failed to read matrix from stream : Expected "[", got "['" File position at start -1, currently -1

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Woody Byun

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Jul 3, 2019, 1:43:59 AM7/3/19
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Hi, I am trying to run steps/segmentation/prepare_targets_gmm.sh for speech activity detection (SAD), but I am stucked at reading matrix part. (Failed to read matrix from stream.  : Expected "[", got "['" File position at start is -1, currently -1 below). I just guess there's a problem at format of matrix file, but I have no idea how to fix this error. 

the exact command line (which is part of our local SAD code) is : 

steps/segmentation/prepare_targets_gmm.sh --stage 5 \
    --train-cmd "$train_cmd" --decode-cmd "$decode_cmd" \
    --nj $nj --reco-nj $reco_nj --lang-test $lang_test \
    --garbage-phones-list $dir/garbage_phones.txt \
    --silence-phones-list $dir/silence_phones.txt \
    --merge-weights "$merge_weights" \
    --graph-dir "$graph_dir" \
    $lang $data_dir $whole_data_dir $sat_model_dir $model_dir $dir


FYI, I am using python 3.5.2 and current version of kaldi is compiled properly. 

Thank you in advance!



# steps/segmentation/internal/merge_segment_targets_to_recording.py --reco2num-frames=/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/reco2num_frames --frame-shift=0.01 --default-targets= /home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/split40reco/reco2utt.25 /home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/split40reco/segments.25 /home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/split40reco/targets.25.scp - | copy-feats ark,t:- ark,scp:/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/targets.25.ark,/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/targets.25.scp
copy-feats ark,t:- ark,scp:/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/targets.25.ark,/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/targets.25.scp
2019-07-03 11:31:50,164 [steps/segmentation/internal/merge_segment_targets_to_recording.py:187 - run - ERROR ] Command 'copy-feats --binary=false /home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_sup_targets/targets.49.ark:241212 -' failed
ERROR (copy-feats[5.5.391~1-fe541]:Read():kaldi-matrix.cc:1617) Failed to read matrix from stream.  : Expected "[", got "['" File position at start is -1, currently -1

[ Stack-Trace: ]
/home/users/lucasjo/_tool_/kaldi/src/lib/libkaldi-base.so(kaldi::MessageLogger::LogMessage() const+0x82c) [0x2b40ac3fa28a]
copy-feats(kaldi::MessageLogger::LogAndThrow::operator=(kaldi::MessageLogger const&)+0x21) [0x414665]
/home/users/lucasjo/_tool_/kaldi/src/lib/libkaldi-matrix.so(kaldi::Matrix<float>::Read(std::istream&, bool, bool)+0x1aca) [0x2b40ac19991c]
copy-feats(kaldi::KaldiObjectHolder<kaldi::Matrix<float> >::Read(std::istream&)+0x290) [0x422bd8]
copy-feats(kaldi::SequentialTableReaderArchiveImpl<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::Next()+0x321) [0x422f0f]
copy-feats(kaldi::SequentialTableReaderArchiveImpl<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x2c3) [0x41f511]
copy-feats(kaldi::SequentialTableReader<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x2b4) [0x41d278]
copy-feats(kaldi::SequentialTableReader<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::SequentialTableReader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x47) [0x41d46b]
copy-feats(main+0x813) [0x411559]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x2b40acdd6830]
copy-feats(_start+0x29) [0x410c79]

WARNING (copy-feats[5.5.391~1-fe541]:Read():util/kaldi-holder-inl.h:84) Exception caught reading Table object. kaldi::KaldiFatalError
WARNING (copy-feats[5.5.391~1-fe541]:Next():util/kaldi-table-inl.h:574) Object read failed, reading archive standard input
WARNING (copy-feats[5.5.391~1-fe541]:Open():util/kaldi-table-inl.h:521) Error beginning to read archive file (wrong filename?): standard input
ERROR (copy-feats[5.5.391~1-fe541]:SequentialTableReader():util/kaldi-table-inl.h:860) Error constructing TableReader: rspecifier is ark,t:-

