GATK version used: GATK4
I tried to run MarkDuplicates like this: picard MarkDuplicates I = $ (FILE) .sort.bam O = $ (FILE) .MD.bam M = $ (FILE) .MD_matrix.txt;
And I got the comment: WARNING 2022-02-06 13:24:09 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three': 'separated fields as numeric values>' did not match read name '2hpf_wt_total_SRR870747.42096'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
And in Matrix only one line came out (I previously ran the command string on the current BAM file and many more lines came out in the matrix).
I tried to run according to previous questions in the forum:
picard ValidateSamFile I = $ (FILE) .sort.bam MODE = SUMMARY;
On the file that came out of sort (before the MarkDuplicates).
And I received:
WARNING 2022-02-06 13:16:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur.
What it means? How can this be fixed? Is the problem with MarkDuplicates related to this?
I would love to help, thank you so much!
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