search

jlab-code / MethylStar

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
GNU General Public License v3.0
32 stars 6 forks source link

Trimmomatic #14

Closed mmageroy closed 3 years ago

mmageroy commented 3 years ago

Hi, I am trying to run spruce WGBS through your pipeline.

Is it possible to run the pipeline without Trimmomatic? My reads are fairly have quality and the adaptors have been trimmed already. I am also having trouble with Trimmomatic not giving any output. See below.

Thanks! Melissa

1 Configuration Summary:

Configured Java location: /usr/bin/java Trimmomatic path: /home/software/Trimmomatic-0.38 Trimmomatic Adapter: /home/software/Trimmomatic-0.38/adapters/TruSeq3-PE.fa Trimmomatic Running mode: PE Trimmomatic ILLUMINACLIP: 1:30:9 Trimmomatic LEADING: 20 Trimmomatic TRAILING: 20 Trimmomatic SLIDINGWINDOW: 4:20 Trimmomatic MINLEN: 36 Trimmomatic Threading: 16 Parallel mode is: Disabled

Do you want continue to run? [y/n] y

Running Trimmomatic Part...

Starting Trimmomatic ... Running Trimmomatic for /data/V300033699_L1_PL2003110001-2_2.fq.gz V300033699_L1_PL2003110001-2_2 : at java.base/java.io.FileInputStream.(FileInputStream.java:157) Trimmomatic finished. Duration 0 Minutes. Running Trimmomatic for /data/V300033699_L1_PL2003110001-2_1.fq.gz V300033699_L1_PL2003110001-2_1 : at java.base/java.io.FileInputStream.(FileInputStream.java:157) Trimmomatic finished. Duration 0 Minutes. Trimmomatic finished. Total time 0 Minutes.

Processing files is finished, You can check the log files in Menu, part 'Trimmomatic-log'

2

    *** Running FastQC Report Part ***

Configuration Summary:

Do you want continue to run? [y/n] y

Running FastQC reports ... ls: cannot access '/results/trimmomatic-files/*.gz': No such file or directory

Starting Fasqc-report ... Running in single mode. (parallel mode disabled.)

QC report finished in 0 minutes. You can find the results in /results/qc-fastq-reports folder.

sort: cannot read: /results/qc-fastq-reports/list-finished.lst: No such file or directory rm: cannot remove '/results/qc-fastq-reports/list-finished.lst': No such file or directory

Processing files are finished.

Please, press ENTER to continue ...

shahryary commented 3 years ago

Hi @mmageroy

Thank you for using our pipeline.

Yes, it is possible to run if you already have Trimmomatic files. Please copy your trimmomatic output files into "Pipeline-RESULT-PATH/ trimmomatic-files/" then run the pipeline and select either "Run QC-Fastq-report" or "Run Bismark Mapper". The pipeline will read all the files from the "trimmomatic-files" directory and will start to run QC or Bismark-mapper.

Regarding the error message, I think the "trimmomatic-files" directory is empty, and when FASTQ is trying to read the files from that directory, you are getting this message. So, if you copy the files as I explained above, it should solve your problem.

Please let me know if you have any questions.