Empty output files although program is running

[ckeuschn]

Hi,

I am trying to get metaDMG running, but cannot get an output when I try to anaylze a sorted and filered bamfile from the filter-bam program. The program seems to run, but the output *.gz are empty although a damage profile seems to be detected?

Any help pointing me in the right direction would be highly appreciated.

Thank you in advance
Best
Christoph

metaDMG-cpp getdamage -n 10 -l 30 -r 1 -o test test_filtered.bam
-> metaDMG version: v0.4-169-g6124f0b-dirty (htslib: 1.22.1) build(Jul 24 2025 12:57:27)
-> metaDMG-cpp getdamage -n 10 -l 30 -r 1 -o test test_filtered.bam
-> ./metaDMG-cpp refName: (null) min_length: 30 print_length: 5 run_mode: 1 out_prefix: test nthreads: 10 ignore_errors: 0
skipping: VL00799:6:AAG7G5WM5:1:1101:7495:19080 failed: flags=1040, this msg is printed: 2 times more
skipping: VL00799:6:AAG7G5WM5:1:1101:8177:16467 failed: flags=1024, this msg is printed: 1 times more
skipping: VL00799:6:AAG7G5WM5:1:1101:8347:27126 failed: flags=1024, this msg is printed: 0 times more
pos A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G
0 0.00000 0.00000 0.00000 0.00000 0.07692 0.00000 0.00000 0.04167 0.00000 0.00000 0.00000 0.14286
1 0.42857 0.00000 0.00000 0.00000 0.05882 0.05882 0.00000 0.07143 0.00000 0.00000 0.00000 0.00000
2 0.14286 0.00000 0.00000 0.05556 0.00000 0.00000 0.00000 0.08333 0.00000 0.00000 0.00000 0.21429
3 0.09091 0.00000 0.00000 0.00000 0.06667 0.06667 0.00000 0.17647 0.05882 0.00000 0.00000 0.00000
4 0.11111 0.00000 0.00000 0.06250 0.06250 0.00000 0.00000 0.00000 0.27273 0.00000 0.00000 0.00000
pos A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G
0 0.00000 0.10000 0.00000 0.07692 0.07692 0.07692 0.10000 0.00000 0.00000 0.05556 0.00000 0.05556
1 0.15385 0.07692 0.00000 0.00000 0.07692 0.00000 0.00000 0.05000 0.00000 0.00000 0.00000 0.00000
2 0.00000 0.00000 0.00000 0.05263 0.00000 0.05263 0.00000 0.11765 0.05882 0.00000 0.00000 0.00000
3 0.10000 0.00000 0.00000 0.00000 0.11765 0.11765 0.00000 0.09091 0.00000 0.00000 0.00000 0.00000
4 0.00000 0.11111 0.00000 0.00000 0.20000 0.00000 0.00000 0.20000 0.00000 0.00000 0.00000 0.00000
-> Will dump: 'test.res.gz' this contains damage patterns for: 9888 items
-> Setting threads to: 10
-> Will dump: 'test.bdamage.gz' this contains damage patterns for: 9888 items
-> Setting threads to: 10
-> Will dump: 'test.rlens.gz' this contains read length distributions for: 9888 items
-> Setting threads to: 10
-> Outputting overall statistic in file: "test.stat.gz"

metaDMG-cpp print test.bdamage.gz -bam test_filtered.bam
-> metaDMG version: v0.4-169-g6124f0b-dirty (htslib: 1.22.1) build(Jul 24 2025 12:57:27)
-> metaDMG-cpp print test.bdamage.gz -bam test_filtered.bam
infile: test.bdamage.gz inbam: test_filtered.bam search: -1 ctga: 0 countout: 0 nodes: (null) names: (null) howmany: 15
-> printlength(howmany) from inputfile: 0
Reference Nalignments Direction Pos AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT