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BaseRecalibrator was able to recalibrate 0 reads

I'm trying to track down why `BaseRecalibrator` isn't able to recalibrate my reads, but am having trouble finding the problem's source. I'm running GATK v 3.5.

Command:
```
strings=(
S1233686
)


for i in "${strings[@]}"; do
echo "${i}"

java -jar /ast/emb/anaconda3/opt/gatk-3.5/GenomeAnalysisTK.jar \
-T BaseRecalibrator \
-R /ast/emb/prtj3/refs/Homo_sapiens_assembly38.fasta \
-I /ast/emb/prtj3/indel_realigned/${i}.bam \
-knownSites /ast/emb/prtj3/refs/Mills_and_1000G_gold_standard.indels.hg38.vcf \
-knownSites /ast/emb/prtj3/refs/1000G_phase1.snps.high_confidence.hg38.vcf \
-o /ast/emb/prtj3/BQSR/${i}.recal.data.table.txt

done
```



Output:
```INFO 14:42:03,137 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:42:03,139 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 14:42:03,139 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:42:03,139 HelpFormatter - For support and documentation go to removed link
INFO 14:42:03,142 HelpFormatter - Program Args: -T BaseRecalibrator -R /ast/emb/well/prjt3/Homo_sapiens_assembly38.fasta -I /ast/emb/prjt3/indel_realigned/S1233686.bam
-knownSites /ast/emb/prjt3/refs/Mills_and_1000G_gold_standard.indels.hg38.vcf -knownSites /ast/emb/prjt3/refs/1000G_phase1.snps.high_confidence.hg38.vcf -o /ast/emb/prjt3/BQSR/S1233686.recal.data.table.txt
INFO 14:42:03,147 HelpFormatter - Executing as [email protected] on Linux 2.6.32-696.el6.centos.plus.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14.
INFO 14:42:03,147 HelpFormatter - Date/Time: 2019/04/10 14:42:03
INFO 14:42:03,147 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:42:03,147 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:42:03,466 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:42:03,650 GenomeAnalysisEngine - Downsampling Settings: No downsampling
INFO 14:42:03,654 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 14:42:03,773 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.12
INFO 14:42:04,552 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files
INFO 14:42:04,556 GenomeAnalysisEngine - Done preparing for traversal
INFO 14:42:04,557 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 14:42:04,557 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 14:42:04,557 ProgressMeter - Location | reads | elapsed | reads | completed | runtime | runtime
INFO 14:42:04,574 BaseRecalibrator - The covariates being used here:
INFO 14:42:04,575 BaseRecalibrator - ReadGroupCovariate
INFO 14:42:04,575 BaseRecalibrator - QualityScoreCovariate
INFO 14:42:04,575 BaseRecalibrator - ContextCovariate
INFO 14:42:04,575 ContextCovariate - Context sizes: base substitution model 2, indel substitution model 3
INFO 14:42:04,575 BaseRecalibrator - CycleCovariate
INFO 14:42:04,650 ReadShardBalancer$1 - Loading BAM index data
INFO 14:42:04,653 ReadShardBalancer$1 - Done loading BAM index data
INFO 14:42:04,663 BaseRecalibrator - Calculating quantized quality scores...
INFO 14:42:04,674 BaseRecalibrator - Writing recalibration report...
INFO 14:42:04,692 BaseRecalibrator - ...done!
INFO 14:42:04,692 BaseRecalibrator - BaseRecalibrator was able to recalibrate 0 reads
INFO 14:42:04,694 ProgressMeter - done 0.0 0.0 s 37.9 h 100.0% 0.0 s 0.0 s
INFO 14:42:04,694 ProgressMeter - Total runtime 0.14 secs, 0.00 min, 0.00 hours
INFO 14:42:05,344 GATKRunReport - Uploaded run statistics report to AWS S3
```


From the Resource Bundle, I retrieved
`Homo_sapiens_assembly38.fasta`,
`Mills_and_1000G_gold_standard.indels.hg38.vcf`, and
`1000G_phase1.snps.high_confidence.hg38.vcf`.



Here I tried validating the input .bam:

Command:
```
java -jar /ast/emb/anaconda3/share/picard-2.18.16-0/picard.jar ValidateSamFile \
I=/ast/emb/prjt3/indel_realigned/S1233686.bam \
MODE=SUMMARY
```

Output:
```
INFO 2019-04-10 15:12:23 ValidateSamFile

********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** removed link
**********
********** The command line looks like this in the new syntax:
**********
********** ValidateSamFile -I /ast/emb/prjt3/indel_realigned/S1233686.bam -MODE SUMMARY
**********


15:12:24.009 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/ast/emb/anaconda3/share/picard-2.18.16-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Wed Apr 10 15:12:24 EDT 2019] ValidateSamFile INPUT=/ast/emb/prjt3/indel_realigned/S1233686.bam MODE=SUMMARY MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Wed Apr 10 15:12:24 EDT 2019] Executing as [email protected] on Linux 2.6.32-696.el6.centos.plus.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.18.16-SNAPSHOT
WARNING 2019-04-10 15:12:24 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
No errors found
[Wed Apr 10 15:12:24 EDT 2019] picard.sam.ValidateSamFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=506462208
```


Prior to running `BaseRecalibrator`, here's what I did with aligned reads:
1. `MarkDuplicates`
2. `SortSam`, `SORT_ORDER=coordinate`
3. `AddOrReplaceReadGroups`
4. `index`
5. GATK
6. `RealignerTargetCreator`
7. `IndelRealigner`
8. `index`

Sorry, the back ticks don't seem to produce code even after using return.

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