Gemini load error

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1

Hi there,

I am very new to Galaxy. I am using it to complete a university assignment but I am having trouble with the Gemini load tool. In my first workflow with Path248 I used it without any issues but when I combined 2 more datasets in a daughter and a sister. but after about an hour It fails and I get this message.

Indexing /mnt/tmp/job_working_directory/002/438/2438919/working/input.vcf.gz with grabix.
Loading 1250792 variants.
Breaking /mnt/tmp/job_working_directory/002/438/2438919/working/input.vcf.gz into 3 chunks.
Loading chunk 0.
Loading chunk 1.
Loading chun

I am looking for some pointers on where I might have gone wrong or some help in solving the error please.

Many thanks,

Kara

2

Hi, to debug this I’d need the full error message.

3

hi wrm75 to the best of my knowledge it is the full message

error.

An error occurred with this dataset:

Indexing /mnt/tmp/job_working_directory/002/438/2438919/working/input.vcf.gz with grabix. Loading 1250792 variants. Breaking /mnt/tmp/job_working_directory/002/438/2438919/working/input.vcf.gz into 3 chunks. Loading chunk 0. Loading chunk 1. Loading chun

4

You need to click the little bug icon attached to the dataset to see the full message.

5

I’m not sure if this is what you were referring too but I found this:

GEMINI load

Dataset Information

Number 43
Name GEMINI load on data 39
Created Wednesday Jun 16th 8:57:47 2021 UTC
Filesize -
Dbkey hg19
Format gemini.sqlite
File contents contents
History Content API ID a174cb07fac4a6e8
History API ID 0671c0977d8a5f5f
UUID 03044cc1-b7a8-4473-8efc-125a8668b8ce
Full Path /mnt/user-data/004/217/dataset_4217274.dat

Tool Parameters

Input Parameter Value
VCF dataset to be loaded in the GEMINI database * 39: SnpEff eff: on data 37 and data 36
The variants in this input are annotated with snpEff
This input comes with genotype calls for its samples True
Choose a gemini annotation source 2020-05-14
Sample and family information in PED format
Load the following optional content into the database GERP scores CADD scores (non-commercial use only; see licensing note below) Gene tables Sample genotypes variant INFO field

Job Information

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/gemini_load/gemini_load/0.20.1+galaxy2
Command Line mkdir gemini && ln -s ‘/mnt/tools-indices/custom-indices/gemini/200/hg19/2020-05-14/gemini/data’ gemini/data && export GEMINI_CONFIG=’/mnt/tools-indices/custom-indices/gemini/200/hg19/2020-05-14’ && bgzip -c ‘/mnt/user-data/004/216/dataset_4216173.dat’ > input.vcf.gz && tabix -p vcf input.vcf.gz && gemini load -v input.vcf.gz -t snpEff --skip-pls --save-info-string --cores ${GALAXY_SLOTS:-4} ‘/mnt/user-data/004/217/dataset_4217274.dat’

(Click to expand)|
|Tool Standard Output|Indexing /mnt/tmp/job_working_directory/002/438/2438919/working/input.vcf.gz with grabix. Loading 1250792 variants. Breaking /mnt/tmp/job_working_directory/002/438/2438919/working/input.vcf.gz into 3 chunks. Loading chunk 0. Loading chunk 1. Loading chunk 2. Done loading 1250792 variants in 3 chunks. 2021-06-16 10:41:11 merging 3 chunks.

