Funcotator error: Only IGRs were produced for this dataset
Answered
Hi
I recently ran to problem with funcotator:
11:57:01.141 INFO Funcotator - Initializing Funcotator Engine...
11:57:01.146 INFO FuncotatorEngine - Using given VCF and Reference. No conversion required.
11:57:01.146 INFO Funcotator - Creating a VCF file for output: file:/srv/DATA/VCFfile/HRR024686.vcf
11:57:01.190 INFO ProgressMeter - Starting traversal
11:57:01.190 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
11:57:11.443 INFO ProgressMeter - NC_000001.11:61875485 0.2 11000 64384.0
11:57:21.691 INFO ProgressMeter - NC_000001.11:183425400 0.3 24000 70243.9
11:57:32.085 INFO ProgressMeter - NC_000002.12:33695464 0.5 38000 73798.3
11:57:42.576 INFO ProgressMeter - NC_000002.12:160124521 0.7 52000 75389.6
11:57:52.960 INFO ProgressMeter - NC_000003.12:21300851 0.9 66000 76493.7
11:58:03.268 INFO ProgressMeter - NC_000003.12:136835081 1.0 80000 77323.3
11:58:13.640 INFO ProgressMeter - NC_000004.12:53461068 1.2 94000 77846.8
11:58:24.294 INFO ProgressMeter - NC_000004.12:182070358 1.4 108000 77975.5
11:58:34.661 INFO ProgressMeter - NC_000005.10:128162281 1.6 122000 78313.9
11:58:44.841 INFO ProgressMeter - NC_000006.12:47453391 1.7 136000 78725.7
11:58:55.056 INFO ProgressMeter - NC_000007.14:904361 1.9 150000 79041.0
11:59:05.267 INFO ProgressMeter - NC_000007.14:103563731 2.1 164000 79306.2
11:59:15.679 INFO ProgressMeter - NC_000008.11:60584391 2.2 178000 79412.3
11:59:25.990 INFO ProgressMeter - NC_000009.12:37486919 2.4 192000 79558.0
11:59:36.137 INFO ProgressMeter - NC_000010.11:12411127 2.6 206000 79769.7
11:59:46.299 INFO ProgressMeter - NC_000010.11:113482961 2.8 220000 79947.2
11:59:56.417 INFO ProgressMeter - NC_000011.10:70238017 2.9 234000 80125.1
12:00:06.529 INFO ProgressMeter - NC_000012.12:32792561 3.1 248000 80285.3
12:00:16.709 INFO ProgressMeter - NC_000013.11:18895365 3.3 262000 80401.4
12:00:27.085 INFO ProgressMeter - NC_000014.9:30605974 3.4 276000 80429.3
12:00:37.452 INFO ProgressMeter - NC_000015.10:47775321 3.6 290000 80458.0
12:00:47.531 INFO ProgressMeter - NC_000016.10:27160763 3.8 304000 80586.4
12:00:57.631 INFO ProgressMeter - NC_000017.11:32718572 3.9 318000 80697.0
12:01:07.792 INFO ProgressMeter - NC_000018.10:49929610 4.1 332000 80777.9
12:01:17.812 INFO ProgressMeter - NC_000019.10:43806368 4.3 346000 80897.2
12:01:27.854 INFO ProgressMeter - NC_000020.11:62943308 4.4 360000 81000.8
12:01:38.144 INFO ProgressMeter - NC_000023.11:23825431 4.6 374000 81024.3
12:01:43.199 INFO ProgressMeter - NW_009646209.1:29696 4.7 380270 80905.9
12:01:43.200 INFO ProgressMeter - Traversal complete. Processed 380270 total variants in 4.7 minutes.
