(base) [mzakeri1@devlangmead1 hprc_v1_separator_indexes]$ /usr/bin/time ~/Movi/build_test/movi build --list reference/hprc_v1.txt --index movi_regular_thresholds.hprc_94/ --separators
[INFO] 20:12:01 - Reverse complement: 1
[INFO] 20:12:01 - Separator: 1
[INFO] 20:12:01 - /data/blangme2/fasta/hprc-v2/fastas/100000_CHM13.pri.fa
[INFO] 20:12:39 - /data/blangme2/fasta/hprc-v2/fastas/110000_GRCh38.pri.fa
[INFO] 20:13:16 - /data/blangme2/fasta/hprc-yr1/HG002.1.fa
[INFO] 20:13:52 - /data/blangme2/fasta/hprc-yr1/HG002.2.fa
[INFO] 20:14:29 - /data/blangme2/fasta/hprc-yr1/HG00438.1.fa
[INFO] 20:15:06 - /data/blangme2/fasta/hprc-yr1/HG00438.2.fa
[INFO] 20:15:43 - /data/blangme2/fasta/hprc-yr1/HG005.1.fa
[INFO] 20:16:19 - /data/blangme2/fasta/hprc-yr1/HG005.2.fa
[INFO] 20:16:55 - /data/blangme2/fasta/hprc-yr1/HG00621.1.fa
[INFO] 20:17:30 - /data/blangme2/fasta/hprc-yr1/HG00621.2.fa
[INFO] 20:18:06 - /data/blangme2/fasta/hprc-yr1/HG00673.1.fa
[INFO] 20:18:41 - /data/blangme2/fasta/hprc-yr1/HG00673.2.fa
[INFO] 20:19:17 - /data/blangme2/fasta/hprc-yr1/HG00733.1.fa
[INFO] 20:19:53 - /data/blangme2/fasta/hprc-yr1/HG00733.2.fa
[INFO] 20:20:29 - /data/blangme2/fasta/hprc-yr1/HG00735.1.fa
[INFO] 20:21:05 - /data/blangme2/fasta/hprc-yr1/HG00735.2.fa
[INFO] 20:21:42 - /data/blangme2/fasta/hprc-yr1/HG00741.1.fa
[INFO] 20:22:18 - /data/blangme2/fasta/hprc-yr1/HG00741.2.fa
[INFO] 20:22:54 - /data/blangme2/fasta/hprc-yr1/HG01071.1.fa
[INFO] 20:23:30 - /data/blangme2/fasta/hprc-yr1/HG01071.2.fa
[INFO] 20:24:06 - /data/blangme2/fasta/hprc-yr1/HG01106.1.fa
[INFO] 20:24:41 - /data/blangme2/fasta/hprc-yr1/HG01106.2.fa
[INFO] 20:25:18 - /data/blangme2/fasta/hprc-yr1/HG01109.1.fa
[INFO] 20:25:52 - /data/blangme2/fasta/hprc-yr1/HG01109.2.fa
[INFO] 20:26:28 - /data/blangme2/fasta/hprc-yr1/HG01123.1.fa
[INFO] 20:27:05 - /data/blangme2/fasta/hprc-yr1/HG01123.2.fa
[INFO] 20:27:41 - /data/blangme2/fasta/hprc-yr1/HG01175.1.fa
[INFO] 20:28:16 - /data/blangme2/fasta/hprc-yr1/HG01175.2.fa
[INFO] 20:28:52 - /data/blangme2/fasta/hprc-yr1/HG01243.1.fa
[INFO] 20:29:26 - /data/blangme2/fasta/hprc-yr1/HG01243.2.fa
[INFO] 20:30:01 - /data/blangme2/fasta/hprc-yr1/HG01258.1.fa
[INFO] 20:30:36 - /data/blangme2/fasta/hprc-yr1/HG01258.2.fa
[INFO] 20:31:12 - /data/blangme2/fasta/hprc-yr1/HG01358.1.fa
[INFO] 20:31:47 - /data/blangme2/fasta/hprc-yr1/HG01358.2.fa
[INFO] 20:32:23 - /data/blangme2/fasta/hprc-yr1/HG01361.1.fa
[INFO] 20:33:00 - /data/blangme2/fasta/hprc-yr1/HG01361.2.fa
[INFO] 20:33:37 - /data/blangme2/fasta/hprc-yr1/HG01891.1.fa
[INFO] 20:34:13 - /data/blangme2/fasta/hprc-yr1/HG01891.2.fa
[INFO] 20:34:50 - /data/blangme2/fasta/hprc-yr1/HG01928.1.fa
[INFO] 20:35:24 - /data/blangme2/fasta/hprc-yr1/HG01928.2.fa
[INFO] 20:36:01 - /data/blangme2/fasta/hprc-yr1/HG01952.1.fa
[INFO] 20:36:35 - /data/blangme2/fasta/hprc-yr1/HG01952.2.fa
[INFO] 20:37:12 - /data/blangme2/fasta/hprc-yr1/HG01978.1.fa
[INFO] 20:37:49 - /data/blangme2/fasta/hprc-yr1/HG01978.2.fa
[INFO] 20:38:25 - /data/blangme2/fasta/hprc-yr1/HG02055.1.fa
[INFO] 20:39:00 - /data/blangme2/fasta/hprc-yr1/HG02055.2.fa
[INFO] 20:39:36 - /data/blangme2/fasta/hprc-yr1/HG02080.1.fa
[INFO] 20:40:11 - /data/blangme2/fasta/hprc-yr1/HG02080.2.fa
[INFO] 20:40:46 - /data/blangme2/fasta/hprc-yr1/HG02109.1.fa
[INFO] 20:41:22 - /data/blangme2/fasta/hprc-yr1/HG02109.2.fa
[INFO] 20:41:57 - /data/blangme2/fasta/hprc-yr1/HG02145.1.fa
[INFO] 20:42:31 - /data/blangme2/fasta/hprc-yr1/HG02145.2.fa
[INFO] 20:43:06 - /data/blangme2/fasta/hprc-yr1/HG02148.1.fa