[ Stack-Trace: ]
/home/users/lucasjo/_tool_/kaldi/src/lib/libkaldi-base.so(kaldi::MessageLogger::LogMessage() const+0x82c) [0x2b40ac3fa28a]
copy-feats(kaldi::MessageLogger::LogAndThrow::operator=(kaldi::MessageLogger const&)+0x21) [0x414665]
copy-feats(kaldi::SequentialTableReader<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::SequentialTableReader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xa1) [0x41d4c5]
copy-feats(main+0x813) [0x411559]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x2b40acdd6830]
copy-feats(_start+0x29) [0x410c79]

kaldi::KaldiFatalErrorTraceback (most recent call last):
  File "steps/segmentation/internal/merge_segment_targets_to_recording.py", line 291, in <module>
    main()
  File "steps/segmentation/internal/merge_segment_targets_to_recording.py", line 285, in main
    run(args)
  File "steps/segmentation/internal/merge_segment_targets_to_recording.py", line 184, in run
    mat = np.matrix(common_lib.read_matrix_ascii(p.stdout),
  File "steps/libs/common.py", line 414, in read_matrix_ascii
    raise RuntimeError
RuntimeError
# Accounting: time=5 threads=1

Daniel Povey

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Jul 3, 2019, 10:36:49 AM7/3/19
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Looks like there is a stray quote in that file.  Are you sure you didn't put that file in an editor and accidentally change it?

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Woody Byun

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Jul 3, 2019, 10:33:46 PM7/3/19
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I'm pretty sure that I didn't do anything regarding editing that file. 

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Atlas LabsㅣWoody Byunㅣ변석현
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Daniel Povey

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Jul 3, 2019, 10:54:56 PM7/3/19
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OK, well you at least have something to debug.  There is a stray quote in that file, apparently.  Is it there for other matrices, or just that one?
If all else fails it could be file system corruption.
Check you didn't change the Kaldi source code.


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Woody Byun

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Jul 3, 2019, 11:06:42 PM7/3/19
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it fails in every single step (all merge_targets_to_reco.*.log), and I also didn't change anything from the previous kaldi SAD code which  perfectly worked well only couple days ago.

If it's file system corruption problem how can i cope with it ? 

Daniel Povey

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Jul 3, 2019, 11:15:42 PM7/3/19
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Go to the top of your repo and do
git status -uno
git log -3
and show the output


On Wed, Jul 3, 2019 at 11:06 PM Woody Byun <wo...@atlaslabs.ai> wrote:
it fails in every single step (all merge_targets_to_reco.*.log), and I also didn't change anything from the previous kaldi SAD code which  perfectly worked well only couple days ago.

If it's file system corruption problem how can i cope with it ? 

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Woody Byun

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Jul 3, 2019, 11:44:19 PM7/3/19
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1. git status -uno:

On branch modify_wer_return
You have unmerged paths.
  (fix conflicts and run "git commit")

Changes to be committed:

