Trimmomatic not displaying summary

Question

[kiddodoraemon]

Hello all, i am a beginner in this field. i'm grateful for your advice and help : i was running Trimmomatic0.36 on terminal using my macbook. however i couldnt find the "input read data..surviving reads...dropped reads..." summary lines on finishing the task. instead the display finished off like this:

Multiple cores found: Using 4 threads
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences

Here's my script: (I also try a simple script without the for loop but i didnt get the summary data either)

curl -O http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
unzip Trimmomatic-0.36.zip
#!/bin/bash
for f1 in *_1.fastq.gz
do
withpath="${f1}"
filename=${withpath##*/}
base="${filename%*_*.fastq.gz}"
echo "${base}"
java -jar ./Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 -trimlog trimmoatic.log "${base}"*_1.fastq.gz "${base}"*_2.fastq.gz "${base}"_1.trimmed.1P.fastq.gz "${base}"_1.trimmed.1U.fastq.gz "${base}"_2.trimmed.2P.fastq.gz "${base}"_2.trimmed.2U.fastq.gz ILLUMINACLIP:./Trimmomatic-0.36/adapters/NexteraPE-PE.fa:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:20:20 MINLEN:50
done

how could i get the summary lines regarding surviving reads, reads dropped etc? Thanks a lot!

Answer 1

[Kevin Blighe]

Hey kiddodoraemon,

I have edited your question to make he code more legible. When posting code or output from a command, highlight the text and then press the '101 010' button.

I have just tested trimmomatic (same version as yours) on my OS (Ubuntu 14.04) and it outputs the surviving reads, etc.to my terminal when the run completes.

I execute in a bash script with the following:

#!/bin/bash

paste files.list | while read fastq
do
    java -jar ./Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 -trimlog MyTrimming.log "${fastq}" . ILLUMINACLIP:./Trimmomatic-0.36/adapters/NexteraPE-PE.fa:2:30:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:20:20 MINLEN:50
done

files.list just contains my FASTQ files (1 per line). As you have paired end, you should be able to run it as:

#!/bin/bash

paste mates1.list mates2.list | while read P1 P2
do
    java -jar ./Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 -trimlog MyTrimming.log "${P1}" "${P2}" et cetera...
done


Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 1444735 Surviving: 1443542 (99,92%) Dropped: 1193 (0,08%)
TrimmomaticSE: Completed successfully

[kiddodoraemon]

Thanks very much Kevin Blighe! its simpler and it works!