Range trimming can be out by 30 secs+

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MyronAub
Posts: 7
Joined: Wed Jan 02, 2019 1:09 pm

Range trimming can be out by 30 secs+

Post by MyronAub »

I will often video capture a load of episodes of a TV show overnight which results in a typically 40GB file the next morning. I then use Handbrake to Deinterlace and trim this large file back into individual episode files.

To trim I play the large file back in VLC and then copy the start and end times in seconds into the Range section of Handbrake. This always works fine with smaller files but recently with larger files the first episode seems fine but as I get to say episode three and four etc. the trimmed file is starting a few seconds too late and eventually as much as 30 seconds out (i.e. I told Handbrake to start at the opening credits but the trimmed file actually starts 10 or 20 seconds into the action.)

Has anyone come across this behaviour before or any ideas how to resolve?

HandBrake version (e.g., 1.0.0): Handbrake 1.2.0

Operating system and version (e.g., Ubuntu 16.04 LTS, macOS 10.13 High Sierra, Windows 10 Creators Update): Windows 7 Pro
rollin_eng
Veteran User
Posts: 4840
Joined: Wed May 04, 2011 11:06 pm

Re: Range trimming can be out by 30 secs+

Post by rollin_eng »

Could you please post your HB logs, instructions can be found here:

https://handbrake.fr/docs/en/latest/hel ... y-log.html
MyronAub
Posts: 7
Joined: Wed Jan 02, 2019 1:09 pm

Re: Range trimming can be out by 30 secs+

Post by MyronAub »

I've just done some double checking and noted actual specifics in case it gives anyone any pointers on perhaps a setting I have set wrong:

24GB .ts Interlaced file (4 hours long) containing 6 x 40 minute episodes.
By the fourth episode I've set the Range in Handbrake to start at 02:01:19 but on comparing the outputted file with the original source the trimmed file actually starts at 02:01:47 so 28 seconds out in this particular case.

Correct activity log below:

Code: Select all

HandBrake 1.2.0 (2018121700)
OS: Microsoft Windows NT 6.1.7601 Service Pack 1
Ram: 16265 MB, 
GPU Information:
  Intel(R) HD Graphics 530 - 21.20.16.4860
Screen: 1920x1080
Temp Dir: C:\Users\Chris\AppData\Local\Temp\
Install Dir: C:\Program Files\HandBrake
Data Dir: C:\Users\Chris\AppData\Roaming\HandBrake

