Gemini load error

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

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

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

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

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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