Errors at the end of the SNP calling

I am following the next steps to call variants in RNA-seq data:

https://software.broadinstitute.org/gatk/guide/article?id=3891

I am runnig the step 6 of variant calling using this command line:

java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R /LUSTRE/usuario/egonzalez/referencias/Zea_mays.AGPv3.22.dna.genome.fasta -I PT_todo_splitN.bam -o PTxB73F1.vcf -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0

And that give me the next errors:

INFO  00:25:28,277 ProgressMeter -     1:301362893    1.766387238E9    33.1 h           67.0 s      100.0%   33.1 h       6.0 s 
INFO  00:25:29,258 VectorLoglessPairHMM - Time spent in setup for JNI call : 33.407765322 
INFO  00:25:29,259 PairHMM - Total compute time in PairHMM computeLikelihoods() : 87411.73185938601 
INFO  00:25:29,259 HaplotypeCaller - Ran local assembly on 221086 active regions 
INFO  00:25:29,756 ProgressMeter -            done    2.067864162E9    33.1 h           57.0 s      100.0%    33.1 h       0.0 s 
INFO  00:25:29,757 ProgressMeter - Total runtime 119221.45 secs, 1987.02 min, 33.12 hours 
INFO  00:25:29,758 MicroScheduler - 93331090 reads were filtered out during the traversal out of approximately 194330945 total reads (48.03%) 
INFO  00:25:29,758 MicroScheduler -   -> 4209 reads (0.00% of total) failing BadCigarFilter 
INFO  00:25:29,758 MicroScheduler -   -> 59464782 reads (30.60% of total) failing DuplicateReadFilter 
INFO  00:25:29,759 MicroScheduler -   -> 604373 reads (0.31% of total) failing FailsVendorQualityCheckFilter 
INFO  00:25:29,759 MicroScheduler -   -> 33257726 reads (17.11% of total) failing HCMappingQualityFilter 
INFO  00:25:29,760 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO  00:25:29,760 MicroScheduler -   -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter 
INFO  00:25:29,760 MicroScheduler -   -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter 
INFO  00:25:29,761 MicroScheduler -   -> 0 reads (0.00% of total) failing UnmappedReadFilter 
INFO  00:25:32,255 GATKRunReport - Uploaded run statistics report to AWS S3

I am using GATK/3.5.0. At the end I have the vcf file and everything looks normal in it, but I am not sure which is the problem with these errors. Do you know which is the problem?