Ryan Lorig-Roach

Ok i will take a closer look at the paper. I just tried rerunning with `--sv-off` and it appears to have reduced these rearrangements.

With `sv-off` I do still get some strange ones though, unfortunately: ``` 2497450 60236 146 29307 - h2tg000005l 111658231 848222 878809 3055 30728 46 tp:A:P cm:i:219 s1:i:2764 s2:i:2331 rl:i:636 2497450...

Thanks @ekg, this is interesting. As it turns out, I've been digging into these issues more and have found that @lh3 was right about many of them being chimeric. A...

To be more specific about the remaining non-chimeric artifacts I mentioned, here are 2 examples: ``` 14617 59497 29 59436 + h2tg000052l 87420292 61492027 61545226 18078 59881 60 tp:A:P cm:i:1359...

I'm getting a similar set of errors on Python 3.10.12 ``` fa2/fa2util.c: In function ‘__Pyx_modinit_type_init_code’: fa2/fa2util.c:10939:32: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 10939 | __pyx_type_3fa2_7fa2util_Node.tp_print =...

I'm not sure if this is the same error or underlying issue but I recently attempted to align NovaSeq reads and got this: ``` [0000] 1. Calling kt_for - worker_bwt...

Sure here they are: **PASS** ``` curl 7.81.0 (x86_64-pc-linux-gnu) libcurl/7.81.0 OpenSSL/3.0.2 zlib/1.2.11 brotli/1.0.9 zstd/1.4.8 libidn2/2.3.2 libpsl/0.21.0 (+libidn2/2.3.2) libssh/0.9.6/openssl/zlib nghttp2/1.43.0 librtmp/2.3 OpenLDAP/2.5.13 Release-Date: 2022-01-05 Protocols: dict file ftp ftps gopher gophers...

It doesn't crash when using this public BAM: `gs://pepper-deepvariant-public/T2T_case_study/chm13.draft_v0.9.hifi_20k.wm_1.11.pri.chr20.bam` (it needs to be fetched in the chr20 contig because there are no alignments elsewhere)

I should say, using my own private gs URI it always fails. Here are some potentially relevant differences I found between the verbose logs (on the same BAM, on different...

oh yes this definitely explains it. In my original script, the first bam would succeed but the second one would fail. They have different URIs, but the same filename (orphaned...