Qiime tools import: paired end file

Hi guys,

I am working with Illumina miseq paired end data.

While I was trying to import fastq files, I got this error: qiime2 qiime tools import is not fasqgzformat file: file is uncompressed.

This is the command I used to import my data:
qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path XXXXX --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path demux-paired-end.qza

As you can see in the picture below my files are fasqgzformat files..

What should I do with this problem? :frowning:

Thanks for your help in advance

hey,
As far as i can see, your files are not zipped to fastq.gz
you should zip them first

good luck

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Just to add to what Yos.Dos said;
use gzip filename to zip em up =D I dont know if straight up zipped files would work properly

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Hi,

I zipped the files but I’m still getting the same error :frowning:

here was a problem importing /media/sf_gvhd/gvhd_raw:

/media/sf_gvhd/gvhd_raw/._A100_S60_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:

File is uncompressed

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Hi @Jeongsu_Kim,

I think you might have some temporary files in your directory, usually these are created by text editors so that if they crash they don’t hurt your real file. Files that start with a dot are typically hidden, so you won’t see them normally.

Would you be able to run:

ls -al

on your directory of fastq files just so we can be sure that those files are not in fact important? I’m expecting them to mostly match a real file name and have a different modified-date than the rest of your data. Once we know that that is the case, we can safely just remove them and your import should work fine (I hope).

Yeah, there are some temporary files.
(qiime2-2018.8) [email protected]:/media/sf_gvhd/gvhd_raw$ ls -al
total 4508844
drwxrwx— 1 root vboxsf 196608 Oct 12 03:12 .
drwxrwx— 1 root vboxsf 4096 Oct 12 02:52 …
-rwxrwx— 1 root vboxsf 4096 Oct 11 03:57 ._A100_S60_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 4096 Oct 11 03:58 ._A100_S60_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 4096 Oct 11 03:56 ._A105_S7_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 4096 Oct 11 03:58 ._A105_S7_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 4096 Oct 11 03:59 ._A107_S57_L001_R1_001.fastq.gz
-rwxrwx— 1 root vboxsf 4096 Oct 11 03:54 ._A107_S57_L001_R2_001.fastq.gz
-rwxrwx— 1 root vboxsf 4096 Oct 11 04:00 ._A10_S3_L001_R1_001.fastq.gz

Thank you for your help!

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Hi @Jeongsu_Kim,

I figured out what those files are. They come from mounting an Apple filesystem in a different operating system. (They are called “resource forks” and contain file metadata).

It looks like you are running VirtualBox on OS X?

If so, I do want to mention it is much less of a hassle to use conda on OS X and install QIIME 2 natively. You won’t have that problem then.

Otherwise, if you have the host system running, you should be able to type dot_clean . in the same directory that you are mounting within VirtualBox. I would avoid deleting these directly for the moment, because they are a part of the filesystem (I believe), but I could be wrong there. If that doesn’t work we can move onto other things to try.


But I would recommend installing QIIME 2 directly on OS X if possible instead.

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