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GATK CountReads Tool

patelsarpatelsar Member
edited August 2013 in Ask the GATK team

Have I done this right? These are the results I received. According to the tutorial if I saw the line that had the word "Walker" in it, then I did it right. But I'm not sure if I'm right or wrong because CountReads gave me the number of reads counted (2075853)

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INFO  18:32:02,582 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  18:32:03,761 GenomeAnalysisEngine - Strictness is SILENT 
INFO  18:32:04,457 GenomeAnalysisEngine - Downsampling Settings: No downsampling 
INFO  18:32:04,469 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO  18:32:04,569 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08 
INFO  18:32:04,933 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO  18:32:04,939 GenomeAnalysisEngine - Done preparing for traversal 
INFO  18:32:04,940 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  18:32:04,940 ProgressMeter -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining 
INFO  18:32:04,944 ReadShardBalancer$1 - Loading BAM index data 
INFO  18:32:04,945 ReadShardBalancer$1 - Done loading BAM index data 
INFO  18:32:35,157 ProgressMeter - NODE_375_length_263320_cov_14.647926:263299        1.75e+06   30.0 s       17.0 s     84.0%        35.0 s     5.0 s 
INFO  18:32:38,826 CountReads - CountReads counted 2075853 reads in the traversal 
INFO  18:32:38,828 ProgressMeter -            done        2.08e+06   33.0 s       16.0 s    100.0%        33.0 s     0.0 s 
INFO  18:32:38,828 ProgressMeter - Total runtime 33.89 secs, 0.56 min, 0.01 hours 
INFO  18:32:38,960 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 2075853 total reads (0.00%) 
INFO  18:32:38,960 MicroScheduler -   -> 0 reads (0.00% of total) failing MalformedReadFilter 
INFO  18:32:39,806 GATKRunReport - Uploaded run statistics report to AWS S3 

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