I am getting ERROR:001 even after correcting as per the suggestion.

Akhil P

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Feb 9, 2024, 3:19:32 PM2/9/24

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Hello,

I am running fuma gwas and have a job submitted yesterday which worked really well but when I am running the same job on a different file I am getting Error 001. Could you help me out regarding this? I have performed all the things that are needed with regards to qc steps of the input file.

Regards
AKHIL

Akhil P

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Feb 9, 2024, 5:26:35 PM2/9/24

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I also tried formating the file again and now I am getting ERROR:ERROR 0

Regards

Akhil

Anastasios Mitsigkolas

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Feb 10, 2024, 10:40:47 AM2/10/24

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Hi there,

please provide the IDs of the faulty jobs so I can assist you further.

Kind regards,
Tasos

Akhil P

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Feb 12, 2024, 11:56:28 AM2/12/24

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Hello Tasos,

Thank you so much for the help and sorry for the delayed response.

Here are the faulty jobs with their errors:

448977 - ERROR:001

448975 - ERROR:0
448973 - ERROR:001
448956 - ERROR:001
448949 - ERROR:001
448942 - ERROR:001
448940 - ERROR:001
448939 - ERROR:001
448937 - ERROR:001

Regards

Akhil

fuma.ctglab

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Feb 12, 2024, 4:16:09 PM2/12/24

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Dear Akhil,

For the jobs with ERROR:001, this is because FUMA expect the rsID to be in rsID format.

In your jobs, you specified ID to be the rsID, but it looks like your ID looks like this: 1:100100094:C:T. This is not the correct rsID format.

Please check the tutorial here: https://fuma.ctglab.nl/tutorial#snp2gene

Column names are automatically detected based on the following headers (case insensitive).

SNP | snpid | markername | rsID: rsID
CHR | chromosome | chrom: chromosome
BP | pos | position: genomic position (hg19)
A1 | effect_allele | allele1 | alleleB: affected allele
A2 | non_effect_allele | allele2 | alleleA: another allele
P | pvalue | p-value | p_value | pval: P-value (Mandatory)
OR: Odds Ratio
Beta | be: Beta
SE: Standard error

You can remove this column and test again.

For the ERROR:0 please see response here: https://groups.google.com/g/fuma-gwas-users/c/PB-M2ZamBAA/m/P-PnVXlgAQAJ

Good luck,
FUMA

Akhil P

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Feb 12, 2024, 9:18:32 PM2/12/24

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Hello,

Thank you so much for the suggestion. I have corrected the file as suggested and reran the analysis and still got the same error. Here is the id: 449665. Please do let me know what could be the issue this time.

Regards

Akhil

Akhil P

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Feb 12, 2024, 9:35:33 PM2/12/24

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Again same issue. I dont have anything other than chromosome, position, alleles, P, beta, and se. Here is the ID 449667.

Regards

Akhil

Anastasios Mitsigkolas

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Feb 13, 2024, 4:27:05 AM2/13/24

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Hi there,

449665: it seems like there is this string "1_KI270766v1_alt" in the CHR column. Please use integers to indicate chromosomes.
449667: same here

Kind regards,
Tasos

Akhil P

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Feb 13, 2024, 1:47:43 PM2/13/24

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Hello,

Thank you so much for the suggestion. Quick question, the job I submitted is in queue for some time(maybe 3 hours). Could you look into it to see if there is a file related issue or general server related queue system? ID is 449885

Regards

Akhil

Akhil P

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Feb 13, 2024, 2:30:51 PM2/13/24

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Hello,

Thank you so much for the help regarding the updates. Unfortunately, I am still getting 001 error when running fuma gwas after the necessary correction. Here is the ID - 449885. Please do let me know of how to resolve this issue.

Regards

Akhil

Anastasios Mitsigkolas

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Feb 14, 2024, 5:57:29 AM2/14/24

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Hi there,

regarding job 449885, the following lines are not recognized by the system

chrY 8725982 CA C 0.2956 0.0679 1.33E-05 +???
chrY 12358262 C CA -0.2753 0.0588 2.86E-06 -???
chrY 13617568 G GAC 0.0762 0.0207 0.0002329 +???
chrY 22207658 A AT 0.1659 0.0474 0.0004657 +???

Kind regards,
Tasos

Akhil P

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Feb 14, 2024, 11:51:24 AM2/14/24

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I have submitted it after removing the variants as suggested. I will keep you posted on the error.

Regards

Akhil

Akhil P

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Feb 14, 2024, 5:41:35 PM2/14/24

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This job is in the queue for a long time. Can you help find out the reason?
JOB ID: 450170

Regards

Akhil

Akhil P

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Feb 14, 2024, 6:06:53 PM2/14/24

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Again the job failed. Even after making corrections as suggested.

Anastasios Mitsigkolas

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Feb 15, 2024, 6:56:55 AM2/15/24

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Hi there,

It seems like those lines are still there:

Y 8725982 CA C 0.2956 0.0679 1.33E-05 +???

Y 12358262 C CA -0.2753 0.0588 2.86E-06 -???

Y 13617568 G GAC 0.0762 0.0207 0.0002329 +???

Y 22207658 A AT 0.1659 0.0474 0.0004657 +???

Could you please remove them entirely and try again?

Kind regards,
Tasos

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