        modified:   ../../.gitignore
        new file:   ../../LICENSE
        new file:   ../../analysis_train_log.ipynb
        new file:   ../../cmd.sh
        new file:   ../../conf/decode.config
        new file:   ../../conf/mfcc.conf
        new file:   ../../conf/mfcc_8kHz.conf
        new file:   ../../conf/mfcc_hires.conf
        new file:   ../../conf/mfcc_hires_8kHz.conf
        new file:   ../../conf/online_cmvn.conf
        new file:   ../../conf/queue.conf
        new file:   ../../conf/vad.conf
        new file:   ../../local/align-visual.py
        new file:   ../../local/align.sh
        new file:   ../../local/analysis_tdnn_train.sh
        new file:   ../../local/apply_segmentation.sh
        new file:   ../../local/buildLM/at_unicode.py
        new file:   ../../local/buildLM/normStep1.py
        new file:   ../../local/buildLM/normStep2.py
        new file:   ../../local/buildLM/normStep3.py
        new file:   ../../local/buildLM/normStep4.py
        new file:   ../../local/buildLM/normStepFinal.py
        new file:   ../../local/buildLM/strip.py
        new file:   ../../local/chain/multi_condition/run_tdnn_1b.sh
        new file:   ../../local/chain/multi_condition/run_tdnn_1f.sh
        new file:   ../../local/chain/multi_condition/run_tdnn_1g.sh
        new file:   ../../local/chain/multi_condition/run_tdnn_1g_zeroth.sh
        new file:   ../../local/chain/multi_condition/run_tdnn_1n.sh
        new file:   ../../local/chain/multi_condition/run_tdnn_lstm_1e.sh
        new file:   ../../local/chain/run_tdnn_1a.sh
        new file:   ../../local/chain/run_tdnn_1b.sh
        new file:   ../../local/chain/run_tdnn_1b_transferlearning_1a.sh
        new file:   ../../local/chain/run_tdnn_1n_transferlearning_1a.sh
        new file:   ../../local/chain/run_tdnn_lstm_1e.sh
        new file:   ../../local/character_tokenizer.sh
        new file:   ../../local/checkDur.sh
        new file:   ../../local/checkHours.sh
        new file:   ../../local/check_mfcc_log.sh
        new file:   ../../local/convKor2Num.py
        new file:   ../../local/copy_lat_dir.sh
        new file:   ../../local/copy_lat_dir_rvb.sh
        new file:   ../../local/data/get_reco2dur.sh
        new file:   ../../local/data_prep.sh
        new file:   ../../local/data_prep_car_clean.sh
        new file:   ../../local/data_prep_noisy01_clean.sh
        new file:   ../../local/data_prep_nospkinfo.sh
        new file:   ../../local/export_sad.sh
        new file:   ../../local/fName_norm.py
        new file:   ../../local/filter.py
        new file:   ../../local/filter_data_dir.sh
        new file:   ../../local/format_lms.sh
        new file:   ../../local/multi_condition/copy_ali_dir.sh
        new file:   ../../local/nnet3/multi_condition/data_augmentation.sh
        new file:   ../../local/nnet3/multi_condition/data_augmentation_v2.sh
        new file:   ../../local/nnet3/multi_condition/run_ivector_common.sh
        new file:   ../../local/nnet3/multi_condition/run_ivector_common_v2.sh
        new file:   ../../local/nnet3/run_ivector_common.sh
        new file:   ../../local/nnet3/segment_and_decode.sh
        new file:   ../../local/prepare_dict.sh
        new file:   ../../local/report_cer.sh
        new file:   ../../local/revert_segmentation.sh
        new file:   ../../local/run_sad_test.sh
        new file:   ../../local/run_sad_training.sh
        new file:   ../../local/score.sh
        new file:   ../../local/segmentation/tuning/train_lstm_asr_sad_1a.sh
        new file:   ../../local/segmentation/tuning/train_stats_asr_sad_1a.sh
        new file:   ../../local/split_dataset.sh
        new file:   ../../path.sh
        new file:   ../../run.sh
        new file:   ../../speechDATA
        new file:   ../../steps
        new file:   ../../utils

Unmerged paths:
  (use "git add <file>..." to mark resolution)

