# make.sra scraps

**URL:** <https://forum.mothur.org/t/make-sra-scraps/2778>\
**Category:** Commands in mothur\
**Created:** [March 22, 2016, 6:10pm UTC](https://forum.mothur.org/t/make-sra-scraps/2778 "2016-03-22T18:10:37Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![akleight2](https://avatars.discourse-cdn.com/v4/letter/a/3e96dc/32.png) [@akleight2](https://forum.mothur.org/u/akleight2)\
**Post date:** [March 22, 2016, 6:10pm UTC](https://forum.mothur.org/t/make-sra-scraps/2778/1 "2016-03-22T18:10:37Z")

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I am finished with my analysis and need to archive my sequences. I am trying to use the make.sra command, but all of my sequences end up in scrap. I am hoping you might be able to help.

Here are some details:

Sequences: MiSeq paired 16s rRNA reads. One forward and one reverse fastq file.

Command: make.sra(file=paired\_fastq.file, oligos=barcodes.oligos, project=My.project, mimark=barcodes\_mimark.txt, pdiffs=1)

My paired\_fastq file looks like: forward\_S1\_R1.fastq reverse\_S1\_R2.fastq

My oligos file (same one used for make.contigs) looks like:  
Primer ATGCA… TGACG… V3V4  
Barcode GTTAC… TCAA… F1R1  
…etc

My mimark file (generated using get.mimarkspackage) looks like:  
F1R1.V3V4 aquatic metagenome …etc  
F1R2.V3V4 aquatic metagenome …etc  
…etc

No errors in output

Output File Names:  
paired\_fasta.scrap.forward.fastq  
paired\_fasta.scrap.reverse.fastq  
paired\_fasta.xml

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [March 24, 2016, 1:27pm UTC](https://forum.mothur.org/t/make-sra-scraps/2778/2 "2016-03-24T13:27:43Z")

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Could you send your input files and log file to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) so I can troubleshoot the issue for you?