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Genome not found #20

@gherrgo

Description

@gherrgo

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!

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