        both added:      ../../README.md

Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        deleted:    ../ami/s5/README
        modified:   ../callhome_diarization/v2/run.sh
        modified:   ../librispeech/s5/cmd.sh
        modified:   ../librispeech/s5/run.sh
        modified:   ../mini_librispeech/s5/cmd.sh
        deleted:    ../zeroth_korean/s5/README.txt
        deleted:    ../zeroth_korean/s5/RESULTS
        deleted:    ../zeroth_korean/s5/cmd.sh
        deleted:    ../zeroth_korean/s5/conf/decode.config
        deleted:    ../zeroth_korean/s5/conf/mfcc.conf
        deleted:    ../zeroth_korean/s5/conf/mfcc_hires.conf
        deleted:    ../zeroth_korean/s5/conf/online_cmvn.conf
        deleted:    ../zeroth_korean/s5/local/chain/compare_wer.sh
        deleted:    ../zeroth_korean/s5/local/chain/run_tdnn.sh
        deleted:    ../zeroth_korean/s5/local/chain/run_tdnn_opgru.sh
        deleted:    ../zeroth_korean/s5/local/chain/tuning/run_tdnn_1a.sh
        deleted:    ../zeroth_korean/s5/local/chain/tuning/run_tdnn_opgru_1a.sh
        deleted:    ../zeroth_korean/s5/local/data_prep.sh
        deleted:    ../zeroth_korean/s5/local/download_and_untar.sh
        deleted:    ../zeroth_korean/s5/local/format_lms.sh
        deleted:    ../zeroth_korean/s5/local/nnet3/run_ivector_common.sh
        deleted:    ../zeroth_korean/s5/local/prepare_dict.sh
        deleted:    ../zeroth_korean/s5/local/score.sh
        deleted:    ../zeroth_korean/s5/local/update_segmentation.sh
        deleted:    ../zeroth_korean/s5/path.sh
        deleted:    ../zeroth_korean/s5/run.sh
        deleted:    ../zeroth_korean/s5/steps
        deleted:    ../zeroth_korean/s5/utils
        modified:   ../../scripts/rnnlm/compute_sentence_scores.sh
        modified:   ../../scripts/rnnlm/lmrescore_nbest.sh
        modified:   ../../scripts/rnnlm/train_rnnlm.sh

2. git log -3 : 

commit f107cdba3252c884d58acc59584df2b75b33fb04
Author: Hosung Park <indr...@gmail.com>
Date:   Sun Apr 21 13:11:54 2019 +0900

    [egs] Improve chain example script for Resource Management (RM) (#3252)

commit c3260f242f0f331d5131dbd7ac9835f391756e06
Author: Soonshin Seo <ss...@sogang.ac.kr>
Date:   Sat Apr 20 04:38:37 2019 +0900

    [egs] Make voxceleb recipe work with latest version of the dataset  (#3249)

commit 84ecd0e1e2a09b3196ebacecee3e2f40505dd067
Author: Hosung Park <indr...@gmail.com>
Date:   Fri Apr 19 12:14:37 2019 +0900

    [egs] Update RM chain recipe with more recent configuration (#3237)

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Daniel Povey

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Jul 4, 2019, 12:03:37 AM7/4/19
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Your repo seems to be a few months old, plus  it looks like you've done some local merging so maybe you changed some code locally.
I suspect you made changes in the matrix/ directory.  You'll have to do tests with copy-feats using the ark,t:- output style and see if it gives you those extra single quotes.

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Woody Byun

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Jul 4, 2019, 1:59:11 AM7/4/19
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well, when I do ". ./path.sh" and run "steps/segmentation/internal/merge_segment_targets_to_recording.py --reco2num-frames=/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/reco2num_frames --frame-shift=0.01 --default-targets= /home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/split40reco/reco2utt.25 /home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/split40reco/segments.25 /home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/split40reco/targets.25.scp - | copy-feats ark,t:- ark,scp:/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/targets.25.ark,/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/targets.25.scp" on command line, it just gives the same error: 

copy-feats ark,t:- ark,scp:/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/targets.25.ark,/home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_whole_sup_targets/targets.25.scp
2019-07-04 14:57:49,023 [steps/segmentation/internal/merge_segment_targets_to_recording.py:187 - run - ERROR ] Command 'copy-feats --binary=false /home/users/woody/kaldi_practice/kaldi_woody/egs/zeroth-sad/exp/segmentation_1a/tri3b_train_100k_sup_targets/targets.49.ark:971270 -' failed

