make.sra command only generate submission.xml and submit.ready files

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ch3coch3
Posts: 31
Joined: Fri Oct 02, 2015 5:02 pm

make.sra command only generate submission.xml and submit.ready files

Post by ch3coch3 » Fri Oct 20, 2017 5:22 pm

Hi,

I've been running problems using make.sra command. It used to work great.

Now I have issues like make.sra only generates submission.xml and submit.ready files, without sequences for each samples.

I used raw sequencing data, make.sra (file=xx.file, project=xx.project, mimark=xx.txt)

my xx.file contains information

name_1 DMP04993_L1_name_1_1.fq.gz DMP04993_L1_name_1_2.fq.gz
name_2 DMP04993_L1_name_2_1.fq.gz DMP04993_L1_name_2_2.fq.gz

If I run make.sra(fastq=xx.fastq, oligos=xx.oligos, project=xx.project, mimark=xx.txt)

the fastq file is made by merging all the raw data(forward and reverse fastq) files together.

All the seqs end up in the scarp file.

How can I correct it, please?

Thanks you so much for your help

westcott
Posts: 1729
Joined: Thu Sep 03, 2009 7:47 am

Re: make.sra command only generate submission.xml and submit.ready files

Post by westcott » Mon Oct 23, 2017 10:31 am

With the following command and the setup of the xx.file, mothur should not create new files for each sample because the samples are already separated by sample.

mothur > make.sra (file=xx.file, project=xx.project, mimark=xx.txt)

my xx.file contains information

name_1 DMP04993_L1_name_1_1.fq.gz DMP04993_L1_name_1_2.fq.gz - sample name_1 forward and reverse files for upload.
name_2 DMP04993_L1_name_2_1.fq.gz DMP04993_L1_name_2_2.fq.gz - sample name_2 forward and reverse files for upload.

ch3coch3
Posts: 31
Joined: Fri Oct 02, 2015 5:02 pm

Re: make.sra command only generate submission.xml and submit.ready files

Post by ch3coch3 » Fri Oct 27, 2017 4:24 pm

westcott wrote:With the following command and the setup of the xx.file, mothur should not create new files for each sample because the samples are already separated by sample.

mothur > make.sra (file=xx.file, project=xx.project, mimark=xx.txt)

my xx.file contains information

name_1 DMP04993_L1_name_1_1.fq.gz DMP04993_L1_name_1_2.fq.gz - sample name_1 forward and reverse files for upload.
name_2 DMP04993_L1_name_2_1.fq.gz DMP04993_L1_name_2_2.fq.gz - sample name_2 forward and reverse files for upload.
Makes sense! Thank you so much!

Guilllg
Posts: 5
Joined: Tue Apr 26, 2016 5:08 am

Re: make.sra command only generate submission.xml and submit.ready files

Post by Guilllg » Mon Oct 08, 2018 3:56 pm

Any luck with your submission last year...?

I believe I'm currently experiencing the same problem. I.e. most of my seqs end up in the scrap file after running the make.sra command, either straight from the fastq with oligos file or using "file=xx.file".

Based on some of your other post (viewtopic.php?f=3&t=10681&p=20941&hilit=make.sra#p20941) I suspect you were trying to submit some of your old "Mr. DNA" fastq files, which is the case for me at the moment.

I followed your advice from the previous post, generating a merge fastq from: make.contigs(ffastq=xx.R1.fastq, rfastq=xx.R2.fastq), trim.seqs(), and make.fastq(fasta=current, qfile="current".qual).

Then using the merged fastq and an oligos file to generate sample/group specific fastq files.

Anyway, any tips would be great!
Thanks.

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