I have a problem with Trimmomatic 0.36 that can't be solved with all the suggestions that I have found so far, since they are for PE mode (such as Trimmomatic not acknowleding commands over Linux cluster, and here they don't fix the problem). So I am posting a separate question for the single end (SE) mode situation.
Problem: I want to remove the first 5 bases of every read (HEADCROP:5) in my fastq file (filename: Preprocessed_110.fastq.gz) using Trimmomatic. For which I run the following code:
touch trimlog110.txt trimmomatic SE -trimlog trimlog110.txt Preprocessed_110.fastq.gz trimmed_110.fq HEADCROP:5 Usage: PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>... or: SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-quiet] <inputFile> <outputFile> <trimmer1>... or: -version
If I check the current directory with "ls", I see the fastq.gz file is still there, no output file is generated and the log.txt file is still empty, as if the program did nothing. I tried removing the "SE", as suggested by some people with the "PE" in paired end mode, and the result is the same. I tried removing the trimlog part to keep it simple, with less commands as possible to trace down the error, and nothing changed. Does anyone identify another thing that might be causing the problem? Thank you.
Regarding the computer specifics: I installed Trimmomatic in MacOS High Sierra. I created a script in the /usr/local/bin directory that calls the .jar file and executes the program, so I could just write "trimmomatic" and not the whole java -jar+path; all this was suggested in the Biostar bioinformatics handbook:
MacBook:bin username$ touch trimmomatic Macbook:bin username$ vi trimmomatic #!/bin/bash java -jar /Users/username/Trimmomatic-0.36/trimmomatic-0.36.jar Macbook:bin username$ chmod +x trimmomatic
This worked, and if you type trimmomatic in any directory, the program runs. That is why I assume is something in the code typinc that comes afterwards that is making trouble.