Hello folks,
Super new to Qiime. Please be patient with me.
I recently installed the new Qime2 release using docker in my Windows 10 Pro computer. I have 10 paired end read samples (total 20 files) that I've used in the past in my Mac and a previous release of Qiime without any issues. I'm trying to import this same data in this new docker setup. I start qiime in docker like this:
PS C:\Users\chiok\desktop\EHDP_Qiime2_KC_2018> docker run -t -i -v ${pwd}:/data qiime2/core:2018.11 bash
(qiime2-2018.11) root@42a728bd3d91:/data# ls
EHDP 2018 metadata.tsv fasta pe-64-manifest.txt
**EHDP_Qiime2_KC_2018 is my current working directory. The metadata file (which needs renaming probably) is the first file on the left. The second "fasta" is the folder where my fasta.gz are. The third file is my manifest pe-64-manifest.txt (1.7 KB). I first check that my fastas are there, like this:
(qiime2-2018.11) root@42a728bd3d91:/data# cd fasta
(qiime2-2018.11) root@42a728bd3d91:/data/fasta# ls
EHDP_10_R1.fastq.gz EHDP_15_R1.fastq.gz EHDP_19_R1.fastq.gz EHDP_3_R1.fastq.gz EHDP_6_R1.fastq.gz
EHDP_10_R2.fastq.gz EHDP_15_R2.fastq.gz EHDP_19_R2.fastq.gz EHDP_3_R2.fastq.gz EHDP_6_R2.fastq.gz
EHDP_13_R1.fastq.gz EHDP_17_R1.fastq.gz EHDP_1_R1.fastq.gz EHDP_4_R1.fastq.gz EHDP_7_R1.fastq.gz
EHDP_13_R2.fastq.gz EHDP_17_R2.fastq.gz EHDP_1_R2.fastq.gz EHDP_4_R2.fastq.gz EHDP_7_R2.fastq.gz
**They're all there. So I go back to my working directory. I used this command to import my data:
(qiime2-2018.11) root@42a728bd3d91:/data# qiime tools import \
> --type 'SampleData[PairedEndSequencesWithQuality]' \
> --input-path pe-64-manifest.txt \
> --output-path paired-end-demux.qza \
> --input-format PairedEndFastqManifestPhred33
**And I get the following error:
There was a problem importing pe-64-manifest.txt:
pe-64-manifest.txt is not a(n) PairedEndFastqManifestPhred33 file:
File referenced on line 2 could not be found (C:\Users\chiok\Desktop\EHDP_Qiime2_KC_2018\fasta\EHDP_1_R1.fastq.gz).
**I've been canvassing the Forum trying to find answers. I checked the files were there and I am executing the command in my working directory, outside the folder that contains my fastas. Is it because of the \ symbols in the file paths specified in the manifest file? I tried changing to / without any luck. I also tried removing the C: from file paths in my manifest. Is it Docker? I am going insane trying to figure out what I'm missing.
Any help is greatly appreciated.
Thank you,
K