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Published 20 hours ago • verified publisher icon soedinglab

Database creation for GTDB not working (Error: createdb died)

Open g0ddengr opened this issue 2 years ago • 2 comments
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Expected Behavior

Completion of download and db creation for GTDB.

Current Behavior

I installed release 14-7e284 via conda yesterday and tried to download various databases via the databases module. The following error messages were generated for GTDB; other databases were generated without errors. I thought problems with GTDB were fixed in previous versions (e.g., see issue #742), but perhaps changes were reverted in the latest release via conda?

Here are the relevant error messages (full output also included below):

09/27 13:21:53 [ERROR] CUID#7 - Download aborted. URI=https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/VERSION Exception: [AbstractCommand.cc:351] errorCode=3 URI=https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/VERSION -> [HttpSkipResponseCommand.cc:218] errorCode=3 Resource not found

09/27 13:21:53 [NOTICE] Download GID#5876f1173053ff82 not complete: tmp/3290078511923703767/version

Download Results: gid |stat|avg speed |path/URI ======+====+===========+======================================================= 5876f1|ERR | 0B/s|tmp/3290078511923703767/version

Status Legend: (ERR):error occurred.

....

The input files have no entry: - tmp/3290078511923703767/tardb Please check your input files. Only files in fasta/fastq[.gz|bz2] are supported Error: createdb died

Steps to Reproduce (for bugs)

mmseqs databases GTDB gtdb tmp

MMseqs Output (for bugs)

Create directory tmp databases GTDB gtdb tmp

MMseqs Version: 14.7e284 Tsv false Force restart with latest tmp false Remove temporary files false Compressed 0 Threads 64 Verbosity 3

09/27 13:21:52 [NOTICE] Downloading 1 item(s)

09/27 13:21:53 [ERROR] CUID#7 - Download aborted. URI=https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/VERSION Exception: [AbstractCommand.cc:351] errorCode=3 URI=https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/VERSION -> [HttpSkipResponseCommand.cc:218] errorCode=3 Resource not found

09/27 13:21:53 [NOTICE] Download GID#5876f1173053ff82 not complete: tmp/3290078511923703767/version

Download Results: gid |stat|avg speed |path/URI ======+====+===========+======================================================= 5876f1|ERR | 0B/s|tmp/3290078511923703767/version

Status Legend: (ERR):error occurred.

aria2 will resume download if the transfer is restarted. If there are any errors, then see the log file. See '-l' option in help/man page for details. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 196 100 196 0 0 245 0 --:--:-- --:--:-- --:--:-- 245

09/27 13:21:54 [NOTICE] Downloading 1 item(s)

09/27 13:21:54 [NOTICE] Allocating disk space. Use --file-allocation=none to disable it. See --file-allocation option in man page for more details. *** Download Progress Summary as of Wed Sep 27 13:22:54 2023 ***

[#2b99bd 207MiB/51GiB(0%) CN:5 DL:10MiB ETA:1h24m8s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:23:54 2023 ***

[#2b99bd 723MiB/51GiB(1%) CN:5 DL:8.7MiB ETA:1h38m40s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:24:56 2023 ***

[#2b99bd 1.1GiB/51GiB(2%) CN:5 DL:6.5MiB ETA:2h11m31s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:25:58 2023 ***

[#2b99bd 1.6GiB/51GiB(3%) CN:5 DL:2.3MiB ETA:6h48s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:26:59 2023 ***

[#2b99bd 2.1GiB/51GiB(4%) CN:5 DL:9.3MiB ETA:1h29m23s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:28:00 2023 ***

[#2b99bd 2.7GiB/51GiB(5%) CN:5 DL:10MiB ETA:1h16m12s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:29:00 2023 ***

[#2b99bd 3.2GiB/51GiB(6%) CN:5 DL:5.8MiB ETA:2h20m52s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:30:00 2023 ***

[#2b99bd 3.7GiB/51GiB(7%) CN:5 DL:9.9MiB ETA:1h21m55s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:31:01 2023 ***

[#2b99bd 4.2GiB/51GiB(8%) CN:5 DL:10MiB ETA:1h18m3s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:32:02 2023 ***

[#2b99bd 4.7GiB/51GiB(9%) CN:5 DL:7.3MiB ETA:1h48m41s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:33:02 2023 ***

[#2b99bd 5.1GiB/51GiB(10%) CN:5 DL:10MiB ETA:1h14m10s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:34:03 2023 ***

[#2b99bd 5.6GiB/51GiB(11%) CN:5 DL:6.4MiB ETA:2h18s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:35:04 2023 ***

[#2b99bd 6.0GiB/51GiB(11%) CN:5 DL:8.6MiB ETA:1h29m12s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:36:08 2023 ***

[#2b99bd 6.3GiB/51GiB(12%) CN:5 DL:0B] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:37:09 2023 ***

[#2b99bd 6.8GiB/51GiB(13%) CN:5 DL:8.9MiB ETA:1h24m59s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:38:09 2023 ***

[#2b99bd 7.2GiB/51GiB(14%) CN:5 DL:9.4MiB ETA:1h19m25s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:39:09 2023 ***

[#2b99bd 7.6GiB/51GiB(14%) CN:5 DL:9.0MiB ETA:1h22m16s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:40:09 2023 ***

[#2b99bd 8.1GiB/51GiB(15%) CN:5 DL:13MiB ETA:56m37s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:41:10 2023 ***

[#2b99bd 8.5GiB/51GiB(16%) CN:5 DL:2.1MiB ETA:5h37m40s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:42:11 2023 ***

[#2b99bd 9.0GiB/51GiB(17%) CN:5 DL:11MiB ETA:1h1m15s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:43:11 2023 ***

[#2b99bd 9.5GiB/51GiB(18%) CN:5 DL:6.7MiB ETA:1h45m50s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:44:11 2023 ***

[#2b99bd 10GiB/51GiB(19%) CN:5 DL:11MiB ETA:1h2m50s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:45:11 2023 ***

[#2b99bd 10GiB/51GiB(20%) CN:5 DL:9.9MiB ETA:1h9m34s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:46:12 2023 ***

[#2b99bd 11GiB/51GiB(22%) CN:5 DL:8.8MiB ETA:1h17m14s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:47:13 2023 ***

[#2b99bd 11GiB/51GiB(23%) CN:5 DL:8.6MiB ETA:1h18m18s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:48:14 2023 ***

[#2b99bd 12GiB/51GiB(24%) CN:5 DL:12MiB ETA:54m33s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:49:16 2023 ***

[#2b99bd 13GiB/51GiB(25%) CN:5 DL:5.9MiB ETA:1h49m11s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:50:17 2023 ***

[#2b99bd 13GiB/51GiB(26%) CN:5 DL:11MiB ETA:58m14s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:51:21 2023 ***

[#2b99bd 14GiB/51GiB(27%) CN:5 DL:6.2MiB ETA:1h42m17s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:52:23 2023 ***

[#2b99bd 14GiB/51GiB(28%) CN:5 DL:5.7MiB ETA:1h49m30s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:53:24 2023 ***

[#2b99bd 15GiB/51GiB(29%) CN:5 DL:10MiB ETA:58m43s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:54:24 2023 ***

[#2b99bd 15GiB/51GiB(31%) CN:5 DL:8.5MiB ETA:1h10m41s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:55:24 2023 ***

[#2b99bd 16GiB/51GiB(32%) CN:5 DL:11MiB ETA:53m59s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:56:25 2023 ***

[#2b99bd 17GiB/51GiB(33%) CN:5 DL:9.5MiB ETA:1h1m30s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:57:27 2023 ***

[#2b99bd 17GiB/51GiB(34%) CN:5 DL:11MiB ETA:51m21s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:58:27 2023 ***

[#2b99bd 18GiB/51GiB(35%) CN:5 DL:9.4MiB ETA:59m37s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 13:59:28 2023 ***

[#2b99bd 18GiB/51GiB(36%) CN:5 DL:8.5MiB ETA:1h5m13s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:00:29 2023 ***

[#2b99bd 19GiB/51GiB(37%) CN:5 DL:11MiB ETA:46m45s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:01:29 2023 ***

[#2b99bd 20GiB/51GiB(39%) CN:5 DL:9.7MiB ETA:54m37s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:02:30 2023 ***

[#2b99bd 20GiB/51GiB(40%) CN:5 DL:9.2MiB ETA:56m15s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:03:30 2023 ***

[#2b99bd 21GiB/51GiB(42%) CN:5 DL:9.8MiB ETA:51m39s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:04:31 2023 ***

[#2b99bd 22GiB/51GiB(43%) CN:5 DL:10MiB ETA:48m28s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:05:33 2023 ***

[#2b99bd 22GiB/51GiB(44%) CN:5 DL:6.7MiB ETA:1h11m54s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:06:34 2023 ***

[#2b99bd 23GiB/51GiB(45%) CN:5 DL:11MiB ETA:39m54s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:07:35 2023 ***

[#2b99bd 24GiB/51GiB(47%) CN:5 DL:15MiB ETA:29m42s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:08:35 2023 ***

