Long Job using minimap2

Hi, I am trying to assemble a plant genome using PacBio CLRs (41 Gb in fastq.gz) in Minimap2. The job started about one month ago and is still shown as running. How can I check if that is really the case? The account quota is indicated as 16% but I am wondering if the limit is exceeded.

Thanks for help,

Hi Helgard,
there were 2 minimap jobs running from you, I killed one of them as it crashed at the beginning of the year.

The other job is running since 28 days and, it has 2 days left before it will be automatically killed. It’s writing data to the disk, also this morning, so it’s working properly from my point of view.

Great! Thank You!

Hi gmauro,

now my minimap2 job ended with an error, terminated by an administrator. I think something went wrong because I had only one minimap job running (pb-ava). (?)

@helgardk minimap2 taking 30 days is very very unusual. Can you explain to us a little bit more what you are doing? Maybe there is another underlying error here?


I have 8.5 million (about 42GB) PacBio CLR-Reads from a plant genome and I started a “pb-ava” assembly in minimap2 where you run the reads against themselves for a de-novo assembly. As this mode has a preset of commands I didn´t add anything else.

In the mean time I have deleted and purged the data to start a test with a subset of the reads. So far everything works.