Hello! Thanks for the cool tool - is it possible to somehow save the printed output from trimmomatic into the log file?
As of now, the log file only has data associated with every read, however, the final summary is not included. Is ther ea way to save this or could you introduce this feature in later versions?
EG I want to somehow be able to automatically record the Trimmomatic printout:
TrimmomaticPE: Started with arguments:
-threads 80 -phred33 -trimlog /media/ali/Intenso/90-961119608/Local/01_Trimmomatic/CAHET1.log -basein /media/ali/Intenso/90-961119608/00_fastq/CAHET1_R1_001.fastq.gz -baseout /media/ali/Intenso/90-961119608/Local/01_Trimmomatic/CAHET1.fastq.gz ILLUMINACLIP:adapters/TruSeq3-PE-2.fa:2:30:10:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30
Using templated Input files: /media/ali/Intenso/90-961119608/00_fastq/CAHET1_R1_001.fastq.gz /media/ali/Intenso/90-961119608/00_fastq/CAHET1_R2_001.fastq.gz
Using templated Output files: /media/ali/Intenso/90-961119608/Local/01_Trimmomatic/CAHET1_1P.fastq.gz /media/ali/Intenso/90-961119608/Local/01_Trimmomatic/CAHET1_1U.fastq.gz /media/ali/Intenso/90-961119608/Local/01_Trimmomatic/CAHET1_2P.fastq.gz /media/ali/Intenso/90-961119608/Local/01_Trimmomatic/CAHET1_2U.fastq.gz
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
Using Long Clipping Sequence: 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
Using Long Clipping Sequence: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 41190641 Both Surviving: 39657113 (96.28%) Forward Only Surviving: 831908 (2.02%) Reverse Only Surviving: 384507 (0.93%) Dropped: 317113 (0.77%)
TrimmomaticPE: Completed successfully
Hello! Thanks for the cool tool - is it possible to somehow save the printed output from trimmomatic into the log file?
As of now, the log file only has data associated with every read, however, the final summary is not included. Is ther ea way to save this or could you introduce this feature in later versions?
EG I want to somehow be able to automatically record the Trimmomatic printout: