Dear all,
I calculated Picard HsMetrics and the FOLD_80_BASE_PENALTY metric had
a question mark ("?").
I have attached the output file to this email.
Do you know what might have happened?
Thank you and best wishes,
Esteban
## net.sf.picard.metrics.StringHeader
# net.sf.picard.analysis.directed.CalculateHsMetrics
BAIT_INTERVALS=EXOMEV3_KAPA_1_microgram_subsample.bait_intervals.txt
TARGET_INTERVALS=EXOMEV3_KAPA_1_microgram_subsample.target_intervals.txt
INPUT=EXOMEV3_KAPA_1_microgram_subsample.srt.mkdups.bam
OUTPUT=EXOMEV3_KAPA_1_microgram_subsample_calculate_hs_metrics.txt
METRIC_ACCUMULATION_LEVEL=[ALL_READS]
REFERENCE_SEQUENCE=/data/annotation/hg19/hg19.fa TMP_DIR=[.]
VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5
MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
## net.sf.picard.metrics.StringHeader
# Started on: Tue May 27 04:02:25 EDT 2014
## METRICS CLASS net.sf.picard.analysis.directed.HsMetrics
BAIT_SET GENOME_SIZE BAIT_TERRITORY TARGET_TERRITORY
BAIT_DESIGN_EFFICIENCY TOTAL_READS PF_READS PF_UNIQUE_READS
PCT_PF_READS PCT_PF_UQ_READS PF_UQ_READS_ALIGNED PCT_PF_UQ_READS_ALIGNED
PF_UQ_BASES_ALIGNED ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES
ON_TARGET_BASES PCT_SELECTED_BASES PCT_OFF_BAIT ON_BAIT_VS_SELECTED
MEAN_BAIT_COVERAGE MEAN_TARGET_COVERAGE PCT_USABLE_BASES_ON_BAIT
PCT_USABLE_BASES_ON_TARGET FOLD_ENRICHMENT ZERO_CVG_TARGETS_PCT
FOLD_80_BASE_PENALTY PCT_TARGET_BASES_2X PCT_TARGET_BASES_10X
PCT_TARGET_BASES_20X PCT_TARGET_BASES_30X PCT_TARGET_BASES_40X
PCT_TARGET_BASES_50X PCT_TARGET_BASES_100X HS_LIBRARY_SIZE HS_PENALTY_10X
HS_PENALTY_20X HS_PENALTY_30X HS_PENALTY_40X HS_PENALTY_50X HS_PENALTY_100X
AT_DROPOUT GC_DROPOUT SAMPLE LIBRARY READ_GROUP
EXOMEV3_KAPA_1_microgram_subsample 3095693983 64190747
63564965 0.990251 1489424 1489424 1488442 1 0.999341
1305549 0.877125 129535097 82223204 32197962
15113931 79685603 0.883322 0.116678 0.718601
1.28092 1.641928 0.555873 0.538717 30.612059
0.339827 ? 0.329202 0.002417 0.000263
0.000061 0.000021 0.00001 0 502957198 -1 -1
-1 -1 -1 -1 0.001777 9.100754
------------------------------------------------------------------------------
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