contigs(file=stability.files, processors=16)”

But this step didn’t create all the files such as stability.contigs.count_table
all other files are made

Because of this I am not able to proceed in the steps.
Kindly help with the issue.

6

Can you post the contents of stability.files?

Pat