(Click to expand)|
|Tool Standard Error|CADD scores are being loaded (to skip use:–skip-cadd). GERP per bp is being loaded (to skip use:–skip-gerp-bp). [W::vcf_parse_format] Extreme FORMAT/AO value encountered and set to missing at chr1:10334 [W::vcf_parse_format] Extreme FORMAT/AO value encountered and set to missing at chr3:194712150 [W::vcf_parse_format] Extreme FORMAT/AO value encountered and set to missing at chr16:24230976 pid 862602: 9999 variants processed. pid 862599: 9999 variants processed. pid 862605: 9999 variants processed. pid 862602: 19999 variants processed. pid 862599: 19999 variants processed. pid 862605: 19999 variants processed. pid 862602: 29999 variants processed. pid 862599: 29999 variants processed. pid 862605: 29999 variants processed. pid 862602: 39999 variants processed. pid 862599: 39999 variants processed. pid 862605: 39999 variants processed. pid 862602: 49999 variants processed. pid 862599: 49999 variants processed. pid 862605: 49999 variants processed. pid 862605: 59999 variants processed. pid 862599: 59999 variants processed. pid 862602: 59999 variants processed. pid 862605: 69999 variants processed. pid 862602: 69999 variants processed. pid 862599: 69999 variants processed. pid 862605: 79999 variants processed. pid 862602: 79999 variants processed. pid 862599: 79999 variants processed. pid 862605: 89999 variants processed. pid 862602: 89999 variants processed. pid 862599: 89999 variants processed. pid 862605: 99999 variants processed. pid 862602: 99999 variants processed. pid 862599: 99999 variants processed. pid 862605: 109999 variants processed. pid 862602: 109999 variants processed. pid 862599: 109999 variants processed. pid 862605: 119999 variants processed. pid 862602: 119999 variants processed. pid 862599: 119999 variants processed. pid 862605: 129999 variants processed. pid 862602: 129999 variants processed. pid 862599: 129999 variants processed. pid 862605: 139999 variants processed. pid 862602: 139999 variants processed. pid 862599: 139999 variants processed. pid 862605: 149999 variants processed. pid 862602: 149999 variants processed. pid 862599: 149999 variants processed. pid 862605: 159999 variants processed. pid 862602: 159999 variants processed. pid 862599: 159999 variants processed. pid 862605: 169999 variants processed. pid 862602: 169999 variants processed. pid 862599: 169999 variants processed. pid 862605: 179999 variants processed. pid 862602: 179999 variants processed. pid 862599: 179999 variants processed. pid 862605: 189999 variants processed. pid 862602: 189999 variants processed. pid 862599: 189999 variants processed. pid 862605: 199999 variants processed. pid 862602: 199999 variants processed. pid 862599: 199999 variants processed. pid 862605: 209999 variants processed. pid 862602: 209999 variants processed. pid 862599: 209999 variants processed. pid 862605: 219999 variants processed. pid 862602: 219999 variants processed. pid 862599: 219999 variants processed. pid 862605: 229999 variants processed. pid 862602: 229999 variants processed. pid 862599: 229999 variants processed. pid 862602: 239999 variants processed. pid 862605: 239999 variants processed. pid 862599: 239999 variants processed. pid 862602: 249999 variants processed. pid 862605: 249999 variants processed. pid 862599: 249999 variants processed. pid 862605: 259999 variants processed. pid 862602: 259999 variants processed. pid 862599: 259999 variants processed. pid 862605: 269999 variants processed. pid 862602: 269999 variants processed. pid 862599: 269999 variants processed. pid 862605: 279999 variants processed. pid 862602: 279999 variants processed. pid 862599: 279999 variants processed. pid 862605: 289999 variants processed. pid 862602: 289999 variants processed. pid 862599: 289999 variants processed. pid 862605: 299999 variants processed. pid 862602: 299999 variants processed. pid 862599: 299999 variants processed. pid 862605: 309999 variants processed. pid 862602: 309999 variants processed. pid 862599: 309999 variants processed. pid 862602: 319999 variants processed. pid 862605: 319999 variants processed. pid 862599: 319999 variants processed. pid 862605: 329999 variants processed. pid 862602: 329999 variants processed. pid 862599: 329999 variants processed. pid 862605: 339999 variants processed. pid 862602: 339999 variants processed. pid 862599: 339999 variants processed. pid 862605: 349999 variants processed. pid 862602: 349999 variants processed. pid 862605: 359999 variants processed. pid 862599: 349999 variants processed. pid 862605: 369999 variants processed. pid 862605: 379999 variants processed. pid 862602: 359999 variants processed. pid 862599: 359999 variants processed. pid 862605: 389999 variants processed. pid 862602: 369999 variants processed. pid 862605: 399999 variants processed. pid 862599: 369999 variants processed. pid 862602: 379999 variants processed. pid 862605: 409999 variants processed. pid 862599: 379999 variants processed. pid 862605: 416932 variants processed. pid 862602: 389999 variants processed. pid 862599: 389999 variants processed. pid 862602: 399999 variants processed. pid 862599: 399999 variants processed. pid 862602: 409999 variants processed. pid 862602: 416930 variants processed. pid 862599: 409999 variants processed. pid 862599: 416930 variants processed. Traceback (most recent call last): File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/bin/gemini”, line 7, in gemini_main.main() File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py”, line 1248, in main args.func(parser, args) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py”, line 346, in mergechunk_fn gemini_merge_chunks.merge_chunks(parser, args) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_merge_chunks.py”, line 229, in merge_chunks merge_db_chunks(args) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_merge_chunks.py”, line 194, in merge_db_chunks append_variant_info(main_curr, db) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_merge_chunks.py”, line 25, in append_variant_info main_curr.execute(cmd) sqlite3.IntegrityError: UNIQUE constraint failed: variants.variant_id Traceback (most recent call last): File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/bin/gemini”, line 7, in gemini_main.main() File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py”, line 1248, in main args.func(parser, args) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_main.py”, line 204, in load_fn gemini_load.load(parser, args) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load.py”, line 49, in load load_multicore(args) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load.py”, line 94, in load_multicore merge_chunks_multicore(chunks, args) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load.py”, line 168, in merge_chunks_multicore wait_until_finished(procs) File “/mnt/tools-indices/tool_dependencies/_conda/envs/__gemini@0.20.1/lib/python2.7/site-packages/gemini/gemini_load.py”, line 359, in wait_until_finished raise ValueError(“Processing failed on GEMINI chunk load”) ValueError: Processing failed on GEMINI chunk load

(Click to expand)|
|Tool Exit Code:|1|
|Job Messages|* { “code_desc”: “”, “desc”: “Fatal error: Exit code 1 ()”, “error_level”: 3, “exit_code”: 1, “type”: “exit_code” }

  • { “code_desc”: null, “desc”: “Fatal error: Matched on Error:”, “error_level”: 3, “match”: “Error:”, “stream”: “stderr”, “type”: “regex” }|
    |Job API ID:|b069d1fb798a3db0|

Dataset Storage

This dataset is stored in the default configured Galaxy object store .

Inheritance Chain

GEMINI load on data 39

Job Dependencies

Dependency Dependency Type Version
gemini conda 0.20.1

Dataset peek

no peek

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