# Manifest importing issue

**URL:** <https://forum.qiime2.org/t/manifest-importing-issue/7051>\
**Category:** Technical Support\
**Tags:** import, fastq-manifest\
**Created:** [November 17, 2018, 2:11pm UTC](https://forum.qiime2.org/t/manifest-importing-issue/7051 "2018-11-17T14:11:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Xio\_Lee](https://forum.qiime2.org/user_avatar/forum.qiime2.org/xio_lee/32/4643_2.png) [@Xio\_Lee](https://forum.qiime2.org/u/Xio_Lee)\
**Post date:** [November 17, 2018, 2:11pm UTC](https://forum.qiime2.org/t/manifest-importing-issue/7051/1 "2018-11-17T14:11:18Z")

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Hi,

I encountered this issue when importing the manifest file in jupyter notebook:

code:  
!qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]'   
--input-path 16SF@16SR\_manifest.csv   
--output-path qiime2\_pipeline/16s/micro\_16s\_sequences.qza   
--input-format PairedEndFastqManifestPhred33

```
There was a problem importing 16SF@16SR_manifest.csv:

  /tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-413rrait is not a(n) SingleLanePerSamplePairedEndFastqDirFmt:

  Contains a subdirectory: O148

```

I have a folder contains 16s reads and ITS reads together. I created a qiime2\_pipeline folder with 2 sub directories for storing the output file. 2 manifest files for each 16s and ITS. They look as below.

[16SF@16SR\_manifest.csv](https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/flex002/uploads/qiime21/original/2X/e/e3cf4c02b73c90aba6cd25f53409bf126abaa8fd.csv) (21.4 KB)

not sure why the format is not correct and why it says containing a subdirectory. Maybe I should separate the reads into two folders?

Many Thanks.

---

<div class="post-metadata">

**Author:** ![Xio\_Lee](https://forum.qiime2.org/user_avatar/forum.qiime2.org/xio_lee/32/4643_2.png) [@Xio\_Lee](https://forum.qiime2.org/u/Xio_Lee)\
**Post date:** [November 17, 2018, 8:04pm UTC](https://forum.qiime2.org/t/manifest-importing-issue/7051/2 "2018-11-17T20:04:48Z")

</div>

I figured out. The sample id can not contain "/", so I changed it to underscore. It is working now.

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<div class="post-metadata">

**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:** [December 19, 2018, 2:18am UTC](https://forum.qiime2.org/t/manifest-importing-issue/7051/3 "2018-12-19T02:18:40Z")

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