Hi! I am struggling trying to import my fastq data!
I am trying to import my data from one file of IONTORRENT data1.fastq.qz which contains 29 samples in it. It has the barcodes as well and is demultiplexed.
The file that is in a file named data in home (home/alejandra/data).
I am using this:
qiime tools import --type MultiplexedSingleEndBarcodeInSequence --input-path data --output-path multiplexed_seqs_single.qza
and I get this error:
There was a problem importing data:
Missing one or more files for MultiplexedPairedEndBarcodeInSequenceDirFmt: âforward.fastq.gzâ
I do not have this file, and I am lost, since afterwards I want to demux and trimm the file. I
Hi @Alejandra_Szabo!
Iâm not clear on what your data looks like, or what commands youâre running. Please help me understand your situation. Do you have:
one file only, called data1.fastq.gz
that one file contains the multiplexed data from all 29 of your samples
the sequences are single-ended
the barcodes are included in the sequences themselves? Or are they in a second, separate file?
Based on your post, it looks like you are trying to import your files as âMultiplexedSingleEndBarCodeInSequenceâ. The error you are getting would most likely occur if you were importing them as paired-end sequences instead.
Please copy/paste or share a screen capture of 1) the actual command you are running, and 2) its complete error message.
If your situation is as I described, your issue may be as simple as file naming. qiime tools import often requires that forward reads be in a file named forward.fastq.gz. If you had paired-end sequences, your reverse reads would be in a file called reverse.fastq.gz.
You might try renaming your file and re-running your import command. Take your time, make sure your command describes your data accurately, and read any error messages that might pop up closely. Theyâre usually pretty helpful.
Yes I have 1 file only called data1.fastq.gz. It contains multiplexed data for 29 samples, single ended, and the barcodes are included in the sequence themselves.
Now i am running the program again and I get this error!
Thatâs not a very clear error message, huh @Alejandra_Szabo? Sorry about that!
It looks like youâve misspelled the semantic type in your command. Compare:
Good: MultiplexedSingleEndBarcodeInSequence
Bad: MultiplexedSingledEndBarcodeInSequence
This error has popped up before on the forum (1, 2, 3), and I figured out how to solve it by searching for part of the error message: âcompatible directory formatâ. The forumâs search feature (at the top right hand corner) is often much faster than posting and waiting for a response, and Iâd encourage you to give it a shot next time you run into an issue like this.
Chris