[INFO] 20:43:42 - /data/blangme2/fasta/hprc-yr1/HG02148.2.fa
[INFO] 20:44:18 - /data/blangme2/fasta/hprc-yr1/HG02257.1.fa
[INFO] 20:44:54 - /data/blangme2/fasta/hprc-yr1/HG02257.2.fa
[INFO] 20:45:31 - /data/blangme2/fasta/hprc-yr1/HG02486.1.fa
[INFO] 20:46:05 - /data/blangme2/fasta/hprc-yr1/HG02486.2.fa
[INFO] 20:46:41 - /data/blangme2/fasta/hprc-yr1/HG02559.1.fa
[INFO] 20:47:18 - /data/blangme2/fasta/hprc-yr1/HG02559.2.fa
[INFO] 20:47:55 - /data/blangme2/fasta/hprc-yr1/HG02572.1.fa
[INFO] 20:48:29 - /data/blangme2/fasta/hprc-yr1/HG02572.2.fa
[INFO] 20:49:04 - /data/blangme2/fasta/hprc-yr1/HG02622.1.fa
[INFO] 20:49:41 - /data/blangme2/fasta/hprc-yr1/HG02622.2.fa
[INFO] 20:50:17 - /data/blangme2/fasta/hprc-yr1/HG02630.1.fa
[INFO] 20:50:53 - /data/blangme2/fasta/hprc-yr1/HG02630.2.fa
[INFO] 20:51:28 - /data/blangme2/fasta/hprc-yr1/HG02717.1.fa
[INFO] 20:52:03 - /data/blangme2/fasta/hprc-yr1/HG02717.2.fa
[INFO] 20:52:40 - /data/blangme2/fasta/hprc-yr1/HG02723.1.fa
[INFO] 20:53:15 - /data/blangme2/fasta/hprc-yr1/HG02723.2.fa
[INFO] 20:53:50 - /data/blangme2/fasta/hprc-yr1/HG02818.1.fa
[INFO] 20:54:25 - /data/blangme2/fasta/hprc-yr1/HG02818.2.fa
[INFO] 20:55:00 - /data/blangme2/fasta/hprc-yr1/HG02886.1.fa
[INFO] 20:55:36 - /data/blangme2/fasta/hprc-yr1/HG02886.2.fa
[INFO] 20:56:13 - /data/blangme2/fasta/hprc-yr1/HG03098.1.fa
[INFO] 20:56:47 - /data/blangme2/fasta/hprc-yr1/HG03098.2.fa
[INFO] 20:57:23 - /data/blangme2/fasta/hprc-yr1/HG03453.1.fa
[INFO] 20:57:59 - /data/blangme2/fasta/hprc-yr1/HG03453.2.fa
[INFO] 20:58:34 - /data/blangme2/fasta/hprc-yr1/HG03486.1.fa
[INFO] 20:59:10 - /data/blangme2/fasta/hprc-yr1/HG03486.2.fa
[INFO] 20:59:45 - /data/blangme2/fasta/hprc-yr1/HG03492.1.fa
[INFO] 21:00:19 - /data/blangme2/fasta/hprc-yr1/HG03492.2.fa
[INFO] 21:00:56 - /data/blangme2/fasta/hprc-yr1/HG03516.1.fa
[INFO] 21:01:33 - /data/blangme2/fasta/hprc-yr1/HG03516.2.fa
[INFO] 21:02:09 - /data/blangme2/fasta/hprc-yr1/HG03540.1.fa
[INFO] 21:02:45 - /data/blangme2/fasta/hprc-yr1/HG03540.2.fa
[INFO] 21:03:22 - /data/blangme2/fasta/hprc-yr1/HG03579.1.fa
[INFO] 21:03:56 - /data/blangme2/fasta/hprc-yr1/HG03579.2.fa
[INFO] 21:04:32 - /data/blangme2/fasta/hprc-yr1/NA18906.1.fa
[INFO] 21:05:09 - /data/blangme2/fasta/hprc-yr1/NA18906.2.fa
[INFO] 21:05:45 - /data/blangme2/fasta/hprc-yr1/NA19240.1.fa
[INFO] 21:06:21 - /data/blangme2/fasta/hprc-yr1/NA19240.2.fa
[INFO] 21:06:58 - /data/blangme2/fasta/hprc-yr1/NA20129.1.fa
[INFO] 21:07:33 - /data/blangme2/fasta/hprc-yr1/NA20129.2.fa
[INFO] 21:08:09 - /data/blangme2/fasta/hprc-yr1/NA21309.1.fa
[INFO] 21:08:45 - /data/blangme2/fasta/hprc-yr1/NA21309.2.fa
[INFO] 21:09:21 - Separators between genomes are added
[INFO] 21:09:21 - The clean fasta with the reverse complement is stored at movi_regular_thresholds.hprc_94//ref.fa
Sending logging messages to file: movi_regular_thresholds.hprc_94//ref.fa.thr.log
==== Parsing. Command: /home/mzakeri1/Movi/build_test/external_repos/pfp-thresholds-build/_deps/bigbwt-build/newscanNT.x movi_regular_thresholds.hprc_94//ref.fa -w 10 -p 100 -t 0 -f -P -s
Elapsed time: 45251.7298
movi_regular_thresholds.hprc_94//ref.fa PFP started!
==== Computing Thresholds. Command: /home/mzakeri1/Movi/build_test/external_repos/pfp-thresholds-build/test/src/pfp_thresholds64 movi_regular_thresholds.hprc_94//ref.fa -w 10 -r
Thresholds Elapsed time: 75584.4277
Total construction time: 120836.1629
==== Deleting temporary files.
==== Done
[INFO] 23:26:57 - Movi index version: 2.0.0

