MarkDuplicates expects to find a pattern in the reads' names (it is used to find the lane, tile and the X,Y position in the lane/tile) https://en.wikipedia.org/wiki/FASTQ_format

With Casava 1.8 the format of the '@' line has changed:

@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG

EAS139 the unique instrument name

(...)

if your reads names don't have a standard format , MarkDuplicates won't be able to find the information. There is an option to fix this:

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.0.4.0/picard_sam_markduplicates_MarkDuplicates.php#--READ_NAME_REGEX

Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim. Note that without optical duplicate counts, library size estimation will be inaccurate. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.