KNx5
commented
5 years ago After digging into the picard.py script, I realize that the output file that this is erroring on is the Anisopodidae_A5.reads-on-target.txt generated by /phyluce_assembly_get_trinity_coverage_for_uce_loci Here's what that looks like:
lane1_coverageXlocus_output]$ more Anisopodidae_A5.reads-on-target.txt
## htsjdk.samtools.metrics.StringHeader
# CollectHsMetrics BAIT_INTERVALS=[/home/feenerlab/katinkaX/DipteraUCEs/Trinity/Coverage/lane1_coverageXlocus_output/Anisopodidae_A5-UCE-matches-interval.list] TARGET_INTERVALS=[/ho
me/feenerlab/katinkaX/DipteraUCEs/Trinity/Coverage/lane1_coverageXlocus_output/Anisopodidae_A5-UCE-matches-interval.list] INPUT=/home/feenerlab/katinkaX/DipteraUCEs/Trinity/Coverage
/trinity_assemblies_lane1/Anisopodidae_A5/Anisopodidae_A5-CL-RG-M-MD.bam OUTPUT=/home/feenerlab/katinkaX/DipteraUCEs/Trinity/Coverage/lane1_coverageXlocus_output/Anisopodidae_A5.rea
ds-on-target.txt VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/home/feenerlab/katinkaX/DipteraUCEs/Trinity/Coverage/trinity_assemblies_lane1/Anisopodidae_A5/contigs.fasta MET
RIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 SAMPLE_SIZE=10000 ALLELE_FRACTIO
N=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT
_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Jan 14 09:02:11 MST 2019
## METRICS CLASS 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_BASES_ALIGNED PF_UQ_BASES_ALIGNED ON_BAIT_BASES NEAR_BAIT_BASES OFF_BAIT_BASES ON_TARGET_BASES PCT_SELECTED_BASES PCT_O
FF_BAIT ON_BAIT_VS_SELECTED MEAN_BAIT_COVERAGE MEAN_TARGET_COVERAGE MEDIAN_TARGET_COVERAGE MAX_TARGET_COVERAGE PCT_USABLE_BASES_ON_BAIT PCT_USABLE_BASES_ON_T
ARGET FOLD_ENRICHMENT ZERO_CVG_TARGETS_PCT PCT_EXC_DUPE PCT_EXC_MAPQ PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_OFF_TARGET FOLD_80_BASE_PENALTY PCT_TARGET_BASES_1X 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_SI
ZE HS_PENALTY_10X HS_PENALTY_20X HS_PENALTY_30X HS_PENALTY_40X HS_PENALTY_50X HS_PENALTY_100X AT_DROPOUT GC_DROPOUT HET_SNP_SENSITIVITY HET_SNP_Q SAMPL
E LIBRARY READ_GROUP
Anisopodidae_A5-UCE-matches-interval 18490144 801063 801063 1 3065018 3065018 2903876 1 0.947425 1552485 0.534625 195891302 177127730 21056453 0 174834849 16781663 0.10749 0.89251 1 26.285639 20.949242 8 662 0.055723 0.04441 2.481097 0.000929 0.095786 0.26605 0.00521 0.05787 0.579549 5.237311 0.996935 0.983925 0.455064 0.260751 0.184424 0.138436 0.106184 0.037855 352253 79.743427 -1 -1 -1 -1 -1 8.004739 4.036515 0.872487 9
## HISTOGRAM java.lang.Integer
coverage_or_base_quality high_quality_coverage_count unfiltered_baseq_count
0 2455 0
1 10422 0
2 48365 0
3 70045 0
4 73957 0
5 67324 0
6 54786 0
7 43036 0
8 35286 0
9 30852 0
10 26443 0
11 23004 0
12 19152 0
...It looks like the python script is expecting only the metrics section and not the histogram section.
Have you come across this before? Is it a GATK/picard version issue?
Thanks!
brantfaircloth
quattrinia
Greetings, Been muddling through the various gatk issues with getting coverage metrics, but now have this error with my output from phyluce_assembly_get_trinity_coverage that is fed into get_trinity_coverage_for_uce_loci . I've included the input and error below, as well as the directory for this taxon and the picard metrics output. Any ideas? Thanks!
Here is the output from the first script
And within Albuquerquea_B4.all.picard-metricsfile.txt