# Weird Illumina MiSeq question, some help with import?

**URL:** https://forum.qiime2.org/t/weird-illumina-miseq-question-some-help-with-import/4329
**Category:** User Support
**Tags:** miseq, multiplexed, importing
**Created:** [May 28, 2018, 1:15pm UTC](https://forum.qiime2.org/t/weird-illumina-miseq-question-some-help-with-import/4329 "2018-05-28T13:15:41Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![ben](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ben/32/1790_2.png) [@ben](https://forum.qiime2.org/u/ben)
#### Post date: [May 28, 2018, 1:15pm UTC](https://forum.qiime2.org/t/weird-illumina-miseq-question-some-help-with-import/4329/1 "2018-05-28T13:15:41Z")

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Long time QIIME1 user, new QIIIME2, trying to understand how to import files. We have 3 files with multiple samples from the Illumina MiSeq sequencer. The Files are R1 - forward, R2 -barcodes, and R3 reverse. Multiple samples are included in these files.

 ![31%20PM](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/5/577e7921b682217a8538bd0399f23b2666a58ee9.png)

head of forward:

@MISEQ01:230:000000000-BJB48:1:1101:15468:1595 1:N:0:  
TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGTCTGTTAAGTCAGCGGTCAAAGCCCGGGGCTCAACCCCGGCCCGCCGTTGAAACTGGCAGTCTCGAGTTGGAGAGAAGTATGCGGAATGCGCGGTG  
+

> 1\>111111B1B110A0AE0FEG000AEG1FG11/AFE121A1/B/A//A//\>//\>/\>0FF221BB21@//?//111BBF//\<@BCEC1GGCC//BCC?@C?CC..DBGD0/\</.\<CD0/0.GE0/0//..CC:00CC.??@E0B.C-?E?  
> @MISEQ01:230:000000000-BJB48:1:1101:15537:1602 1:N:0:  
> CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

- 

AABCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFADFFFFFFAC  
@MISEQ01:230:000000000-BJB48:1:1101:18142:1620 1:N:0:  
TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTGCGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTACCGAACTAGAGTGTCGGAGAGGTAAGTGGAATTCCTAGT

I have been trying to import these files into QIIME2 and have been using qiime2 import using:

qiime tools import --type EMPPairedEndSequences --input-path ~/QIIME2\_2\_fastq --output-path ~/QIIME2\_2\_fastq/emp-paired-end-sequences.qza

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path ~/QIIME2\_2\_fastq --source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path ~/QIIME2\_2\_fastq/emp-paired-end-sequences.qza

Neither one works, both error respectively with:

Missing one or more files for EMPPairedEndDirFmt: 'barcodes.fastq.gz'

Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+\_.+\_L[0-9][0-9][0-9]\_R[12]\_001\.fastq\.gz'

I'm just wondering what the issue is? Should I demultiplex the samples in each of the runs? Should I create a manifest? Thank you.

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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [May 28, 2018, 1:27pm UTC](https://forum.qiime2.org/t/weird-illumina-miseq-question-some-help-with-import/4329/2 "2018-05-28T13:27:45Z")

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Hi @ben,

> [@ben](#):
>
> I’m just wondering what the issue is? Should I demultiplex the samples in each of the runs? Should I create a manifest? Thank you.

The issue is simply that the file names are incorrect for EMP format, even though the format is correct. Try this:

1. Make a new directory `raw-seqs`
2. run the following commands (you will probably need to change the filepaths):

```auto
cp lane1_NoIndex_R1_001.fastq raw-seqs/forward.fastq.gz
cp lane1_NoIndex_R1_002.fastq raw-seqs/barcodes.fastq.gz
cp lane1_NoIndex_R1_003.fastq raw-seqs/reverse.fastq.gz

```

1. Try importing again as EMP format

Let me know if that helps!

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<div class="post-metadata">

### Author: ![ben](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ben/32/1790_2.png) [@ben](https://forum.qiime2.org/u/ben)
#### Post date: [May 29, 2018, 2:26am UTC](https://forum.qiime2.org/t/weird-illumina-miseq-question-some-help-with-import/4329/3 "2018-05-29T02:26:23Z")

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Great, works like a charm - it's kind of funny because I tried this before and I think it had something to do with the way the files are formatted. I think that it was this issue, some formatting I did and voila, it works. Thank you again.

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [June 29, 2018, 8:40am UTC](https://forum.qiime2.org/t/weird-illumina-miseq-question-some-help-with-import/4329/4 "2018-06-29T08:40:50Z")

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