I am trying to analyze my RNAseq reads for defective genomes and I use this program (http://www.di-tector.cyame.eu/) that is suggested by Beauclair et al (https://pubmed.ncbi.nlm.nih.gov/30012569/) for that.
After downloading a .py script and running it with the following command:
sudo python3 DI-tector_06.py /mnt/e/nastya/SLX066-02/sequence.fasta /mnt/e/nastya/SLX066-02/B-dVMV-RIG-1/B-dVMV-RIG-1_ACAGTG_L008_R1_001.rc.fastq.gz
It says at the beginning that
================================= Program: DI-tector Version: 0.6 - Last modified 25/05/2018 ================================= Requirement: (must be in your $PATH) -bwa -samtools Optional: (must be in your $PATH) -bedtools
I have tried to install bwa using:
sudo apt-get update -y sudo apt-get install -y bwa
and samtools using
cd /usr/local/bin sudo wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 sudo tar -vxjf samtools-1.9.tar.bz2 cd samtools-1.9 sudo make
I did not get exactly what does that mean: (must be in your $PATH) but I have searched here and there and discovered that it might mean
The program starts and, after some calculations it gives me the following error:
Input file: /mnt/e/nastya/SLX066-02/B-dVMV-RIG-1/B-dVMV-RIG-1_ACAGTG_L008_R1_001.rc.fastq.gz Host reference: None Virus reference: /mnt/e/nastya/SLX066-02/sequence.fasta Remove segment: < 15 nt Remove reads with MAPQ: < 25 Allow InDel. length: > 1 nt ================================= Reading gziped input file... ================================= Number of reads in input file: 18,035,544 ================================= ================================= Step 1/5 : Alignment against Viral reference...Filtering... ================================= [E::bwa_idx_load_from_disk] fail to locate the index files Traceback (most recent call last): File "DI-tector_06.py", line 183, in <module> Popen(["samtools", "view", "-Sb", "-F", "4"], stdin=out_file_onVirus, stdout=out_file_Virus).communicate() File "/usr/lib/python3.6/subprocess.py", line 709, in __init__ restore_signals, start_new_session) File "/usr/lib/python3.6/subprocess.py", line 1344, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) PermissionError: [Errno 13] Permission denied: 'samtools'
I have no idea how samtools must be accessed, I tried
sudo command with python3 but it did not work.