Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:27
The following output files were created (click the filename to view/download a copy):
CollectAlignmentSummaryMetrics.log
CollectAlignmentSummaryMetrics.metrics.txt

Picard on line resources

Picard output (transposed to make it easier to see)
## net.sf.picard.metrics.StringHeader
# net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 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: Fri Nov 11 08:07:22 EST 2011
## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics
CATEGORYFIRST_OF_PAIR 
TOTAL_READS5 
PF_READS5 
PCT_PF_READS1 
PF_NOISE_READS0 
PF_READS_ALIGNED0 
PCT_PF_READS_ALIGNED0 
PF_ALIGNED_BASES0 
PF_HQ_ALIGNED_READS0 
PF_HQ_ALIGNED_BASES0 
PF_HQ_ALIGNED_Q20_BASES0 
PF_HQ_MEDIAN_MISMATCHES0 
PF_MISMATCH_RATE0 
PF_HQ_ERROR_RATE0 
PF_INDEL_RATE0 
MEAN_READ_LENGTH13 
READS_ALIGNED_IN_PAIRS0 
PCT_READS_ALIGNED_IN_PAIRS0 
BAD_CYCLES0 
STRAND_BALANCE0 
PCT_CHIMERAS0 
PCT_ADAPTER0 
SAMPLE 
LIBRARY 
READ_GROUP  
Picard Tool Run Log
INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true  ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat returned status 0 and nothing on stderr
The freely available Picard software generated all outputs reported here running as a Galaxy tool