ablab
Spades finished abnormally, err code: -7
I am attempting to run Spades with both short, paired end reads and Oxford Nanopore long reads. The genome is estimated to be around 1.5 Gbp using GenomeScope. This is an organism with a relatively high degree of heterozygosity, around 1.5%.
I've tried running Spades with the following:
3182196758 paired Illumina reads with 151 bp average read length 14,247,894 ONT reads with span of 95,637,220,134, minimum length of 3,001 bp, maximum length of 1,045,012 bp, and median length of 5,652 bp.
I am running in careful mode on 192 threads with 4,096 Gb of RAM.
I get the following error:
== Error == system call for: "['/
So, Spades has successfully handled K21, K33, and K55, but cannot complete K77.
One other thing I did note was during K55. I received the following message numerous times:
The impossible happened : collision on 128 bit hashes... please switch to safe branch, and play the lottery.Another more likely explanation might be that you have duplicate keys in your input. If so, you can ignore this message, but be aware that too many duplicate keys will increase ram usage
In a previous thread, it was suggested that err code -7 might relate to insufficiency in RAM resources available... I'm finding it hard to believe that 4,096 Gb of RAM would be insufficient for my assembly.
Thoughts? Thank you for your time.
Hello
Please at least attach the files mentioned in the error message. Without them no thoughts could be generated.
