I am processing ~200 million WGS aligned reads with Picard's ValidateSamFile, with the following options:
MODE=VERBOSE MAX_OUTPUT=10000000 TMP_DIR=[/local2/tmp] IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
However, the job ends prematurely without any errors and says it is complete -- after processing only 300K or so reads.
I have used this tool before without any issues for alignments with multimillions of reads.
Please advise, any help would be much appreciated!