Trimmomatic errors

Question

[marion.ryan]

Any ideas here, I have run this code and keep getting errors cannot execute binary file. Is this a problem with my input files or TRIMMOMATIC itself

module load trimmomatic
module load jdk/1.8.0.221 export
TRIMMOMATIC=/opt/software/trimmomatic/0.39/trimmomatic-0.39.jar
java -jar $TRIMMOMATIC PE \
  -phred33 \
  /scratch/marionr/Raw_Muscle_2021/41_L4_R1_001.fastq \
  /scratch/marionr/Raw_Muscle_2021/41_L4_R2_001.fastq \
  /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R1_paired.fastq \
  /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R1_unpaired.fastq \
  /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R2_paired.fastq \
  /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R2_unpaired.fastq \
  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35

Output

Loading trimmomatic/0.39
  Loading requirement: jdk/1.8.0.221
Usage: 
       PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
   or: 
       SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
   or: 
       -version
/var/spool/slurm/d/job1302460/slurm_script: line 25: /scratch/marionr/Raw_Muscle_2021/41_L4_R1_001.fastq.gz: cannot execute binary file
/var/spool/slurm/d/job1302460/slurm_script: line 26: /scratch/marionr/Raw_Muscle_2021/41_L4_R2_001.fastq.gz: cannot execute binary file
/var/spool/slurm/d/job1302460/slurm_script: line 27: /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R1_paired.fastq: No such file or directory
/var/spool/slurm/d/job1302460/slurm_script: line 28: /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R1_unpaired.fastq: No such file or directory
/var/spool/slurm/d/job1302460/slurm_script: line 29: /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R2_paired.fastq: No such file or directory
/var/spool/slurm/d/job1302460/slurm_script: line 30: /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R2_unpaired.fastq: No such file or directory
/var/spool/slurm/d/job1302460/slurm_script: line 31: LEADING:3: command not found

Answer 1

[Pierre Lindenbaum]

it looks like yourtrimmomatic command is spanning several lines

/software/trimmomatic/0.39/trimmomatic-0.39.jar java -jar $TRIMMOMATIC PE-phred33 /scratch/marionr/Raw_Muscle_2021/41_L4_R1_001.fastq
/scratch/marionr/Raw_Muscle_2021/41_L4_R2_001.fastq /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R1_paired.fastq
(...)

instead of

/software/trimmomatic/0.39/trimmomatic-0.39.jar java -jar $TRIMMOMATIC PE-phred33 /scratch/marionr/Raw_Muscle_2021/41_L4_R1_001.fastq \
/scratch/marionr/Raw_Muscle_2021/41_L4_R2_001.fastq /scratch/marionr/Raw_Muscle_2021/trimmed_41_L004_R1_paired.fastq \
(...)