Seqal Counters

Seqal provides a number of counters that can be consulted as it runs and at the end of a job. Here is an explanation of what they mean.

Counter name	Explanation
DUPLICATE FRAGMENTS	Number of unpaired fragments identified as duplicates. The fragment may be “unpaired” because its mate was unmapped.
DUPLICATE PAIRS	Number of pairs identified as duplicates.
EMITTED SAM RECORDS	SAM records written to the output files.
MAPPED COORDINATES	Number of mapped reads.
READS FILTERED: LOW QUALITY	Number of reads discarded because of mapq score under the minimum threshold.
READS FILTERED: UNMAPPED	Number of reads discarded because they were unmapped.
READS PROCESSED	Number of reads processed by Seqal (may not be the same as the ones processed by PairReadsQSeq, since it filters as well).
RMDUP UNIQUE FRAGMENTS	Number of unique unpaired reads written to output after duplicate identification.
RMDUP UNIQUE PAIRS	Number of unique read pairs written to output after duplicate identification.
TIME_ANALYZE_PAIRS (CAL_+SW+REFGAP+PROCESS)	Total number of milliseconds (all nodes summed together) spent aligning, filtering, and writing the mapper output.
TIME_BUILD_BWSA	Total number of ms spent converting input to BWA in-memory structures.
TIME_CAL_PAC_POS_PE	Total number of ms spent generating paired alignments.
TIME_CAL_SA_REG_GAP	Total number of ms spent calculating SA position.
TIME_COUNT_BASES	Total number of ms spent counting bases.
TIME_DESTROY_SEQUENCES	Total number of ms spent freeing sequence memory.
TIME_PAIRED_SW	Total number of ms spent performing Smith-Waterman alignment.
TIME_REFINE_GAPPED	Total number of ms spent refining gapped alignments.
TIME_RESTORE_INDEX	Total number of ms spent loading the reference index.
TIME_RESTORE_REFERENCE	Total number of ms spent loading the reference sequence.
TOTAL BASES	Number of bases processes.
TRIMMED BASES	Number of bases trimmed (when read trimming is enabled).