pyatac ins output returning all zero values

[NatashaJansz]

Hello. I'm hoping someone might see this and be able to help me out!

I'm running pyatac ins which seems to run just fine with no errors, however my output is a bedfile with all zeros. I have plenty of reads in the regions I'm trying to analyse, so I definitely expect to have non-zero values in my output.

When I run pyatac ins on the example data that comes with nucleatac, I get the expected values, so it must be a problem with my input files.

I've copied the head of each file. Can anyone see anything wrong? Thank you.

INPUT:
--bed
chr1 10000 10468 (TAACCC)n 463.000000 + hg38_rmsk exon . gene_id "(TAACCC)n"
chr1 10468 11447 TAR1 3612.000000 - hg38_rmsk exon . gene_id "TAR1"; transcript_id "TAR1";
chr1 11504 11675 L1MC5a 484.000000 - hg38_rmsk exon . gene_id "L1MC5a"
chr1 11677 11780 MER5B 239.000000 - hg38_rmsk exon . gene_id "MER5B"
chr1 15264 15355 MIR3 318.000000 - hg38_rmsk exon . gene_id "MIR3"
chr1 15797 15849 (TGCTCC)n 18.000000 + hg38_rmsk exon . gene_id "(TGCTCC)n"
chr1 16712 16744 (TGG)n 18.000000 + hg38_rmsk exon . gene_id "(TGG)n"; transcript_id "(TGG)n";
chr1 18906 19048 L2a 239.000000 + hg38_rmsk exon . gene_id "L2a"; transcript_id "L2a_dup29";
chr1 19971 20405 L3 994.000000 + hg38_rmsk exon . gene_id "L3"; transcript_id "L3_dup3";
chr1 20530 20679 Plat_L3 270.000000 + hg38_rmsk exon . gene_id "Plat_L3"; transcript_id "Plat_L3"

--bam

SRR5487871.10911061 16 chr1 9996 7 51M * 0 0 AGACAGAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC IGHEIGFBIIJIHFJIJIHFIGCGGFGHFFGFJJIGGFHHHHFDFFFFBB@ MD:Z:0N0N0N0N0N0T45 PG:Z:MarkDuplicates XG:i:0 NM:i:6 XM:i:6 XN:i:5 XO:i:0 AS:i:-10 XS:i:-16 YT:Z:UU
SRR5487873.93330727 16 chr1 9996 0 51M * 0 0 AGAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC JJIIIJJJJJJJHGJJJJHGJJJIGFJJIIHFJJHHGEHHHHFBFFFFB@B MD:Z:0N0N0N0N0N0T1A43 PG:Z:MarkDuplicates XG:i:0 NM:i:7 XM:i:7 XN:i:5 XO:i:0 AS:i:-17 XS:i:-17 YT:Z:UU
SRR5487871.86506019 16 chr1 9997 0 51M * 0 0 GAGACAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC JIHEJIIIJIIIHJJIHFCIIHEF?JIHGHGJIIGHFIHHHFDFFFDD?BB MD:Z:0N0N0N0N0T1A44 PG:Z:MarkDuplicates XG:i:0 NM:i:6 XM:i:6 XN:i:4 XO:i:0 AS:i:-16 XS:i:-23 YT:Z:UU
SRR5487871.167501667 16 chr1 9998 2 51M * 0 0 AGACAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC JIIJJJJJJIGHJJJIHGJJJIHFJJIHFEJJIHGFJJHHHFHFFDDBC@B MD:Z:0N0N0N0T1A45 PG:Z:MarkDuplicates XG:i:0 NM:i:5 XM:i:5 XN:i:3 XO:i:0 AS:i:-15 XS:i:-17 YT:Z:UU
SRR5487873.208726844 16 chr1 9998 2 51M * 0 0 AGACAGCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCC JJJJJJJJJIHGJJIJIHJIJIHGJJHGFFIJJIHFJIFHHFHFFFDDCBB MD:Z:0N0N0N0T1A45 PG:Z:MarkDuplicates XG:i:0 NM:i:5 XM:i:5 XN:i:3 XO:i:0 AS:i:-15 XS:i:-17 YT:Z:UU
SRR5487873.196275616 16 chr1 9999 0 4M2I45M * 0 0 TATAAGAGACAAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC JJJIJJJIIJJHFJJIIGFIJIIHFJJIHGFJJJIHGJHHHFFFFFDDB@B MD:Z:0N0N3C0C1T40 PG:Z:MarkDuplicates XG:i:2 NM:i:7 XM:i:5 XN:i:2 XO:i:1 AS:i:-31 YT:Z:UU
SRR5487873.210949433 0 chr1 10002 1 51M * 0 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC CCCFFFFFHGHHGJJJIJJEIJIIJDEHIGIIIIIGIIIJIIJEIJGIJGH MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
SRR5487871.107151502 16 chr1 10002 1 51M * 0 0 AACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC CBIHDDFBIHHGGGIHGAD?JHEFC<JIIFEAJIGAGCHHHFFDFFFF@@@ MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
SRR5487873.177373414 16 chr1 10002 1 51M * 0 0 AGACATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC ##########BB@FGGHDC:IGGE?+HGBCA+GGHGC<HFBDD=DDDD@@@ MD:Z:1A0C1C46 PG:Z:MarkDuplicates XG:i:0 NM:i:3 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-6 YT:Z:UU
SRR5487873.169069869 0 chr1 10003 1 51M * 0 0 ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC @CCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJIJJJJJJJ MD:Z:51 PG:Z:MarkDuplicates XG:i:0 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU

OUTPUT:

chr1 4499007 4499279 0.0
chr1 4499594 4499845 0.0
chr1 4500030 4500340 0.0
chr1 4500499 4500575 0.0
chr1 4500630 4500721 0.0
chr1 4501176 4501406 0.0
chr1 4501450 4501827 0.0
chr1 4501956 4502385 0.0
chr1 4502622 4502866 0.0
chr1 4503055 4503261 0.0