Traceback (most recent call last):
  File "steps/segmentation/internal/merge_segment_targets_to_recording.py", line 291, in <module>
ERROR (copy-feats[5.5.391~1-fe541]:Read():kaldi-matrix.cc:1617) Failed to read matrix from stream.  : Expected "[", got "['" File position at start is -1, currently -1

[ Stack-Trace: ]
/home/users/lucasjo/_tool_/kaldi/src/lib/libkaldi-base.so(kaldi::MessageLogger::LogMessage() const+0x82c) [0x7f6a22b7728a]

copy-feats(kaldi::MessageLogger::LogAndThrow::operator=(kaldi::MessageLogger const&)+0x21) [0x414665]
/home/users/lucasjo/_tool_/kaldi/src/lib/libkaldi-matrix.so(kaldi::Matrix<float>::Read(std::istream&, bool, bool)+0x1aca) [0x7f6a22dc491c]

copy-feats(kaldi::KaldiObjectHolder<kaldi::Matrix<float> >::Read(std::istream&)+0x290) [0x422bd8]
copy-feats(kaldi::SequentialTableReaderArchiveImpl<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::Next()+0x321) [0x422f0f]
copy-feats(kaldi::SequentialTableReaderArchiveImpl<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x2c3) [0x41f511]
copy-feats(kaldi::SequentialTableReader<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x2b4) [0x41d278]
copy-feats(kaldi::SequentialTableReader<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::SequentialTableReader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x47) [0x41d46b]
copy-feats(main+0x813) [0x411559]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f6a22012830]

copy-feats(_start+0x29) [0x410c79]

WARNING (copy-feats[5.5.391~1-fe541]:Read():util/kaldi-holder-inl.h:84) Exception caught reading Table object. kaldi::KaldiFatalError
WARNING (copy-feats[5.5.391~1-fe541]:Next():util/kaldi-table-inl.h:574) Object read failed, reading archive standard input
WARNING (copy-feats[5.5.391~1-fe541]:Open():util/kaldi-table-inl.h:521) Error beginning to read archive file (wrong filename?): standard input
    main()

ERROR (copy-feats[5.5.391~1-fe541]:SequentialTableReader():util/kaldi-table-inl.h:860) Error constructing TableReader: rspecifier is ark,t:-

[ Stack-Trace: ]
/home/users/lucasjo/_tool_/kaldi/src/lib/libkaldi-base.so(kaldi::MessageLogger::LogMessage() const+0x82c) [0x7f6a22b7728a]

copy-feats(kaldi::MessageLogger::LogAndThrow::operator=(kaldi::MessageLogger const&)+0x21) [0x414665]
copy-feats(kaldi::SequentialTableReader<kaldi::KaldiObjectHolder<kaldi::Matrix<float> > >::SequentialTableReader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xa1) [0x41d4c5]
copy-feats(main+0x813) [0x411559]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f6a22012830]
copy-feats(_start+0x29) [0x410c79]


  File "steps/segmentation/internal/merge_segment_targets_to_recording.py", line 285, in main
kaldi::KaldiFatalError    run(args)

  File "steps/segmentation/internal/merge_segment_targets_to_recording.py", line 184, in run
    mat = np.matrix(common_lib.read_matrix_ascii(p.stdout),
  File "steps/libs/common.py", line 414, in read_matrix_ascii
    raise RuntimeError
RuntimeError
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Daniel Povey

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Jul 4, 2019, 11:10:16 AM7/4/19
to kaldi-help
I suspect you might have edited the file write_matrix_ascii in the file steps/libs/common.py, somewhere in your branch, by adding an extra single quote.


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Woody Byun

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Jul 4, 2019, 9:37:59 PM7/4/19
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I resolved the problem. thanks!

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kartik sharma

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Jan 16, 2020, 12:52:44 AM1/16/20
to kaldi-help
how did you solve??
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