Job Failed without email-running SNP2GENE with QTL data

William Casazza

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May 6, 2021, 1:39:03 PM5/6/21

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Hello,

I ran the SNP2GENE jobs 128876 and 128878 on a set of QTLs. The SNPs were mapped to their minimum P value for association with DNA methylation, there were about 14 million rows.

I didn't receive any email stating why the job failed, so I was wondering if anyone could help me figure out what went wrong.

Best,

Will

d.p.wi...@vu.nl

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May 11, 2021, 3:56:23 AM5/11/21

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Hi Will,

Both of those jobs were stopped because they took longer than the time limit. I recommend choosing to skip the magma step because that took up all of the alloted time.

Cheers,

Doug

William Casazza

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May 27, 2021, 1:36:26 PM5/27/21

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Thanks Doug,

I've come across another issue for job 131513. The issue states it may be due to formatting but I am sure that the column names I specified are correct. I also ensured that I had no repeat SNPs and that each variant had an RSID, although I didn't check if it was an ID present in dbSNP 146. In order to save time, would you be able to tell me the exact error message here?

Best,

Will

d.p.wi...@vu.nl

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Jun 11, 2021, 10:08:10 AM6/11/21

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Hi Will,

Sorry for my slow reply. The error is difficult to discern, the problem arises when the start of the genomic locus needs to be defined. Is it possible for you to share your input file with me so I can try to recreate the issue? (d.p.wi...@vu.nl). I have seen this error once before but it was due to the predefined lead snps using the positions from build GRCh38 and not GRCh37 but your job does not use predefined lead snps.