-------------------------------------------


# Starting Encode ...

[09:19:07] hb_init: starting libhb thread
[09:19:07] 1 job(s) to process
[09:19:07] json job:
{
  "Audio": {
    "AudioList": [
      {
        "DRC": 0.0,
        "Encoder": "copy:ac3",
        "Gain": 0.0,
        "Mixdown": -1,
        "NormalizeMixLevel": false,
        "Samplerate": 48000,
        "Track": 0,
        "DitherMethod": 0
      },
      {
        "Bitrate": 160,
        "DRC": 0.0,
        "Encoder": "av_aac",
        "Gain": 0.0,
        "Mixdown": 4,
        "NormalizeMixLevel": false,
        "Samplerate": 48000,
        "Track": 0,
        "DitherMethod": 0
      }
    ],
    "CopyMask": [
      "copy:aac",
      "copy:ac3",
      "copy:dtshd",
      "copy:dts",
      "copy:eac3",
      "copy:flac",
      "copy:mp3",
      "copy:truehd"
    ],
    "FallbackEncoder": "ac3"
  },
  "Destination": {
    "ChapterList": [
      {
        "Name": "Chapter 1"
      }
    ],
    "ChapterMarkers": true,
    "AlignAVStart": true,
    "File": "K:\\Videos5\\Captures\\HandBrake\\Criminal Minds S13e10.m4v",
    "Mp4Options": {
      "IpodAtom": false,
      "Mp4Optimize": false
    },
    "Mux": "mp4"
  },
  "Filters": {
    "FilterList": [
      {
        "ID": 4,
        "Settings": {
          "mode": "7"
        }
      },
      {
        "ID": 3,
        "Settings": {
          "block-height": "16",
          "block-thresh": "40",
          "block-width": "16",
          "filter-mode": "2",
          "mode": "3",
          "motion-thresh": "1",
          "spatial-metric": "2",
          "spatial-thresh": "1"
        }
      },
      {
        "ID": 11,
        "Settings": {
          "crop-bottom": "2",
          "crop-left": "0",
          "crop-right": "0",
          "crop-top": "0",
          "height": "1078",
          "width": "1920"
        }
      },
      {
        "ID": 6,
        "Settings": {
          "mode": "0"
        }
      }
    ]
  },
  "PAR": {
    "Num": 1,
    "Den": 1
  },
  "Metadata": {},
  "SequenceID": 0,
  "Source": {
    "Angle": 1,
    "Range": {
      "Type": "time",
      "Start": 655110000,
      "End": 873720000
    },
    "Title": 1,
    "Path": "K:\\Videos5\\Captures\\criminal minds s13e7.ts"
  },
  "Subtitle": {
    "Search": {
      "Burn": true,
      "Default": false,
      "Enable": true,
      "Forced": true
    },
    "SubtitleList": []
  },
  "Video": {
    "Encoder": "x264",
    "Level": "4.0",
    "TwoPass": false,
    "Turbo": false,
    "ColorMatrixCode": 0,
    "Options": "",
    "Preset": "veryslow",
    "Profile": "high",
    "Quality": 20.0,
    "QSV": {
      "Decode": false,
      "AsyncDepth": 0
    }
  }
}
[09:19:07] CPU: Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
[09:19:07]  - Intel microarchitecture Skylake
[09:19:07]  - logical processor count: 8
[09:19:07] Intel Quick Sync Video support: yes
[09:19:07]  - Intel Media SDK hardware: API 1.23 (minimum: 1.3)
[09:19:07]  - H.264 encoder: yes
[09:19:07]     - preferred implementation: hardware (any) via D3D11
[09:19:07]     - capabilities (hardware):  breftype vsinfo opt1 opt2+mbbrc+extbrc+trellis+ib_adapt+nmpslice
[09:19:07]  - H.265 encoder: no
[09:19:07] hb_scan: path=K:\Videos5\Captures\criminal minds s13e7.ts, title_index=1
udfread ERROR: ECMA 167 Volume Recognition failed
src/libbluray/disc/disc.c:323: failed opening UDF image K:\Videos5\Captures\criminal minds s13e7.ts
src/libbluray/disc/disc.c:424: error opening file BDMV\index.bdmv
src/libbluray/disc/disc.c:424: error opening file BDMV\BACKUP\index.bdmv
[09:19:07] bd: not a bd - trying as a stream/file instead
libdvdnav: Using dvdnav version 6.0.0
libdvdread: Encrypted DVD support unavailable.
libdvdread:DVDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.IFO failed
libdvdread:DVDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.BUP failed
libdvdread: Can't open file VIDEO_TS.IFO.
libdvdnav: vm: failed to read VIDEO_TS.IFO
[09:19:07] dvd: not a dvd - trying as a stream/file instead
[09:19:07] file is MPEG Transport Stream with 188 byte packets offset 0 bytes
[09:19:07] Found the following PIDS
[09:19:07]     Video PIDS :
[09:19:07]       0x1011 type H.264 (0x1b) (PCR)
[09:19:07]     Audio PIDS :
[09:19:07]       0x1100 type AC3 (0x81)
[09:19:07]     Subtitle PIDS :
[09:19:07]     Other PIDS :
[09:19:07] stream id 0x1100 (type 0x81 substream 0x0) audio 0x1100
[09:19:08] scan: decoding previews for title 1
[09:19:08] file is MPEG Transport Stream with 188 byte packets offset 0 bytes
[09:19:08] scan: audio 0x1100: ac3, rate=48000Hz, bitrate=384000 Unknown (AC3) (2.0 ch)
[09:19:09] stream: 94 good frames, 0 errors (0%)
[09:19:09] scan: 10 previews, 1920x1080, 25.000 fps, autocrop = 0/2/0/0, aspect 16:9, PAR 1:1
[09:19:09] scan: supported video decoders: avcodec qsv
[09:19:09] libhb: scan thread found 1 valid title(s)
[09:19:09] Skipping subtitle scan.  No suitable subtitle tracks.
[09:19:09] starting job
[09:19:09] decomb filter thread started for segment 0
[09:19:09] decomb filter thread started for segment 1
[09:19:09] decomb filter thread started for segment 2
[09:19:09] decomb filter thread started for segment 3
[09:19:09] decomb filter thread started for segment 4
[09:19:09] decomb filter thread started for segment 5
[09:19:09] decomb filter thread started for segment 6
[09:19:09] decomb filter thread started for segment 7
[09:19:09] decomb check thread started for segment 0
[09:19:09] decomb check thread started for segment 1
[09:19:09] decomb check thread started for segment 2
[09:19:09] decomb check thread started for segment 3
[09:19:09] decomb check thread started for segment 4
[09:19:09] decomb check thread started for segment 5
[09:19:09] decomb check thread started for segment 6
[09:19:09] decomb check thread started for segment 7
[09:19:09] mask filter thread started for segment 0
[09:19:09] mask filter thread started for segment 1
[09:19:09] mask filter thread started for segment 2
[09:19:09] mask filter thread started for segment 3
[09:19:09] mask filter thread started for segment 4
[09:19:09] mask filter thread started for segment 5
[09:19:09] mask filter thread started for segment 7
[09:19:09] mask filter thread started for segment 6
[09:19:09] mask erode thread started for segment 0
[09:19:09] mask erode thread started for segment 1
[09:19:09] mask erode thread started for segment 2
[09:19:09] mask erode thread started for segment 3
[09:19:09] mask erode thread started for segment 4
[09:19:09] mask erode thread started for segment 5
[09:19:09] mask erode thread started for segment 6
[09:19:09] mask erode thread started for segment 7
[09:19:09] mask dilate thread started for segment 0
[09:19:09] mask dilate thread started for segment 1
[09:19:09] mask dilate thread started for segment 2
[09:19:09] mask dilate thread started for segment 3
[09:19:09] mask dilate thread started for segment 4
[09:19:09] mask dilate thread started for segment 5
[09:19:09] mask dilate thread started for segment 7
[09:19:09] yadif thread started for segment 0
[09:19:09] mask dilate thread started for segment 6
[09:19:09] yadif thread started for segment 1
[09:19:09] yadif thread started for segment 2
[09:19:09] yadif thread started for segment 3
[09:19:09] yadif thread started for segment 4
[09:19:09] yadif thread started for segment 5
[09:19:09] yadif thread started for segment 6
[09:19:09] yadif thread started for segment 7
[09:19:09] work: only 1 chapter, disabling chapter markers
[09:19:09] job configuration:
[09:19:09]  * source
[09:19:09]    + K:\Videos5\Captures\criminal minds s13e7.ts
[09:19:09]    + title 1, start 02:01:19.00 stop 02:41:48.00
[09:19:09]  * destination
[09:19:09]    + K:\Videos5\Captures\HandBrake\Criminal Minds S13e10.m4v
[09:19:09]    + container: MPEG-4 (libavformat)
[09:19:09]      + align initial A/V stream timestamps
[09:19:09]  * video track
[09:19:09]    + decoder: h264
[09:19:09]      + bitrate 200 kbps
[09:19:09]    + filters
[09:19:09]      + Comb Detect (mode=3:spatial-metric=2:motion-thresh=1:spatial-thresh=1:filter-mode=2:block-thresh=40:block-width=16:block-height=16)
[09:19:09]      + Decomb (mode=39)
[09:19:09]      + Framerate Shaper (mode=0)
[09:19:09]        + frame rate: same as source (around 25.000 fps)
[09:19:09]      + Crop and Scale (width=1920:height=1078:crop-top=0:crop-bottom=2:crop-left=0:crop-right=0)
[09:19:09]        + source: 1920 * 1080, crop (0/2/0/0): 1920 * 1078, scale: 1920 * 1078
[09:19:09]    + Output geometry
[09:19:09]      + storage dimensions: 1920 x 1078
[09:19:09]      + pixel aspect ratio: 1 : 1
[09:19:09]      + display dimensions: 1920 x 1078
[09:19:09]    + encoder: H.264 (libx264)
[09:19:09]      + preset:  veryslow
[09:19:09]      + profile: high
[09:19:09]      + level:   4.0
[09:19:09]      + quality: 20.00 (RF)
[09:19:09]      + color profile: 1-1-1
[09:19:09]  * audio track 1
[09:19:09]    + decoder: Unknown (AC3) (2.0 ch) (track 1, id 0x1100)
[09:19:09]      + bitrate: 384 kbps, samplerate: 48000 Hz
[09:19:09]    + AC3 Passthru
[09:19:09]  * audio track 2
[09:19:09]    + decoder: Unknown (AC3) (2.0 ch) (track 1, id 0x1100)
[09:19:09]      + bitrate: 384 kbps, samplerate: 48000 Hz
[09:19:09]    + mixdown: Stereo
[09:19:09]    + dither: none
[09:19:09]    + encoder: AAC (libavcodec)
[09:19:09]      + bitrate: 160 kbps, samplerate: 48000 Hz
[09:19:09] file is MPEG Transport Stream with 188 byte packets offset 0 bytes
[09:19:09] sync: expecting 60750 video frames
[09:19:09] encx264: encoding at constant RF 20.000000
[09:19:09] encx264: unparsed options: level=4.0:ref=4:bframes=8:b-adapt=2:direct=auto:analyse=all:me=umh:merange=24:subme=10:trellis=2:vbv-bufsize=31250:vbv-maxrate=25000:rc-lookahead=60
x264 [info]: using SAR=1/1
x264 [info]: using cpu capabilities: MMX2 SSE2Fast SSSE3 SSE4.2 AVX FMA3 BMI2 AVX2
x264 [info]: profile High, level 4.0, 4:2:0, 8-bit
[09:21:33] stream: error near frame 83759: next_packet: sync lost @ 2889679004, regained after 156 bytes
[09:22:36] stream: error near frame 122823: next_packet: sync lost @ 4240179228, regained after 160 bytes
[09:23:37] stream: error near frame 159231: next_packet: sync lost @ 5489885208, regained after 40 bytes
[09:24:52] stream: error near frame 203577: next_packet: sync lost @ 7024476232, regained after 52 bytes
[09:24:59] stream: error near frame 207972: next_packet: sync lost @ 7176781852, regained after 88 bytes
[09:25:20] stream: 40 new errors (0%) up to frame 217972: next_packet: sync lost @ 7522484376, regained after 80 bytes
[09:26:09] stream: error near frame 238258: next_packet: sync lost @ 8225226788, regained after 152 bytes
[09:29:32] stream: error near frame 362225: next_packet: sync lost @ 12504072216, regained after 164 bytes
[09:29:34] sync: first pts audio 0x1100 is 0
[09:29:34] sync: first pts video is 1559
[09:29:34] sync: first pts audio 0x1100 is 1559
[09:45:22] stream: error near frame 381453: next_packet: sync lost @ 13159628904, regained after 116 bytes
[09:45:28] sync: audio 0x1100 time went backwards 32 ms, dropped 1 frames. PTS 31570715
[09:45:29] sync: video time went backwards 80 ms, dropped 2 frames. PTS 31616759
[09:45:30] sync: audio 0x1100 time went backwards 192 ms, dropped 6 frames. PTS 31613762
[10:23:07] sync: video time went backwards 40 ms, dropped 1 frames. PTS 102092527
[11:00:46] sync: video time went backwards 40 ms, dropped 1 frames. PTS 172602127
[11:13:25] stream: error near frame 472824: next_packet: sync lost @ 16321937540, regained after 56 bytes
[11:22:44] stream: error near frame 483866: next_packet: sync lost @ 16702636092, regained after 128 bytes
[11:22:46] sync: video time went backwards 80 ms, dropped 2 frames. PTS 215900759
[11:22:46] sync: video time went backwards 40 ms, dropped 1 frames. PTS 215907959
[11:22:46] sync: video time went backwards 40 ms, dropped 1 frames. PTS 215915159
[11:22:47] sync: video time went backwards 40 ms, dropped 1 frames. PTS 215922359
[11:22:47] sync: video time went backwards 40 ms, dropped 1 frames. PTS 215929559
[11:22:48] sync: video time went backwards 40 ms, dropped 1 frames. PTS 215936759
[11:22:48] sync: video time went backwards 80 ms, dropped 2 frames. PTS 215943959
[11:22:48] sync: video time went backwards 40 ms, dropped 1 frames. PTS 215958359
[11:24:13] sync: reached video pts 218611559, exiting early
[11:24:13] sync: reached audio 0x1100 pts 218612160, exiting early
[11:24:13] sync: reached audio 0x1100 pts 218612162, exiting early
[11:24:35] work: average encoding speed for job is 8.829632 fps
[11:24:35] comb detect: heavy 58665 | light 624 | uncombed 1443 | total 60732
[11:24:35] decomb: deinterlaced 58665 | blended 624 | unfiltered 1443 | total 60732
[11:24:35] vfr: lost time: 0 (0 frames)
[11:24:35] vfr: gained time: 0 (0 frames) (0 not accounted for)
[11:24:35] stream: 495464 good frames, 73 errors (0%)
[11:24:35] ac3-decoder done: 309495 frames, 0 decoder errors
[11:24:35] ac3-decoder done: 309495 frames, 0 decoder errors
[11:24:35] h264-decoder done: 247655 frames, 0 decoder errors
[11:24:35] sync: got 60732 frames, 60750 expected
[11:24:35] sync: framerate min 25.000 fps, max 245.902 fps, avg 25.003 fps
x264 [info]: frame I:488   Avg QP:16.96  size:126845
x264 [info]: frame P:13095 Avg QP:19.85  size: 47569
x264 [info]: frame B:47149 Avg QP:22.09  size: 16198
x264 [info]: consecutive B-frames:  2.0%  2.1%  3.2% 44.3%  9.8%  8.9%  5.3% 23.3%  1.2%
x264 [info]: mb I  I16..4: 15.9% 73.9% 10.2%
x264 [info]: mb P  I16..4:  7.5% 20.1%  1.0%  P16..4: 42.5%  9.7%  8.1%  0.1%  0.0%    skip:11.0%
x264 [info]: mb B  I16..4:  0.8%  2.0%  0.1%  B16..8: 41.7%  4.5%  0.7%  direct: 8.2%  skip:42.0%  L0:46.0% L1:50.5% BI: 3.5%
x264 [info]: 8x8 transform intra:70.2% inter:80.4%
x264 [info]: direct mvs  spatial:100.0% temporal:0.0%
x264 [info]: coded y,uvDC,uvAC intra: 48.8% 47.4% 7.4% inter: 15.8% 21.2% 0.3%
x264 [info]: i16 v,h,dc,p: 26% 26% 15% 33%
x264 [info]: i8 v,h,dc,ddl,ddr,vr,hd,vl,hu: 15% 15% 21%  6%  8%  9%  8%  8%  9%
x264 [info]: i4 v,h,dc,ddl,ddr,vr,hd,vl,hu: 19% 15%  7%  7% 11% 11% 11%  8% 10%
x264 [info]: i8c dc,h,v,p: 37% 34% 23%  7%
x264 [info]: Weighted P-Frames: Y:1.8% UV:1.2%
x264 [info]: ref P L0: 59.7%  9.3% 20.5% 10.3%  0.2%  0.0%
x264 [info]: ref B L0: 87.1% 10.7%  2.2%
x264 [info]: ref B L1: 93.9%  6.1%
x264 [info]: kb/s:4770.77
[11:24:35] mux: track 0, 60732 frames, 1448506174 bytes, 4770.63 kbps, fifo 2048
[11:24:35] mux: track 1, 75907 frames, 116593152 bytes, 384.00 kbps, fifo 2048
[11:24:35] mux: track 2, 113860 frames, 48521183 bytes, 159.80 kbps, fifo 4096
[11:24:35] libhb: work result = 0

# Encode Completed ...

mduell
Veteran User
Posts: 8187
Joined: Sat Apr 21, 2007 8:54 pm

Re: Range trimming can be out by 30 secs+

Post by mduell »

1) Upgrade to the latest release, 1.2.0 isn't really supported, although I don't expect this to fix the problem.

2) The TS is full of stream errors, as you'd expect for broadcasts, so run it through VideoReDo's Quick Stream Fix first.
MyronAub
Posts: 7
Joined: Wed Jan 02, 2019 1:09 pm

Re: Range trimming can be out by 30 secs+

Post by MyronAub »

mduell wrote: Sat Mar 16, 2019 1:35 pm 1) Upgrade to the latest release, 1.2.0 isn't really supported, although I don't expect this to fix the problem.
Hmmm, thanks, clicking the "Check for Updates" button returns "There are no new updates at this time" so if you hadn't of mentioned 1.2.0 was out of date I would never have known!
mduell wrote: Sat Mar 16, 2019 1:35 pm 2) The TS is full of stream errors, as you'd expect for broadcasts, so run it through VideoReDo's Quick Stream Fix first.
Thanks, I'll investigate.
Woodstock
Veteran User
Posts: 4614
Joined: Tue Aug 27, 2013 6:39 am

Re: Range trimming can be out by 30 secs+

Post by Woodstock »

1.2.2 is current. See this topic: viewtopic.php?f=33&p=182902#p182902
mduell
Veteran User
Posts: 8187
Joined: Sat Apr 21, 2007 8:54 pm

Re: Range trimming can be out by 30 secs+

Post by mduell »

MyronAub wrote: Sat Mar 16, 2019 5:40 pm
mduell wrote: Sat Mar 16, 2019 1:35 pm 1) Upgrade to the latest release, 1.2.0 isn't really supported, although I don't expect this to fix the problem.
Hmmm, thanks, clicking the "Check for Updates" button returns "There are no new updates at this time" so if you hadn't of mentioned 1.2.0 was out of date I would never have known!
The updater has not worked reliably for years. It's a real amateur hour with one problem after another.
rollin_eng
Veteran User
Posts: 4840
Joined: Wed May 04, 2011 11:06 pm

Re: Range trimming can be out by 30 secs+

Post by rollin_eng »

mduell wrote: Sun Mar 17, 2019 10:37 am The updater has not worked reliably for years. It's a real amateur hour with one problem after another.
Patches welcome.
mduell
Veteran User
Posts: 8187
Joined: Sat Apr 21, 2007 8:54 pm

Re: Range trimming can be out by 30 secs+

Post by mduell »

Don't use it, don't want it, but I can easily observe it doesn't work from all the complaints.
MyronAub
Posts: 7
Joined: Wed Jan 02, 2019 1:09 pm

Re: Range trimming can be out by 30 secs+

Post by MyronAub »

mduell wrote: Sat Mar 16, 2019 1:35 pm 1) Upgrade to the latest release, 1.2.0 isn't really supported, although I don't expect this to fix the problem.
You were right, 1.2.2 didn't fix the problem, apparently due to inherent errors in the source so not the fault of HB...
mduell wrote: Sat Mar 16, 2019 1:35 pm 2) The TS is full of stream errors, as you'd expect for broadcasts, so run it through VideoReDo's Quick Stream Fix first.
Bingo! Ran QuickStream Fix first and, hey presto, HandBrake can now trim the file at the exact same places viewed in VLC so all good. Many thanks for suggesting this. :D

Does anyone know if there's any possibility of HandBrake incorporating QuickStream Fix functionality in the future? I've no problem with purchasing VideoReDo but it would be more convenient if HB could automatically fix errors first without having to use another step/app to pre-process every large file.
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s55
HandBrake Team
Posts: 10350
Joined: Sun Dec 24, 2006 1:05 pm

Re: Range trimming can be out by 30 secs+

Post by s55 »

There are no plans to incorporate any Redo's functionality in this area.While there is always a chance someone will contribute patches out the blue, it seems unlikley.
mduell
Veteran User
Posts: 8187
Joined: Sat Apr 21, 2007 8:54 pm

Re: Range trimming can be out by 30 secs+

Post by mduell »

MyronAub wrote: Sun Mar 17, 2019 12:06 pmDoes anyone know if there's any possibility of HandBrake incorporating QuickStream Fix functionality in the future? I've no problem with purchasing VideoReDo but it would be more convenient if HB could automatically fix errors first without having to use another step/app to pre-process every large file.
Sure it's possible; as someone else said above, patches welcome.

However it's neither easy nor are the core HB developers sufficiently interested in it, so it's unlikely to happen without your involvement.
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JohnAStebbins
HandBrake Team
Posts: 5712
Joined: Sat Feb 09, 2008 7:21 pm

Re: Range trimming can be out by 30 secs+

Post by JohnAStebbins »

For your use case, fixing the video really needs to be a done with a separate program and not built in to HandBrake. Look at your process. You found the cut points you wanted with VLC, then cut it with HandBrake. If HandBrake and VLC do not see the same video (which was the case when the stream had errors because HandBrake and VLC handle errors differently) then the cut points will not be accurate. You must fix the video *before* finding your cut points with VLC.

It would be nice to have better error recovery built into HandBrake. But it wouldn't have helped you.
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