gatk baserecalibrator no error reported, but no output generated
Hi, gatk developers! I run gatk baserecalibrator as the code below (gatk installed by mamba and activated when in use; the output file exists; and other file path correct), and the finally outputs were as shown on screen, not in file:
gatk BaseRecalibrator \
-R /path/hg38/v0/Homo_sapiens_assembly38.fasta \
-I /path/sample.sorted.markdup.bam \
--known-sites /path/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
--known-sites /path/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
--known-sites /path/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf \
-O /path/05.BQSR/sample.bqsr.recal.table
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There is supposedly an error message in the logs. Can you capture that log and post it here so that we can diagnose the issue?
Regards.
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Hi Celik, thanks too much for fast response! actually i didn't add log while running, I will add it to re-run; And after checking some online sharings, may I know if my codes below is complete and correct, thanks!!
1. samtools faidx /path/hg38/v0/Homo_sapiens_assembly38.fasta
2. tabix -p vcf /path/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz
3. gatk CreateSequenceDictionary -R output/index/ref.fasta -O output/index/ref.dictthen, to run the gatk BaseRecalibrator \xxx? Thank you so much!!
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Hi again.
The log and the error message will tell us what is wrong but it is most likely an incompatible reference or input error.
Let's see what comes out.
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Hi Celik, thanks so much, i re-run it but showing the log was 0 size, with the below codes:
gatk BaseRecalibrator \
-R /path/hg38/v0/Homo_sapiens_assembly38.fasta \
-I /path/sample.sorted.markdup.bam \
--known-sites /path/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz \
--known-sites /path/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
--known-sites /path/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf \
-O /path/05.BQSR/sample.bqsr.recal.table \ >/path/sample.log -
Hi again.
Log is written to stderr so you need to capture stderr messages. You can add
2$>1
to the end of the command after the log file designation and stderr messages will also get loaded into the log file. Also you can copy and paste the console output as text here.
Regards.
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Hi Celik, I found the issue from log, which is due to the hg38.fasta I used in bwa mem from UCSC, while not from gatk bundle. I rerun these and finally the baserecalibrator succeed! Thanks!!
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