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4.7 years ago
laurapeaz_21315
•
0
Hola soy nueva usando trimmomatic y linnux use la siguiente linea de comando :
lau@DESKTOP-1B4G2I6:/mnt/c/Users/acer/Documents/doctorado/Genoma 4IGSN1/4IgSN1$ java -jar /usr/share/java/trimmomatic.jar PE -threads 8 -phred33 1_HIg5N1_S1_L001_R1_001.fastq 2_HIg5N1_S1_L001_R2_001.fastq 1_HIg5N1_S1_L001_R1_001_paired.fastq 1_HIg5N1_S1_L001_R1_001_unpaired.fastq 2_HIg5N1_S1_L001_R2_001_paired.fastq 2_HIg5N1_S1_L001_R2_001_unpaired.fastq ILLUMINACLIP:../trimmomatichome/adapters/TruSeq3-PE.fa:2:40:15 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:27 MINLEN:75
pero tengo estos 2 errores y no se como solucionarlos:
TrimmomaticPE: Started with arguments: -threads 8 -phred33 1_HIg5N1_S1_L001_R1_001.fastq 2_HIg5N1_S1_L001_R2_001.fastq 1_HIg5N1_S1_L001_R1_001_paired.fastq 1_HIg5N1_S1_L001_R1_001_unpaired.fastq 2_HIg5N1_S1_L001_R2_001_paired.fastq 2_HIg5N1_S1_L001_R2_001_unpaired.fastq ILLUMINACLIP:../trimmomatichome/adapters/TruSeq3-PE.fa:2:40:15 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:27 MINLEN:75
E: Could not find '../trimmomatichome/adapters/TruSeq3-PE.fa'.
Biostars is mainly an English language site so you may want to post (translate) your questions in English. Google translate should do a reasonable job, if you are not confident about posting in English.
Here the error is clear: A file trimmomatic needs can't be found. Check and adjust file path as needed.
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por eso: Could not find '../trimmomatichome/adapters/TruSeq3-PE.fa'. el archivo no existe en esto lugar.
yes, i already corrected that part with this: lau@DESKTOP-1B4G2I6:/mnt/c/Users/acer/Documents/doctorado/Genoma 4IGSN1/4IgSN1$ java -jar /usr/share/java/trimmomatic.jar PE -threads 8 -phred33 -trimlog 1_HIg5N1_S1_L001_R1_001.fastq 2_HIg5N1_S1_L001_R2_001.fastq 1_HIg5N1_S1_L001_R1_001_paired.fastq 1_HIg5N1_S1_L001_R1_001_unpaired.fastq 2_HIg5N1_S1_L001_R2_001_paired.fastq 2_HIg5N1_S1_L001_R2_001_unpaired.fastq ILLUMINACLIP /mnt/c/Users/acer/Documents/doctorado/Genoma\ 4IGSN1/4IgSN1/trimmomatichome/adapters/TruSeq3-PE.fa:2:40:15 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:27 MINLEN:75
but i had this: TrimmomaticPE: Started with arguments: -threads 8 -phred33 -trimlog 1_HIg5N1_S1_L001_R1_001.fastq 2_HIg5N1_S1_L001_R2_001.fastq 1_HIg5N1_S1_L001_R1_001_paired.fastq 1_HIg5N1_S1_L001_R1_001_unpaired.fastq 2_HIg5N1_S1_L001_R2_001_paired.fastq 2_HIg5N1_S1_L001_R2_001_unpaired.fastq ILLUMINACLIP /mnt/c/Users/acer/Documents/doctorado/Genoma 4IGSN1/4IgSN1/trimmomatichome/adapters/TruSeq3-PE.fa:2:40:15 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:27 MINLEN:75 Exception in thread "main" java.lang.RuntimeException: Unknown trimmer: /mnt/c/Users/acer/Documents/doctorado/Genoma 4IGSN1/4IgSN1/trimmomatichome/adapters/TruSeq3-PE.fa at org.usadellab.trimmomatic.trim.TrimmerFactory.makeTrimmer(TrimmerFactory.java:70) at org.usadellab.trimmomatic.Trimmomatic.createTrimmers(Trimmomatic.java:59) at org.usadellab.trimmomatic.TrimmomaticPE.run(TrimmomaticPE.java:536) at org.usadellab.trimmomatic.Trimmomatic.main(Trimmomatic.java:80) `
I think this previous biostar post might help you with the "Unknown trimmer" runtime exception: Trimmomatic - unknown trimmer?