TrimGalore!/FastQC/MultiQC - Illumina HiSeq Genome Sequencing Data Continued

The previous attempt at this was interrupted by a random glitch with our Mox HPC node.

I removed the last files processed by TrimGalore!, just in case they were incomplete. I updated the slurm script to process only the remaining files that had not been processed when the Mox glitch happened (including the files I deemed “incomplete”).

As in the initial run, I kept the option in TrimGalore! to automatically run FastQC on the trimmed output files.

TrimGalore! slurm script:

MultiQC was run locally once the files were copied to Owl.


Job completed on 20180404.

Trimmed FASTQs: 20180328_trim_galore_illumina_hiseq_geoduck/

MD5 checksums: 20180328_trim_galore_illumina_hiseq_geoduck/checksums.md5

  • MD5 checksums were generated on Mox node and verified after copying to Owl.

Slurm output file:

TrimGalore! output: 20180328_trim_galore_illumina_hiseq_geoduck/20180404_trimgalore_reports/

FastQC output: 20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck/

MultiQC output: 20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck/multiqc_data/

MultiQC HTML report: 20180328_trim_galore_illumina_hiseq_geoduck/20180328_fastqc_trimmed_hiseq_geoduck/multiqc_data/multiqc_report.html

Trimming completed and the FastQC results look much better than before.

Will proceed with full-blown assembly!