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: 20180401_trim_galore_illumina_geoduck_hiseq_slurm.sh
MultiQC was run locally once the files were copied to Owl.
Results:
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: 20180401_trim_galore_illumina_geoduck_hiseq_slurm.sh
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!