Trimmomatic "no such file or directory" error with reverse input

Question

[emilyc]

I have run trimmomatic before and I did not experience this issue previously.

My script is:

for i in D465_S13 D466_S14 D467_S15 D468_S16 D469_S17 D470_S18 D471_S19 D472_S20

do

    java -jar /home/emily/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 -trimlog home/emily/pipe/$i/Trim/trim_log /home/emily/pipe/$i/"$i"_L001_R1_001.fastq.gz home/emily/pipe/$i/"$i"_L001_R2_001.fastq.gz home/emily/pipe/$i/Trim/"$i" _output_for_paired.fq.gz home/emily/pipe/$i/Trim/"$i"_output_for_unpaired.fq.gz home/emily/pipe/$i/Trim/"$i"_output_rev_paired.fq.gz home/emily/pipe/$i/Trim/"$i"_output_rev_unpaired.fq.gz ILLUMINACLIP:/home/emily/Trimmomatic-0.38/adapters/NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
done

For each sample I am running, i, I get:

Exception in thread "main" java.io.FileNotFoundException: home/emily/pipe/D472_S20/D472_S20_L001_R2_001.fastq.gz (No such file or directory)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at org.usadellab.trimmomatic.fastq.FastqParser.parse(FastqParser.java:135)
    at org.usadellab.trimmomatic.TrimmomaticPE.process(TrimmomaticPE.java:268)
    at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:555)
    at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80)

However the these files DO exist, e.g.

locate D472_S20_L001_R2_001.fastq.gz
/home/emily/pipe/D472_S20/D472_S20_L001_R2_001.fastq.gz

Any help is appreciated. For some reason it is always the input for the reverse file (R2), on each sample I run (S13-S20).

Answer 1

[finswimmer]

You are missing a / at the start of your input files. It must be /home/... and not home/../

fin swimmer

[emilyc]

Oh my GOD. Thank you. I was staring at this for hours - I guess that is the first day back from holidays for you. I'm so happy it was just a silly and simple error.

All the best!