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Genome not found #20
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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:
-- Genome Reference name: hg38.fa
-- 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
-- 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
-- Minimum read coverage: 1
-- Methimpute Intermediate : Enabled
-- Methimpute probability(Intermediate): constrained
-- Methimpute Fit reports: Disabled
-- Methimpute Enrichment plots: Disabled
-- Methimpute Full report: Disabled
-- Methimpute Context: All
Thanks!
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