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Oshlack/STRetch
coverage issues

One or more parallel stages aborted. The following messages were reported: --------------------------------- median_cov_region ( 11_L001 ) ---------------------------------- Command in stage median_cov_region ...
  • wangDanHua1
  • Opened 
    on Feb 22, 2024
  • #73

Oshlack/STRetch
Data analysis query

Hi Harriet, It s so nice of you to develop such an easy pipeline for exome data analysis. I m trying to analyse the data generated by STRetch I m not getting any significant p-value with my samples. Also ...
  • aakritis0212
  • 3
  • Opened 
    on Dec 20, 2022
  • #72

Oshlack/STRetch
Memory error

Hi, I am trying to run the exome pipeline. When I run it for 2 or 3 samples it runs correctly. But, when I run a command for about 20 samples I get the following error. This is the command: /data/NGS/Reanalysis-Package/STRetch-master/tools/bin/bpipe ...
  • ZohrehFattahi
  • 1
  • Opened 
    on Nov 7, 2022
  • #71

Oshlack/STRetch
Error while installation

Hi team, Hope you are all well. Recently we ve been trying to install STRetch into HPC system. But it continues to fail. Please see the error message below. [dleo2939@login3 ~]$ [dleo2939@login3 ~]$ ...
  • ichauchcc
  • 3
  • Opened 
    on Jun 1, 2022
  • #70

Oshlack/STRetch
ERROR with test run (hg19.STRdecoys.sorted.fasta.sa missing from test dataset)

Hi, I am trying to test run STRetch using the dataset at https://ndownloader.figshare.com/articles/4762489?private_link=cc7347f4637d9a7fe22d and running into the foll. error. (PFA). Basically, the tool ...
  • hchetia
  • 9
  • Opened 
    on Oct 28, 2021
  • #67

Oshlack/STRetch
difference between stretch and strling?

Could you elaborate on the differences between STRetch and STRling?
  • hchetia
  • 2
  • Opened 
    on Oct 28, 2021
  • #66

Oshlack/STRetch
TypeError: ("<lambda>() got an unexpected keyword argument 'result_type'", 'occurred at index chr1-10000-10468')

Hi, I m generating a pipeline using STRetch. When I run STRetch on fastqs, it fails in the last step (estimateSTR.py) with the following error. I searched the error and apparently this might be related ...
  • ghost
  • 4
  • Opened 
    on Apr 28, 2021
  • #65

Oshlack/STRetch
Errors in running

Hi, When I run ../tools/bin/bpipe run -p EXOME_TARGET= SCA8_region.bed ../pipelines/STRetch_exome_pipeline.groovy *.fastq.gz for testing, it return such errors: File /opt/STRetch/tools/miniconda/envs/STR/lib/python3.7/site-packages/Bio/Alphabet/init.py ...
  • biosciences
  • 2
  • Opened 
    on Apr 13, 2021
  • #64

Oshlack/STRetch
Error in running

Dear friend: I have successfully installed the software, but when I run the pipeline with the following command line: pipeline= /work/Software/STRetch-master bampath= /work//bam $pipeline/tools/bin/bpipe ...
  • baoyl818
  • 2
  • Opened 
    on Mar 27, 2021
  • #63

Oshlack/STRetch
exome_bam_pipeline cram support

Hi Harriet, I realized that the exome bam pipeline does not support cram files. I added the following two lines in STRetch_exome_bam_pipeline.groovy in my copy of STRetch and it is working with cram files. ...
  • bharatij
  • 2
  • Opened 
    on Apr 24, 2020
  • #60
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