Question: ustacks problem "Error: Unable to load data from"
gravatar for atikahfm15
7 days ago by
atikahfm150 wrote:

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/

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'.
snp next-gen genome • 49 views
ADD COMMENTlink modified 7 days ago by genomax89k • written 7 days ago by atikahfm150

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?

ADD REPLYlink modified 7 days ago • written 7 days ago by genomax89k

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

ADD REPLYlink written 6 days ago by atikahfm150
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