We are using Trimmomatic 0.39 on an HPC cluster. This is the latest version available via EasyBuild (its module name is Trimmomatic/0.39-Java-11). We have noticed that the output that we would expect to go to STDOUT in fact goes to STDERR. Any output we would expect to go to STDERR also goes there (correctly).
For example, running against a dummy 100-line fastq file using the following command:
java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar SE -threads 6 W3.0_rep1.fastq.short W3.0_rep1_trimmed.fastq.short ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 MINLEN:50 1>stdout 2>stderr
...produces nothing to STDOUT, but the following to STDERR:
TrimmomaticSE: Started with arguments:
-threads 6 W3.0_rep1.fastq.short W3.0_rep1_trimmed.fastq.short ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 MINLEN:50
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Quality encoding detected as phred33
Input Reads: 25 Surviving: 25 (100.00%) Dropped: 0 (0.00%)
TrimmomaticSE: Completed successfully
Are we calling this correctly, or is there some muddle in the code regarding output destinations?
We are using Trimmomatic 0.39 on an HPC cluster. This is the latest version available via EasyBuild (its module name is Trimmomatic/0.39-Java-11). We have noticed that the output that we would expect to go to STDOUT in fact goes to STDERR. Any output we would expect to go to STDERR also goes there (correctly).
For example, running against a dummy 100-line fastq file using the following command:
java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.39.jar SE -threads 6 W3.0_rep1.fastq.short W3.0_rep1_trimmed.fastq.short ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 MINLEN:50 1>stdout 2>stderr...produces nothing to STDOUT, but the following to STDERR:
Are we calling this correctly, or is there some muddle in the code regarding output destinations?