REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:
java -jar /home/ozy/gatk-18.104.22.168/gatk-package-22.214.171.124-local.jar BaseRecalibrator -I /home/ozy/SRR5296488/markedduplikatereadsortedcıktı_2_38.bam -R /home/ozy/hg38/hg38.fasta --known-sites /home/ozy/hg38/baseRecalibrator_dosyaları/hg38.known_indels.vcf --known-sites /home/ozy/hg38/baseRecalibrator_dosyaları/standard.indels.hg38.vcf --known-sites /home/ozy/hg38/baseRecalibrator_dosyaları/all_populations.poly.hg38.vcf --known-sites /home/ozy/hg38/baseRecalibrator_dosyaları/hapmap_3.3.hg38.vcf --known-sites /home/ozy/hg38/baseRecalibrator_dosyaları/hg38.dbsnp138.vcf --maximum-cycle-value -max-cycle 5000 -O recal_data.table
c) Entire program log:
A USER ERROR has occurred: The maximum allowed value for the cycle is 500, but a larger cycle (501) was detected. Please use the --maximum-cycle-value argument (when creating the recalibration table in BaseRecalibrator) to increase this value (at the expense of requiring more memory to run)
While I was trying to use BaseRecalibrator tool I had an error of “A USER ERROR has occurred: The maximum allowed value for the cycle is 500, but a larger cycle (501) was detected. Please use the --maximum-cycle-value argument (when creating the recalibration table in BaseRecalibrator) to increase this value (at the expense of requiring more memory to run)”
Therefore I decided to increase the cycle number by adding the “--maximum-cycle-value -max-cycle 5000” script and performed the analysis. However, I could not understand the consequences of rising the max cycle from 500 to 5000. If I have enough memory is it a problem to rise it? In other words why it is adjusted to 500 in default?
Thank for the comments,
All the best,
If you have enough memory, you can increase the value if you would like. More cycles could potentially help the model, but unless you are having issues with the model, I don't think you need to change the default. We usually optimize the memory requirements so that the tools do not require too much memory while still getting good results.
Also, make sure you are only specifying the argument name once. You don't need to write --maximum-cycle-value -max-cycle 5000, just --maximum-cycle-value 5000. One other note probably unrelated to your issue is that we recommend using the GATK wrapper script instead of calling the jar file: https://gatk.broadinstitute.org/hc/en-us/articles/360035531892-GATK4-command-line-syntax.
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