- ERROR: link_clusters.pl failed.

[fengyuchengdu]

I have a large dataset (~13000 genomes). The program somehow stopped due to low space of disk during "parsing paralogues" and I wanted to re-run the analysis without re-creating pangenome and classifying paralogues using the command below

PIRATE -i ./13383_gff/ -o ./13383_pirate_output -t 32 --pan-off --para-off

however it always threw out an error saying "

Linking clusters between thresholds:

• subsetting loci file for parallel - /home/zong/Desktop/aac_koc/20211206/comparative_genomics/13383_pirate_output/loci_list.tab
• 0 clusters to exclude
• 57697 gene families to process
• ERROR: link_clusters.pl failed. " and lots of "killed" after that

since there was no other informative message from the log, I'm wondering how I can solve this problem

Many thanks,

Feng Yu

[SionBayliss]

Hi,

If you had an issue with available space then a file may have not been correctly formed which is likely contributing to this error. I would suggest recreating the pangenome and ensuring you have additional space.

All the best, Sion