Entering edit mode
3.6 years ago
atikahfm15
•
0
Hi, everyone! I just started to learn STACKS for ddRAD Sequencing data. I have problem in ustacks stage.
my script:
./stacks-2.41/ustacks -m 3 -M 2 -i 1 -p 15 -o ./ustacks -f ./outputstacks/
AmphinM_49.1.fq.gz/AmphinM_49.1.fq
The result:
stacks parameters selected:
Input file: './outputstacks/AmphinM_49.1.fq.gz/AmphinM_49.1.fq'
Sample ID: 1
Min depth of coverage to create a stack (m): 3
Repeat removal algorithm: enabled
Max distance allowed between stacks (M): 2
Max distance allowed to align secondary reads: 4
Max number of stacks allowed per de novo locus: 3
Deleveraging algorithm: disabled
Gapped assembly: enabled
Minimum alignment length: 0.8
Model type: SNP
Alpha significance level for model: 0.05
Loading RAD-Tags...Error opening input file './outputstacks/AmphinM_49.1.fq.gz/AmphinM_49.1.fq'
Error: Unable to load data from './outputstacks/AmphinM_49.1.fq.gz/AmphinM_49.1.fq'.
Looks like you are using wrong input source
./outputstacks/AmphinM_49.1.fq.gz/AmphinM_49.1.fq
. Why would you make a directory with the gzipped file name and then have the actual data file inside it?actually that directory is the result from process_radtags. do you think I did wrong from the process_radtags step? my script for process_radtags is below:
./stacks-2.41/process_radtags -P -1 ./raw/Index_AAAAG_R1_002.fastq.gz -2 ./raw/Index_AAAAG_R2_002.fastq.gz -b Barcodes.csv -c -q -r -o ./outputstacks -E phred64 --renz_1 sbfI --renz_2 haeIII -i gzfastq