12:01:43.200 WARN Funcotator - ================================================================================
12:01:43.200 WARN Funcotator - _ _ _ __ __ _ _ _ _
12:01:43.200 WARN Funcotator - | || || | \ \ / /_ _ _ __ _ __ (_)_ __ __ _ | || || |
12:01:43.200 WARN Funcotator - | || || | \ \ /\ / / _` | '__| '_ \| | '_ \ / _` | | || || |
12:01:43.200 WARN Funcotator - |_||_||_| \ \V V / (_| | | | | | | | | | | (_| | |_||_||_|
12:01:43.200 WARN Funcotator - (_)(_)(_) \_/\_/ \__,_|_| |_| |_|_|_| |_|\__, | (_)(_)(_)
12:01:43.200 WARN Funcotator - |___/
12:01:43.200 WARN Funcotator - --------------------------------------------------------------------------------
12:01:43.201 WARN Funcotator - Only IGRs were produced for this dataset. This STRONGLY indicates that this
12:01:43.201 WARN Funcotator - run was misconfigured.
12:01:43.201 WARN Funcotator - You MUST check your data sources to make sure they are correct for these data.
12:01:43.201 WARN Funcotator - ================================================================================
12:01:43.202 INFO VcfFuncotationFactory - dbSNP 9606_b150 cache hits/total: 0/0
12:01:43.400 INFO Funcotator - Shutting down engine
[September 16, 2022 at 12:01:43 PM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 4.82 minutes.
Runtime.totalMemory()=2315255808
Tool returned:
true
This is the command I ran:
~/gatk-4.2.6.1/gatk Funcotator --variant output.vcf --reference /srv/hg38/GCF_000001405.40_GRCh38.p14_genomic.fna --ref-version hg38 --data-sources-path /srv/funcotator_dataSources.v1.6.20190124s --output HRR024686.vcf --output-file-format VCF
my gatk version is 4.2.6.1
I use funcotator_dataSources.v1.6.20190124s data source version
and my reference is hg38
I searched for the same issue in previous questions and I already applied FilterMutectCalls and SelectVariants for my VCF file but the problem is still exists.
I am in such a hurry for analyzing my data. please help me with this issue
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Hi Mina,
Thank you for writing to the GATK forum! I hope that we can help you sort this out. I recognize that you are in a rush, so let us see what we can do.
Firstly, it looks like you are not using the most up-to-date version of Funcotator data sources; please find the latest version below.
funcotator_dataSources.v1.7.20200521s.tar.gzIt also appears that there may be some inconsistencies between your references. I brought the issue you encountered to our developers; they provided the following suggestions.
- Try comparing your sequence dictionary in your vcf file to that of the hg38 reference that we use: (gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta)
- Specifically, try looking for whether your contigs have the chr prefixes.
I hope this helps! Please let me know if this leads you to success. If not, I'll return this to the developers for the next steps.
Best,
Anthony
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Hi Anthony
Thank you kindly for your response. I also use the latest version data sources (v1.7) but still got the same error. I think the problem is the format of my hg38 reference (GCF_000001405.40_GRCh38.p14_genomic.fna). In the VCF file the "CHROM" column has refseq name of chromosomes (such as NC_000001.11). I changed chromosome names in VCF file with prefix of chr by bcftools but it didn't help and I still get the same error.
Just to note I didn't encounter any problems with this reference in previous steps such as (alignment with BWA or variant calling with Mutect2)
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Hi Mina,
Thank you for your much-appreciated patience! I brought this back to our developers; they have some follow-up questions and things for you to try.
- Did you update the sequence dictionary in addition to the vcf header after changing chromosome names to chr?
- Did you re-index after you edited the CHROM call in the vcf?
In the vcf header, there should be declarations for all the contigs; if the sequence dictionary is not also updated, you will encounter the same problem because GATK uses the sequence dictionary. Furthermore, if you do not re-index after editing the vcf, the index likely does not have the updated names.
Please try to verify that all are consistent and then attempt to re-run. I hope this helps bring you across the finish line! If not, please let me know, and we will figure out our next steps.
Best,
Anthony
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Hi Mina,
We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!
Kind regards,
Anthony
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