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):
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 | 
| CATEGORY | FIRST_OF_PAIR | 
| TOTAL_READS | 5 | 
| PF_READS | 5 | 
| PCT_PF_READS | 1 | 
| PF_NOISE_READS | 0 | 
| PF_READS_ALIGNED | 0 | 
| PCT_PF_READS_ALIGNED | 0 | 
| PF_ALIGNED_BASES | 0 | 
| PF_HQ_ALIGNED_READS | 0 | 
| PF_HQ_ALIGNED_BASES | 0 | 
| PF_HQ_ALIGNED_Q20_BASES | 0 | 
| PF_HQ_MEDIAN_MISMATCHES | 0 | 
| PF_MISMATCH_RATE | 0 | 
| PF_HQ_ERROR_RATE | 0 | 
| PF_INDEL_RATE | 0 | 
| MEAN_READ_LENGTH | 13 | 
| READS_ALIGNED_IN_PAIRS | 0 | 
| PCT_READS_ALIGNED_IN_PAIRS | 0 | 
| BAD_CYCLES | 0 | 
| STRAND_BALANCE | 0 | 
| PCT_CHIMERAS | 0 | 
| PCT_ADAPTER | 0 | 
| 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