Re: [stacks] Process_radtags unable to allocate Seq object error

[Catchen, Julian]

Hi Carolyn,

 

This error message means that process_radtags does not understand the file format you supplied. Are these files:

 

NS.1834.004.D705---B504.Vander_1_R1.fastq.gz

And

NS.1834.004.D705---B504.Vander_1_R2.fastq.gz

 

actually compressed? Or are they plain text files that have had the “.gz” suffix manually added?

 

Your screenshots imply the latter, but I’m not sure what program you are using to show them. You can explicitly specify the input file format using “-i” as 'fastq' or 'gzfastq' (gzipped fastq).

 

julian

 

 

From: stacks...@googlegroups.com <stacks...@googlegroups.com> on behalf of Carolyn Vandervelde <carolynva...@gmail.com>
Date: Friday, April 15, 2022 at 9:39 PM
To: Stacks <stacks...@googlegroups.com>
Subject: [stacks] Process_radtags unable to allocate Seq object error

Hello,

I am incredibly new to bioinformatics and seem to be getting stuck at the first step even having goe over the stacks manual and combing through other threads in this group. 

I have paired-end ddRAD (enzymes PstI and MspI) data run on the NovaSeq 6000 platform at Genome Quebec. I think my data is demultiplexed for the lanes with inline barcodes on the R1 file. I have attached the head of my R1 and R2 files and my barcode files. 

I ran the following code on stacks 2.60:

process_radtags -i fastq.gz -P -1 ./raw/NS.1834.004.D705---B504.Vander_1_R1.fastq.gz -2 ./raw/NS.1834.004.D705---B504.Vander_1_R2.fastq.gz -b ./info/Vander_1_Barcode.txt -o ./cleaned/ -c -q -r --inline_null --renz_1 pstI --renz_2 mspI

And I got this error:

Processing paired-end data.

Using Phred+33 encoding for quality scores.

Found 1 paired input file(s).

Searching for single-end, inlined barcodes.

Loaded 384 barcodes (0-8bp).

Will attempt to recover barcodes with at most 1 mismatches.

Processing file 1 of 1 [NS.1834.004.D705---B504.Vander_1_R1.fastq.gz]

  Reading data from:

  ./raw/NS.1834.004.D705---B504.Vander_1_R1.fastq.gz and

  ./raw/NS.1834.004.D705---B504.Vander_1_R2.fastq.gz

Attempting to read first pair of input records, unable to allocate Seq object (Was the correct input type specified?).

 

Perhaps Im wrong about the barcodes on the R1 and R2 files? Honestly Im just very lost and any insight would be extremely helpful.

 

Thank you in advanced

Carolyn

 

[Chuan Lei]

Hi all, just wondering is there any solution for this issue as I am experencing the same issue here. 

Cheers 

[Diana Elizabeth]

intenta esto:

ejemplo:

 process_radtags -P -p ./Raw/Plate1 -o ./samples/Plate1/ -b ./barcodes/plate1/Barcode.txt -e apeKI -r -c -q -D

 donde -P es pair-end 

            -p en Raw estan los archivos .fastq de R1 y R2

Espero AYUDE,

DIANA

--
Stacks website: http://catchenlab.life.illinois.edu/stacks/
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