No output when choosing the option '--all_mapped_reads'
alexhbnr opened this issue · 4 comments
When running DamageProfiler (v0.4.4) with the option --all_mapped_reads and keeping all other options as set by default, DamageProfiler is not able to produce is any output. The end of the log file looks like this:
2019-03-06 14:42:56 INFO StartCalculations:108 - 0 Reads processed.
2019-03-06 14:42:56 INFO StartCalculations:108 - 0 Reads processed.
2019-03-06 14:42:56 INFO StartCalculations:108 - 0 Reads processed.
2019-03-06 14:42:56 INFO StartCalculations:108 - 0 Reads processed.
2019-03-06 14:42:56 INFO StartCalculations:952 - Values normalized ....
2019-03-06 14:42:56 INFO StartCalculations:126 - -------------------
2019-03-06 14:42:56 INFO StartCalculations:127 - # reads used for damage calculation: 0
2019-03-06 14:42:56 WARN StartCalculations:333 - No reads processed. Can't create any output
2019-03-06 14:42:56 INFO StartCalculations:276 - Runtime of Module was: 3 seconds.
When running the same file with the same options but --all_mapped_reads, DamageProfiler runs through smoothly and is able to produce all other output files.
Can you send me the beginning of the header of your bam/sam entry? I think that's the problem.
Here are the header lines without the @PG tags.
@HD VN:1.5 SO:coordinate
@SQ SN:MT LN:16569
@RG ID:I0071 SM:I0071 PL:illumina
Is this what you were looking for?
Sorry, my fault. I mean the beginning of the SAM entry. The option --all_mapped_reads only considers entries starting with 'M_'. I think your entries start differently and therefore zero reads are processed.
Hm, actually it makes no sense to name this 'mapped reads'. It should be 'mapped_and_merged_reads'. The idea of this option is that only mapped and merged reads are used to calculate the damage profile.
OK, this makes sense then. My reads indeed don't start with "M_". It might be worth mentioning this in the help text or just read over it.