Seg fault on running Kraken2

[TimFulcher]

Hi guys,

I wonder if anyone has any ideas what is causing this: Processed 26958 sequences (8114358 bp) ...Segmentation fault: 11 Command was: kraken --use-names --db minikraken2_v1_8GB --report Kraken2Mini8GB_report.txt --output Kraken2MiniTest.txt 1118_S37_L001_R1_001.fastq

So whether by redirect or using the --output (or just letting it scroll) kraken2 does most of the job, looking at a kraken1 run. The only thing missing is the final summary. However, this blocks the --report switch, and I still haven't figured out how to reproduce that functionality. So if someone could point me to some suggestions I can try them out. Either to run the analysis to get the report structure out or to figure out what's stopping the run.

I'll point out that this is on a mac, so I suspect there's something missing somewhere - currently upgraded bash, installed BLAST, libomp etc.

Thanks Tim

[ramay]

Hi I am also getting a segmentation error while running kraken2.

Processed 1960932 sequences (192886784 bp) ...Segmentation fault (core dumped) and the command used was: kraken2 --use-names --threads 28 --db kraken2db_2020_02_26 --report vaginal_sample test.fa > vaginal_sample.kraken Please guide me if there is a solution? I have also tried the miniKraken database but the error is the same.

Thanks! Hena

[khemlalnirmalkar]

Hi, I got the same problem. Did any of you get the solution? I have tried with many different threads but didn't work. I have 64 . Thanks, Khem

[jenniferlu717]

If you are using kraken2, please open this issue on the kraken2 github: https://github.com/DerrickWood/kraken2/

Please try running without --use-names option?

[khemlalnirmalkar]

If you are using kraken2, please open this issue on the kraken2 github: https://github.com/DerrickWood/kraken2/

Please try running without --use-names option?

Thank you, i will give a try without --use-names. If the error continues, i will open the issue in https://github.com/DerrickWood/kraken2/.

Khem