IntelInflater.java spits out "WARN - Zero Bytes Written : 0" whenever reading the terminal block of a bam file for all tools

[lucifer9288]

Instructions

it‘s my first time to run the pipline for RNA-seq data.
the log of SplitNCigarReads makes me confused which said '00:39:03.278 WARN IntelInflater - Zero Bytes Written : 0' at below.
i don't know weather this step works will or just return the files same as last step？
maybe someone know what's happened，I'm very grateful for someone to help me answer this question！

00:35:09.127 INFO ProgressMeter - 23:27354557 12.4 29918000 2404017.7
00:35:19.176 INFO ProgressMeter - 23:39821286 12.6 30308000 2403016.1
00:35:29.182 INFO ProgressMeter - unmapped 12.8 30712000 2403270.9
00:35:39.184 INFO ProgressMeter - 25:18185455 12.9 31112000 2403222.6
00:35:49.196 INFO ProgressMeter - 25:35485074 13.1 31463000 2399411.3
00:35:59.205 INFO ProgressMeter - 26:15194951 13.3 31932000 2404584.5
00:36:09.210 INFO ProgressMeter - 26:39796753 13.4 32325000 2403995.1
00:36:19.234 INFO ProgressMeter - 27:19938980 13.6 33035000 2426647.2
00:36:29.429 INFO ProgressMeter - 28:32806413 13.8 33417000 2424444.0
00:36:39.586 INFO ProgressMeter - unmapped 14.0 33821000 2423984.0
00:36:49.602 INFO ProgressMeter - 29:43615735 14.1 34294000 2428825.2
00:36:59.630 INFO ProgressMeter - X:20297509 14.3 34746000 2432052.2
00:37:09.635 INFO ProgressMeter - X:79368355 14.5 35002000 2421702.8
00:37:19.744 INFO ProgressMeter - unmapped 14.6 35364000 2418555.7
00:37:29.986 INFO ProgressMeter - MT:4752 14.8 36632000 2476365.0
00:37:39.989 INFO ProgressMeter - MT:6105 15.0 37831000 2528917.2
00:37:50.172 INFO ProgressMeter - MT:6537 15.1 38943000 2574051.7
00:38:00.172 INFO ProgressMeter - MT:7097 15.3 40049000 2618311.9
00:38:10.174 INFO ProgressMeter - MT:8432 15.5 41100000 2658052.2
00:38:20.250 INFO ProgressMeter - MT:9258 15.6 42088000 2692704.3
00:38:30.365 INFO ProgressMeter - MT:11181 15.8 43055000 2725181.1
00:38:40.367 INFO ProgressMeter - MT:13120 16.0 44100000 2762177.2
00:38:50.424 INFO ProgressMeter - MT:14886 16.1 45149000 2798500.4
00:39:00.640 INFO ProgressMeter - MT:15825 16.3 46271000 2838093.5
00:39:03.278 WARN IntelInflater - Zero Bytes Written : 0
00:39:03.284 INFO SplitNCigarReads - 0 read(s) filtered by: AllowAllReadsReadFilter

00:39:03.586 INFO OverhangFixingManager - Overhang Fixing Manager saved 60712 reads in the first pass
00:39:03.589 INFO SplitNCigarReads - Starting traversal pass 2
00:39:10.673 INFO ProgressMeter - 1:58494939 16.5 47045000 2856275.5
00:39:21.853 INFO ProgressMeter - 1:80508954 16.7 47317000 2840650.5
00:39:31.864 INFO ProgressMeter - 1:118661332 16.8 47631000 2831142.5
00:39:42.395 INFO ProgressMeter - 1:135587841 17.0 47895000 2817441.3
00:39:52.406 INFO ProgressMeter - 1:144426574 17.2 48184000 2806892.2
00:40:02.431 INFO ProgressMeter - 2:17749449 17.3 48428000 2793912.3
00:40:12.445 INFO ProgressMeter - 2:85957479 17.5 48718000 2783838.0
00:40:22.634 INFO ProgressMeter - 2:98466734 17.7 48963000 2770949.4
00:40:32.811 INFO ProgressMeter - 2:120118461 17.8 49221000 2759065.9
00:40:42.823 INFO ProgressMeter - 2:135574270 18.0 49526000 2750438.5
00:40:52.830 INFO ProgressMeter - 3:12568695 18.2 49858000 2743462.7
00:41:02.839 INFO ProgressMeter - 3:22877295 18.3 50127000 2733176.3
00:41:14.396 INFO ProgressMeter - 3:39868739 18.5 50376000 2718205.3

[jamesemery]

Hi @lucifer9288. Thanks for pointing this out as its a very confusing message. Its an oversight in our logging that causes that error message and it should not mean that your execution of SplitNCigarReads was invalid. The inflater in this message is referring to the fact that one of the compressed blocks gets uncompressed with zero output bytes which happens with the very last block of a properly formatted BGZF file (as a your input bam should be). It looks like the issue is an errant message in the GKL intel inflater.

[jamesemery]

Doing some digging it seems the message was added in the IntelInflater.inflate() update as of our upgrade to gkl:0.8.8. This is a very minor logging bug but we should probably ask for that warning to be removed as its confusing to users.