hsigeman
commented
1 year ago Hi!
It looks like you are using the configuration file from the test dataset, in which the already small fastq files are subsampled (to 1888226 bp in total).
To avoid subsampling your fastq files, set the "trim_and_subsample" parameter in the config file to false and the "trim_reads" parameter to true. If you don't want to trim or subsample the reads, set both of those parameters to false.
Hope this solves your issue! Hanna
MohdKhairulNizam
FindZX run was completed successfully but when I checked the output files, I could not see any difference between the male and female samples (kindly refer to the pdfs attached). I repeated the analysis twice and I kept getting the same output files. Next, I checked the log file from the server (attached) and I saw a warning message appeared at job 28 (Calculates number of heterozygous sites per individual and 5kb window) and this is followed by an error message in job 79 (Calculate heterozygosity): Error in rule het_calc_genome. Do you have any suggestions as to why this error occured and how to fix this?
4_sexDifferences.25000bp.window.highlight.pdf 2_sexesSeparate.genomeWide.50000bp.window.verticalXaxis.pdf 4_sexDifferences.50000bp.window.pdf findZX_e337712.txt 3_sexDifferences.chromosome.pdf 4_sexDifferences.50000bp.window.highlight.pdf 4_sexDifferences.25000bp.window.pdf 2_sexesSeparate.genomeWide.25000bp.window.verticalXaxis.pdf