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BQSR; ERROR MESSAGE : Bad input: The GATK report has no version specified in the header

FabriceBesnardFabriceBesnard ParisMember
edited October 2014 in Ask the GATK team

Hi,
I am using GATK version 3.2-2-gec30cee.
I have a pb with BQSR. Whwn I run the first step (analyze covariates), everything seems to be fine according to the INFO given by the walker:
Command used:
java -jar -Xmx16g $GATK -T BaseRecalibrator -R ./assembly/spades_reapr.genome.abv500.fna -I BAMsort-RG-dedup-realign_Miseq300.bam -knownSites CEW1_Miseq300_HC0.vcf -o CEW1_Miseq300_BQSR1.table
INFOs read on shell:

INFO 16:11:41,114 BaseRecalibrator - ...done!
INFO 16:11:41,115 BaseRecalibrator - BaseRecalibrator was able to recalibrate 33940210 reads
INFO 16:11:41,116 ProgressMeter - done 3.3941981E7 86.9 m 2.6 m 100.0% 86.9 m 0.0 s
INFO 16:11:41,117 ProgressMeter - Total runtime 5214.59 secs, 86.91 min, 1.45 hours
INFO 16:11:41,117 MicroScheduler - 2144047 reads were filtered out during the traversal out of approximately 36086028 total reads (5.94%)
INFO 16:11:41,118 MicroScheduler - -> 1567207 reads (4.34% of total) failing DuplicateReadFilter
INFO 16:11:41,118 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter
INFO 16:11:41,119 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter
INFO 16:11:41,119 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter
INFO 16:11:41,120 MicroScheduler - -> 546586 reads (1.51% of total) failing MappingQualityZeroFilter
INFO 16:11:41,120 MicroScheduler - -> 30254 reads (0.08% of total) failing NotPrimaryAlignmentFilter
INFO 16:11:41,121 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter
INFO 16:11:42,763 GATKRunReport - Uploaded run statistics report to AWS S

But the generated table (CEW1_Miseq300_BQSR1.table) is empty: it is a blank file, as if something went wrong in the previous step...

As expected, when I go to calculate remaining covariates afer plot:
java -jar -Xmx16g $GATK -T BaseRecalibrator -R ./assembly/spades_reapr.genome.abv500.fna -I BAMsort-RG-dedup-realign_Miseq300.bam -knownSites CEW1_Miseq300_HC0.vcf -BQSR CEW1_Miseq300_BQSR1.table -o CEW1_Miseq300_post-BQSR1.table
I get the following error message:

ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):
ERROR
ERROR This means that one or more arguments or inputs in your command are incorrect.
ERROR The error message below tells you what is the problem.
ERROR
ERROR If the problem is an invalid argument, please check the online documentation guide
ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
ERROR
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
ERROR
ERROR MESSAGE: Bad input: The GATK report has no version specified in the header
ERROR ------------------------------------------------------------------------------------------

Do you know what's happening?
Could you help fix this?

Many thanks!

Fabrice

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