Question: error en trimmomatic
0
gravatar for laurapeaz_21315
3 months ago by
laurapeaz_213150 wrote:

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'.
error trimmomatic • 171 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by laurapeaz_213150

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.

E: Could not find '../trimmomatichome/adapters/TruSeq3-PE.fa'.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax85k

Please use the formatting bar (especially the code option) to present your post better.
code_formatting

Thank you!

ADD REPLYlink written 3 months ago by genomax85k

por eso: Could not find '../trimmomatichome/adapters/TruSeq3-PE.fa'. el archivo no existe en esto lugar.

ADD REPLYlink written 3 months ago by Michael Dondrup47k

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) `

ADD REPLYlink modified 3 months ago • written 3 months ago by laurapeaz_213150

I think this previous biostar post might help you with the "Unknown trimmer" runtime exception: Trimmomatic - unknown trimmer?

ADD REPLYlink written 3 months ago by newbio17110
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