JOB FAILED - job ID 259303 and 259148

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Luheng Qian

Jun 11, 2023, 1:40:11 AMJun 11
to FUMA GWAS users
I received the JOB FAILED for job ID 259148. The input file was some meQTLs I found (about 2 million). And I wanted to perform positional mapping only. At first, I thought maybe there were too many SNPs. So I sampled 250,000 SNPs and ran again (job ID 259303). However, it also failed. Could you review the log for these jobs and let me know the cause of error so I can fix the input file?
My best,

Jul 20, 2023, 3:55:29 AMJul 20
to FUMA GWAS users
Hi Luheng,

Your job took longer than the allowed time limit so it was killed leading to job failed. We allow jobs to run for 6 hours and your job was running for 14 hours when it was killed. It was stuck trying to define genomic risk loci. From looking at the results it appears that there are over 2 million significant variants which makes creating genomic risk loci very computationally intensive leading to a long run time. Unfortunately, FUMA was built in 2017 with the assumption that there will be 10s-100 risk loci and does not deal well with so many significant variants dispursed evenly through the genome.

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