Other than trial & error, how do you know what to set MINIMUM_PCT at for picard.jar CollectInsertSizeMetrics?   With this data-set it crashes at 0.15 but works for 0.16.  I had to run the job about 7 times to get that answer.  Is there a more intelligent way of figuring this out?  

Can you please provide

a) GATK version used

picard-1.134 but question applies to all versions of CollectInsertSizeMetrics

b) Exact GATK commands used  java -Djava.io.tmpdir=/data1/BIOINFORMATICS/TEMP/ -Xmx20g -jar SOFTWARE/broadinstitute-picard-1.134/broadinstitute-picard-a7a08c4/dist/picard.jar CollectInsertSizeMetrics INPUT=R3e_MARK_DUPLICATES/79130_Met_fixmate_novosort_dupsrm.bam TMP_DIR=/data1/BIOINFORMATICS/TEMP/ OUTPUT=R3_STATS/79130_Met_fixmate_novosort_dupsrm.bam_insert_size_metrics.txt HISTOGRAM_FILE=R3_STATS/79130_Met_fixmate_novosort_dupsrm.bam_insert_size_metrics.pdf REFERENCE_SEQUENCE=/data1/BIOINFORMATICS/REFERENCES/NIMBLEGEN/HumanGenome/HG-38/hg38.fa LEVEL=ALL_READS ASSUME_SORTED=true METRIC_ACCUMULATION_LEVEL=READ_GROUP VALIDATION_STRINGENCY=LENIENT MINIMUM_PCT=0.15
c) The entire error log if applicable.

INFO 2020-02-03 00:51:33 SinglePassSamProgram Processed 16,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 3s. Last read position: chr11:1,199,353
INFO 2020-02-03 00:51:36 SinglePassSamProgram Processed 17,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr11:113,449,929
INFO 2020-02-03 00:51:40 SinglePassSamProgram Processed 18,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 3s. Last read position: chr12:88,058,943
INFO 2020-02-03 00:51:44 SinglePassSamProgram Processed 19,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 3s. Last read position: chr14:20,456,519
INFO 2020-02-03 00:51:47 SinglePassSamProgram Processed 20,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 3s. Last read position: chr15:20,566,510
INFO 2020-02-03 00:51:51 SinglePassSamProgram Processed 21,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 3s. Last read position: chr16:1,592,172
INFO 2020-02-03 00:51:54 SinglePassSamProgram Processed 22,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 3s. Last read position: chr16:30,291,085
INFO 2020-02-03 00:51:58 SinglePassSamProgram Processed 23,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 3s. Last read position: chr17:40,820,286
INFO 2020-02-03 00:52:02 SinglePassSamProgram Processed 24,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 3s. Last read position: chr18:44,526,992
INFO 2020-02-03 00:52:05 SinglePassSamProgram Processed 25,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 3s. Last read position: chr19:51,169,649
INFO 2020-02-03 00:52:09 SinglePassSamProgram Processed 26,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 3s. Last read position: chr21:10,482,682
INFO 2020-02-03 00:52:12 SinglePassSamProgram Processed 27,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: chrX:46,118,588
INFO 2020-02-03 00:52:16 SinglePassSamProgram Processed 28,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 3s. Last read position: chrX:110,055,319
INFO 2020-02-03 00:54:37 RExecutor Executing R script via command: Rscript /data1/BIOINFORMATICS/TEMP/script3814707552746657418.R /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3_STATS/79130_Met_fixmate_novosort_dupsrm.bam_insert_size_metrics.txt /data/BIOINFORMATICS/PROJECT_PROD_JN/CAS-0010688777/snakemake-ez-dpops/R3_STATS/79130_Met_fixmate_novosort_dupsrm.bam_insert_size_metrics.pdf 79130_Met_fixmate_novosort_dupsrm.bam
INFO 2020-02-03 00:54:38 ProcessExecutor [1] "Not creating insert size PDF as there are duplicated header names: All_Reads"
INFO 2020-02-03 00:54:38 ProcessExecutor [2] "Not creating insert size PDF as there are duplicated header names: unknown"
[Mon Feb 03 00:54:38 EST 2020] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 4.13 minutes.
Runtime.totalMemory()=7563378688