[PROGRESS] 23:27:11 - Reading thresholds..
[██████████████████████████████████████████████████] 100% (4,245,138,623/4,245,138,623)
[SUCCESS] 23:29:19 - Successfully read 4245138624 thresholds

[INFO] 23:29:19 - Building starts...
[INFO] 23:29:39 - Number of BWT runs: 4245138624

[1/5] 23:29:47 - Computing total length of the BWT..
[██████████████████████████████████████████████████] 100% (4,245,138,623/4,245,138,623)
[PROGRESS] 23:32:00 - Successfully computed total BWT length: 579302018723
[INFO] 23:32:36 - The main bit vector (bits) is initialized.
[INFO] 23:34:30 - The bits vector is updated by thresholds.

[2/5] 23:36:24 - Detecting the move row boundaries..
[██████████████████████▌                           ] 45% (1,916,000,000/4,245,138,623)MAX_RUN_LENGTH
[██████████████████████████████████████████████████] 100% (4,245,138,623/4,245,138,623)
[PROGRESS] 00:38:00 - Successfully detected 0 move row boundaries
[INFO] 00:38:00 - All the characters are indexed.
[INFO] 00:38:01 - Number of runs added by thresholds splitting: 445430857
[INFO] 00:38:01 - Main statistics of the index:
[INFO] 00:38:01 -       n: 579302018723
[INFO] 00:38:01 -       r: 4708172685
[INFO] 00:38:01 -       n/r:    123.041795
[INFO] 00:38:01 -       original_r: 4245138624

[3/5] 00:38:25 - Finding the run heads information..
[██████████████████████████████████████████████████] 100% (4,708,172,684/4,708,172,684)
[PROGRESS] 00:41:00 - Successfully processed 4708172685 runs

[4/5] 00:43:20 - Building Movi rows..
[██████████████████████████████████████████████████] 100% (4,708,172,684/4,708,172,684)
[PROGRESS] 00:51:19 - Successfully built 4708172685 move structure rows

[5/5] 00:51:19 - Updating the thresholds for move rows..
[██████████████████████████████████████████████████] 100% (4,708,172,683/4,708,172,683)
[PROGRESS] 01:02:24 - Successfully updated the thresholds in all the rows.

[SUCCESS] 01:02:24 - The Movi index building is done.


[SUCCESS] 01:02:59 - The Movi index is successfully stored at movi_regular_thresholds.hprc_94/

[INFO] 01:02:59 - Generating the null statistics...
[INFO] 01:03:11 - Successfully generated null statistics with PML
[INFO] 01:03:11 - Successfully generated null statistics with ZML
5352.95user 447.76system 1:37:10elapsed 99%CPU (0avgtext+0avgdata 277705340maxresident)k
14737864inputs+73573680outputs (12major+82402040minor)pagefaults 0swaps
(base) [mzakeri1@devlangmead1 hprc_v1_separator_indexes]$