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1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping RG line that has a repeated ID field.
WARNING: Duplicate Tags, overwritting XA:C:123 with XA:S:456
WARNING: Duplicate Tags, overwritting RR:Z:myID1 with RR:Z:myID2
WARNING: Duplicate Tags, overwritting MD:Z:30A0C5 with MD:Z:2T1N0
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping RG line that has a repeated ID field.
WARNING: Duplicate Tags, overwritting XA:C:123 with XA:S:456
WARNING: Duplicate Tags, overwritting RR:Z:myID1 with RR:Z:myID2
Suppressing rest of Duplicate Tag warnings.
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping RG line that has a repeated ID field.
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping RG line that has a repeated ID field.
ERROR: Missing required tag: SN.
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failed to store SQ record.
ERROR: Missing required tag: LN.
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failed to store SQ record.
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping SQ line that has a repeated SN field.
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping SQ line that has a repeated SN field.
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: multiple HD records.
Can't modify the key tag, SN from chr20 to
ERROR: Missing required tag: VN.
Can't modify the key tag, ID from pid to pid1
Can't modify the key tag, ID from pid to pid1
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping PG line that has a repeated ID field.
Can't modify the key tag, ID from rgID to rgID1
1 invalid SAM/BAM Header lines were skipped due to:
SAM/BAM Header line failure: Skipping RG line that has a repeated ID field.
Can't modify the key tag, ID from rgID1 to rgID111
SamCoordOutput::flush, no output file/header is set, so records removed without being written
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