Dear community, i run meryl for k-mer coverage counting due to the following workflow: Galaxy | Europe | Accessible Workflow | Kcov . When doing so with a paired end Illumina dataset it first work well, i got results. When repating the same workflow with more data the job does not failed (no erro…

Hi @fruitphytodoc , the error seems to be related to the compressed files; I opened an issue about it Meryl: wrong outputs with compressed FASTQ files · Issue #3801 · galaxyproject/tools-iuc · GitHub . Could you try to decompress the fastq.gz files and relaunch the analysis? You can uncompress your f…

Hi @fruitphytodoc , it seems a memory issue. Could you try to run meryl count on the collection instead of collapsing the collection in a single datafile? After that you can merge the collection of .meryldb files by using operation on kmers:union-sum. Regards

Dear @gallardoalba , thanx i will try this! Give you a reply when I did it. All the Best thomas

Hi @hexylena , @gaalardoalba, so due to the problem “possible error in meryl”, it is still persistent also after using a smaller dataset, without and with collapsing th datasets. When using Illumina reads for k-mer counting the tool creates an output, which you can then use as input for histogram c…