Trimmomatic error
Looking back at the log files, there seems to be an error with trimmomatic. It seems to be looking for the adapter sequences in the wrong folder...
TrimmomaticPE: Started with arguments: -threads 4 build/Preprocessing/MT.R1.fq build/Preprocessing/MT.R2.fq build/Preprocessing/MT.R1.trimmed.fq build/Preprocessing/MT.SE1.trimmed.fq build/Preprocessing/MT.R2.trimmed.fq build/Preprocessing/MT.SE2.trimmed.fq ILLUMINACLIP:db/trimmomatic/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:1:3 MINLEN:40 MAXINFO:40:0.5
Apr 22, 2015 5:56:12 AM org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer makeIlluminaClippingTrimmer
SEVERE: null
java.io.FileNotFoundException: /home/imp/integrated-metaomic-pipeline/db/trimmomatic/TruSeq3-PE.fa (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:146)
at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:107)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:70)
at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:27)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:495)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:35)
Quality encoding detected as phred33
Input Read Pairs: 824670 Both Surviving: 791684 (96.00%) Forward Only Surviving: 26157 (3.17%) Reverse Only Surviving: 4593 (0.56%) Dropped: 2236 (0.27%)
TrimmomaticPE: Completed successfully
TrimmomaticPE: Started with arguments: -threads 4 build/Preprocessing/MG.R1.fq build/Preprocessing/MG.R2.fq build/Preprocessing/MG.R1.uniq.trimmed.fq build/Preprocessing/MG.SE1.uniq.trimmed.fq build/Preprocessing/MG.R2.uniq.trimmed.fq build/Preprocessing/MG.SE2.uniq.trimmed.fq ILLUMINACLIP:db/trimmomatic/TruSeq3-PE.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:1:3 MINLEN:40 MAXINFO:40:0.5
Apr 22, 2015 6:04:13 AM org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer makeIlluminaClippingTrimmer
SEVERE: null
java.io.FileNotFoundException: /home/imp/integrated-metaomic-pipeline/db/trimmomatic/TruSeq3-PE.fa (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:146)
at org.usadellab.trimmomatic.fasta.FastaParser.parse(FastaParser.java:54)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.loadSequences(IlluminaClippingTrimmer.java:107)
at org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer.makeIlluminaClippingTrimmer(IlluminaClippingTrimmer.java:70)
at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:27)
at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:495)
at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:35)