Importing data troubles and qz files

[Rosanne_Arends]

Hi all,

I'm relatively new to QIIME2, however, I have run QIIME2 Galaxy before but on data that was already imported by someone else or with a tuorial. Im struggeling with importing this data:

@M01687:237:000000000-JDY6B:1:1101:18699:1975 1:N:0:ACTCGCTA+TCGACTAG
GCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCGTGAAATTATCAACTCTCCCTTTTCTATTGAGGTAGAGCTTGGACTTGGGGATTTGCAGGTCCTTGTGCCGGCTTCCCTTGAATGCATTAGCTGGAACCTGATTTGCAGCATATATGCGGTGTGATAATGTCTTCACTGCGTGGCTCAAGTCATCTGGCTTCAAACCGTCTTCGGAC
+
CCCCCGGGGGGGGGGGGGGGGGGGGGGGGG>,<FA,FGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGCFFGFFGGGGGGGCFCFGF9FEFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGFGGGGGGGGFGGGGFGFGGFFFFFGFFFFFFFFFFFBFFFF6?FFFF7

I have multiple files, containing these types of sequences. My guess, that it is demultiplexed single end sequences with quality. So far, so good. When selecting this, I get an error that has to do with the name.

Also, I need the files to be qz files. I have compressed one single file, with 7zip. However, it is not possible using this programme to zip multiple files to .qz. As I am not very confident in using Windows Powershell, I would like to use something with buttons.

Thanks!

[jphagen (Johannah Hagen)]

Hi @Rosanne_Arends,
Is ARA_S1_L1001_R1_001 the full name of the file? it looks like the regex is expecting .fastq.gz at the end and that could be why it is providing this error? Check the file names and let me know what you find.
-Hannah

[Rosanne_Arends]

Hi @jphagen,

Thanks for your reply. I have made some progress, however, im running into other problems now.

I figured out, that when using Galaxy, the use of an manifest is not possible. q2-galaxy file import troubles - #4 by colinbrislawn

So, I try using the casava format on my samples. This is an example of a file name: 2_D08_89711-D08_CGAGGCTGACTGCATA_L001_R2_001_KFPJJ.filt.fastq.qz

Im not sure if this is the right format. I'm now uploading using SequenceswithQuality, and pairing the collection as suggested by improving fastq import experience for Galaxy users - #2 by gregcaporaso, and then using the casava format. I get an error saying: Unexpected error importing data:
Missing one or more files for CasavaO
neEightSingleLanePerSampleDirFmt: '.+
_.+_L[0-9][0-9][0-9]_R[12]_001\.fast
q\.gz'

1. What method of uploading do I use with my paired samples, with names like: 2_D08_89711-D08_CGAGGCTGACTGCATA_L001_R2_001_KFPJJ.filt.fastq.qz
2. What method of importing do I use, and what type can I use when not using a manifest?
   3.What does this error code tell me?

Thanks in advance!

[Rosanne_Arends]

Tbh, I have been trying to upload my data in Galaxy for three days straight now, and I kinda feel like giving up. Would there be another way of uploading the data, using the comand line for example, and then later on use galaxy again?

[Rosanne_Arends]

Oops, sorry I didn't reply directly to your message!

This is a random name I picked from a forum elsewhere, to check if this was the name galaxy would be expecting.

So, the full name of the samples is 2_D08_89711-D08_CGAGGCTGACTGCATA_L001_R2_001_KFPJJ.filt.fastq.qz

Hope this helps!

[jphagen (Johannah Hagen)]

If you would like to give the command line a try you will need to install qiime2 on your machine by following the installing Qiime2 directions. Then the importing data tutorial will teach you how to import your data into qiime! I am here to help if you get stuck going this route.
-Hannah