Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Genome not found #20

Open
gherrgo opened this issue Dec 16, 2022 · 0 comments
Open

Genome not found #20

gherrgo opened this issue Dec 16, 2022 · 0 comments

Comments

@gherrgo
Copy link

gherrgo commented Dec 16, 2022

Hello,

I have properly formatted all of the parameters necessary for running the program (see below), but somehow am still getting the error message:
./src/bash/preparing.sh: 5: ./src/bash/tmp.conf: genome/: not found

Any ideas on why this is happening? My ref genome is hg38 formatted as a .fa file from UCSC.

============================================================
Here is summary of configuration parameters:

  • RAW files location: /media/grayson/data1/grayson/WGBS
  • Number and Size of the data-set: 64 Files and Total size: 566.0 Gigabyte
  • The directory of results: /
  • Genome type: Human
  • Genome folder location: /media/grayson/data1/grayson/Reference genome/
    -- Genome Reference name: hg38.fa
  • Paired End: Enabled
  • Trimmomatic location: /bin/Trimmomatic-Src-0.39/trimmomatic-0.39
    -- JAVA path: /usr/bin/java
    -- ILLUMINACLIP: /bin/Trimmomatic-Src-0.39/trimmomatic-0.39/adapters/TruSeq3-PE.fa:1:30:9
    -- LEADING: 20
    -- TRAILING: 20
    -- SLIDINGWINDOW: 4:20
    -- MINLEN: 36
    -- Number of Threads: 8
  • QC-Fastq path: /bin/fastqc_v0.11.8/FastQC/fastqc
  • Bismark parameters: /bin/Bismark-0.19.1
    -- scBS-Seq (--pbat)? Disabled
    -- Nucleotide status: false
    -- Number of Parallel: 8 Threads.
    -- Buffer size: 40 Gigabyte.
    -- Samtools Path: /bin/samtools
    -- Bedtools Path: /usr/bin/bedtools
    -- Intermediate for MethExtractor: Disabled
  • Methylation extraction parameters( Only for quick run)
    -- Minimum read coverage: 1
  • Methimpute Part:
    -- Methimpute Intermediate : Enabled
    -- Methimpute probability(Intermediate): constrained
    -- Methimpute Fit reports: Disabled
    -- Methimpute Enrichment plots: Disabled
    -- Methimpute Full report: Disabled
    -- Methimpute Context: All
  • Parallel mode is: Disabled
  • E-mail notification: Disabled
  • MethylStar version: 1.1.1
    Thanks!
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant