diff --git a/tests/fate-run.sh b/tests/fate-run.sh
index 931150b5a6..9aa9a22395 100755
--- a/tests/fate-run.sh
+++ b/tests/fate-run.sh
@@ -142,10 +142,17 @@ crc(){
     ffmpeg "$@" -f crc -
 }
 
-md5(){
+md5pipe(){
     ffmpeg "$@" md5:
 }
 
+md5(){
+    encfile="${outdir}/${test}.out"
+    cleanfiles="$cleanfiles $encfile"
+    ffmpeg "$@" $encfile
+    do_md5sum $encfile | awk '{print $1}'
+}
+
 pcm(){
     ffmpeg "$@" -vn -f s16le -
 }
diff --git a/tests/fate/filter-audio.mak b/tests/fate/filter-audio.mak
index 5d15b31e0b..8030641ed6 100644
--- a/tests/fate/filter-audio.mak
+++ b/tests/fate/filter-audio.mak
@@ -215,7 +215,7 @@ fate-filter-channelmap-one-int: SRC = $(TARGET_PATH)/tests/data/asynth-44100-6.w
 fate-filter-channelmap-one-int: tests/data/asynth-44100-6.wav
 fate-filter-channelmap-one-int: CMD = md5 -i $(SRC) -filter_complex_script $(TARGET_PATH)/tests/data/filtergraphs/channelmap_one_int -f wav -fflags +bitexact
 fate-filter-channelmap-one-int: CMP = oneline
-fate-filter-channelmap-one-int: REF = 428b8f9fac6d57147069b97335019ef5
+fate-filter-channelmap-one-int: REF = 8cfe553d65ed4696756d8c1b824fcdd3
 
 FATE_FILTER_CHANNELMAP += fate-filter-channelmap-one-str
 fate-filter-channelmap-one-str: tests/data/filtergraphs/channelmap_one_str
@@ -223,7 +223,7 @@ fate-filter-channelmap-one-str: SRC = $(TARGET_PATH)/tests/data/asynth-44100-2.w
 fate-filter-channelmap-one-str: tests/data/asynth-44100-2.wav
 fate-filter-channelmap-one-str: CMD = md5 -i $(SRC) -filter_complex_script $(TARGET_PATH)/tests/data/filtergraphs/channelmap_one_str -f wav -fflags +bitexact
 fate-filter-channelmap-one-str: CMP = oneline
-fate-filter-channelmap-one-str: REF = e788890db6a11c2fb29d7c4229072d49
+fate-filter-channelmap-one-str: REF = 0ea3052e482c95d5d3bd9da6dac1b5fa
 
 FATE_AFILTER-$(call FILTERDEMDECENCMUX, CHANNELMAP, WAV, PCM_S16LE, PCM_S16LE, WAV) += $(FATE_FILTER_CHANNELMAP)
 
diff --git a/tests/fate/matroska.mak b/tests/fate/matroska.mak
index 48b710c26c..2747496e1e 100644
--- a/tests/fate/matroska.mak
+++ b/tests/fate/matroska.mak
@@ -2,7 +2,7 @@
 # properties in remuxing (-c:v copy)
 # It also tests automatic insertion of the vp9_superframe bitstream filter
 FATE_MATROSKA-$(call DEMMUX, MATROSKA, MATROSKA) += fate-matroska-remux
-fate-matroska-remux: CMD = md5 -i $(TARGET_SAMPLES)/vp9-test-vectors/vp90-2-2pass-akiyo.webm -color_trc 4 -c:v copy -fflags +bitexact -strict -2 -f matroska
+fate-matroska-remux: CMD = md5pipe -i $(TARGET_SAMPLES)/vp9-test-vectors/vp90-2-2pass-akiyo.webm -color_trc 4 -c:v copy -fflags +bitexact -strict -2 -f matroska
 fate-matroska-remux: CMP = oneline
 fate-matroska-remux: REF = 1ed49a4f2b6790357fac268938357353
 
diff --git a/tests/fate/subtitles.mak b/tests/fate/subtitles.mak
index fc2b192e5d..11cbb82b24 100644
--- a/tests/fate/subtitles.mak
+++ b/tests/fate/subtitles.mak
@@ -14,7 +14,7 @@ FATE_SUBTITLES_ASS-$(CONFIG_ASS_DEMUXER) += fate-sub-ssa-to-ass-remux
 fate-sub-ssa-to-ass-remux: CMD = fmtstdout ass -i $(TARGET_SAMPLES)/sub/a9-misc.ssa -c copy
 
 FATE_SUBTITLES-$(call ALLYES, ASS_DEMUXER, MATROSKA_MUXER) += fate-binsub-mksenc
-fate-binsub-mksenc: CMD = md5 -i $(TARGET_SAMPLES)/sub/1ededcbd7b.ass -c copy -f matroska -flags +bitexact -fflags +bitexact
+fate-binsub-mksenc: CMD = md5pipe -i $(TARGET_SAMPLES)/sub/1ededcbd7b.ass -c copy -f matroska -flags +bitexact -fflags +bitexact
 
 FATE_SUBTITLES_ASS-$(call DEMDEC, JACOSUB, JACOSUB) += fate-sub-jacosub
 fate-sub-jacosub: CMD = fmtstdout ass -i $(TARGET_SAMPLES)/sub/JACOsub_capability_tester.jss
diff --git a/tests/fate/wavpack.mak b/tests/fate/wavpack.mak
index 32ae3f6100..e4e8d47128 100644
--- a/tests/fate/wavpack.mak
+++ b/tests/fate/wavpack.mak
@@ -89,12 +89,12 @@ FATE_WAVPACK-$(call DEMDEC, MATROSKA, WAVPACK) += fate-wavpack-matroskamode
 fate-wavpack-matroskamode: CMD = md5 -i $(TARGET_SAMPLES)/wavpack/special/matroska_mode.mka -f s16le
 
 FATE_WAVPACK-$(call DEMMUX, WV, MATROSKA) += fate-wavpack-matroska_mux-mono
-fate-wavpack-matroska_mux-mono: CMD = md5 -i $(TARGET_SAMPLES)/wavpack/num_channels/mono_16bit_int.wv -c copy -fflags +bitexact -f matroska
+fate-wavpack-matroska_mux-mono: CMD = md5pipe -i $(TARGET_SAMPLES)/wavpack/num_channels/mono_16bit_int.wv -c copy -fflags +bitexact -f matroska
 fate-wavpack-matroska_mux-mono: CMP = oneline
 fate-wavpack-matroska_mux-mono: REF = 11773e2a518edc788475f3880d849230
 
 FATE_WAVPACK-$(call DEMMUX, WV, MATROSKA) += fate-wavpack-matroska_mux-61
-fate-wavpack-matroska_mux-61: CMD = md5 -i $(TARGET_SAMPLES)/wavpack/num_channels/eva_2.22_6.1_16bit-partial.wv -c copy -fflags +bitexact -f matroska
+fate-wavpack-matroska_mux-61: CMD = md5pipe -i $(TARGET_SAMPLES)/wavpack/num_channels/eva_2.22_6.1_16bit-partial.wv -c copy -fflags +bitexact -f matroska
 fate-wavpack-matroska_mux-61: CMP = oneline
 fate-wavpack-matroska_mux-61: REF = 9641abdf596c10c2e21bd9b026d4bade
 
diff --git a/tests/ref/fate/mapchan-6ch-extract-2-downmix-mono b/tests/ref/fate/mapchan-6ch-extract-2-downmix-mono
index a47c85cd6b..9ac4dba261 100644
--- a/tests/ref/fate/mapchan-6ch-extract-2-downmix-mono
+++ b/tests/ref/fate/mapchan-6ch-extract-2-downmix-mono
@@ -1 +1 @@
-2727e5418eb5b8f89954f140d9f3a19a
+6ededcfc9f0b26d200a7295205e87663
diff --git a/tests/ref/fate/mapchan-silent-mono b/tests/ref/fate/mapchan-silent-mono
index f720c318f4..93f519e0ee 100644
--- a/tests/ref/fate/mapchan-silent-mono
+++ b/tests/ref/fate/mapchan-silent-mono
@@ -1 +1 @@
-16dc73c037897dff9b1d3e3d8561dc73
+b6b034fffa8639e64d79be84f16d9ebe
diff --git a/tests/ref/fate/mpeg4-bsf-unpack-bframes b/tests/ref/fate/mpeg4-bsf-unpack-bframes
index 162d436625..703ae3a8e8 100644
--- a/tests/ref/fate/mpeg4-bsf-unpack-bframes
+++ b/tests/ref/fate/mpeg4-bsf-unpack-bframes
@@ -1 +1 @@
-c9535e459c2ee4ead6d84b93bc7e9f46
+a0c4ba21ab9d68966b8fce7cc848e2c6
diff --git a/tests/ref/fate/time_base b/tests/ref/fate/time_base
index eec4b21aa5..7923556b35 100644
--- a/tests/ref/fate/time_base
+++ b/tests/ref/fate/time_base
@@ -1 +1 @@
-ef9896ce045941607782e895aea930b6
+d26a35b141551b36c5b8bd716451cfcb
diff --git a/tests/ref/fate/v410enc b/tests/ref/fate/v410enc
index 139da7b875..9fddf5a35c 100644
--- a/tests/ref/fate/v410enc
+++ b/tests/ref/fate/v410enc
@@ -1 +1 @@
-5fd2d9a7b3311f5c19dbdd647bb9eae6
+465bcc7477104a8295f47b35f1b987df