STAR solo bam file throws sorting error but successfully finishes?

[Tonya Brunetti]

Hello Alex,

Great software!  I have been a STAR user for several, several years and I love the great documentation and how well it works, so thank you!  Lately, I have been using STAR solo and my bam files map perfectly fine, but sometimes at the sorting stage, it throws this error:

[W::sam_hdr_read] bgzf_check_EOF: Invalid argument
[E::bam_hdr_read] invalid BAM binary header

However, it continues to run (no seg faults) eventually the STAR log will still output the following, indicating it is successful:

Dec 25 10:51:26 ..... started STAR run
Dec 25 10:51:27 ..... loading genome
Dec 25 10:52:41 ..... started mapping
Dec 25 12:08:03 ..... finished mapping
Dec 25 12:08:06 ..... started Solo counting
Dec 25 12:13:59 ..... finished Solo counting
Dec 25 12:13:59 ..... started sorting BAM
Dec 25 19:21:01 ..... finished successfully

And it still produces a bam file and Log.final.out file.

Since there is no seg fault and it seems to produce a bam and a Log.final.out file, is it ok to use the bam output or will there be other problems with it?

Thanks!

Tonya

[Alexander Dobin]

Hi Tonya,

It looks like there was an issue with sorting. It took really long time (>7 hours). Please send me the Log.out file.