[#2b99bd 24GiB/51GiB(48%) CN:5 DL:9.7MiB ETA:45m59s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:09:36 2023 ***

[#2b99bd 25GiB/51GiB(49%) CN:5 DL:11MiB ETA:38m9s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:10:38 2023 ***

[#2b99bd 26GiB/51GiB(51%) CN:5 DL:10MiB ETA:40m36s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:11:39 2023 ***

[#2b99bd 26GiB/51GiB(52%) CN:5 DL:8.7MiB ETA:47m37s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:12:39 2023 ***

[#2b99bd 27GiB/51GiB(53%) CN:5 DL:11MiB ETA:35m22s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:13:39 2023 ***

[#2b99bd 28GiB/51GiB(54%) CN:5 DL:8.6MiB ETA:46m7s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:14:40 2023 ***

[#2b99bd 28GiB/51GiB(55%) CN:5 DL:7.5MiB ETA:51m57s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:15:41 2023 ***

[#2b99bd 29GiB/51GiB(56%) CN:5 DL:6.5MiB ETA:58m22s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:16:41 2023 ***

[#2b99bd 29GiB/51GiB(57%) CN:5 DL:7.2MiB ETA:51m11s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:17:43 2023 ***

[#2b99bd 30GiB/51GiB(58%) CN:5 DL:8.8MiB ETA:41m7s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:18:44 2023 ***

[#2b99bd 30GiB/51GiB(59%) CN:5 DL:10MiB ETA:35m4s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:19:45 2023 ***

[#2b99bd 30GiB/51GiB(60%) CN:5 DL:6.2MiB ETA:55m53s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:20:45 2023 ***

[#2b99bd 31GiB/51GiB(61%) CN:5 DL:10MiB ETA:32m44s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:21:46 2023 ***

[#2b99bd 32GiB/51GiB(62%) CN:5 DL:7.4MiB ETA:44m7s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:22:47 2023 ***

[#2b99bd 32GiB/51GiB(63%) CN:5 DL:6.7MiB ETA:47m37s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:23:47 2023 ***

[#2b99bd 33GiB/51GiB(64%) CN:5 DL:13MiB ETA:23m43s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:24:48 2023 ***

[#2b99bd 33GiB/51GiB(65%) CN:5 DL:9.9MiB ETA:30m8s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:25:49 2023 ***

[#2b99bd 34GiB/51GiB(67%) CN:5 DL:9.9MiB ETA:29m] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:26:49 2023 ***

[#2b99bd 35GiB/51GiB(68%) CN:5 DL:12MiB ETA:22m6s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:27:50 2023 ***

[#2b99bd 35GiB/51GiB(69%) CN:5 DL:13MiB ETA:20m10s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:28:51 2023 ***

[#2b99bd 36GiB/51GiB(71%) CN:5 DL:14MiB ETA:17m20s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:29:51 2023 ***

[#2b99bd 37GiB/51GiB(72%) CN:5 DL:12MiB ETA:19m22s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:30:51 2023 ***

[#2b99bd 38GiB/51GiB(74%) CN:5 DL:12MiB ETA:18m14s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:31:52 2023 ***

[#2b99bd 38GiB/51GiB(75%) CN:5 DL:10MiB ETA:21m4s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:32:53 2023 ***

[#2b99bd 39GiB/51GiB(76%) CN:5 DL:9.6MiB ETA:21m9s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:33:54 2023 ***

[#2b99bd 39GiB/51GiB(77%) CN:5 DL:7.9MiB ETA:24m25s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:34:54 2023 ***

[#2b99bd 40GiB/51GiB(78%) CN:5 DL:7.8MiB ETA:23m42s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:35:55 2023 ***

[#2b99bd 40GiB/51GiB(79%) CN:5 DL:7.5MiB ETA:23m39s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:36:56 2023 ***

[#2b99bd 41GiB/51GiB(80%) CN:5 DL:7.0MiB ETA:24m11s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:37:57 2023 ***

[#2b99bd 41GiB/51GiB(81%) CN:5 DL:8.1MiB ETA:20m] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:38:57 2023 ***

[#2b99bd 42GiB/51GiB(82%) CN:5 DL:7.6MiB ETA:20m13s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:39:57 2023 ***

[#2b99bd 42GiB/51GiB(83%) CN:5 DL:7.6MiB ETA:19m18s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:40:58 2023 ***

[#2b99bd 43GiB/51GiB(84%) CN:5 DL:12MiB ETA:10m45s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:41:59 2023 ***

[#2b99bd 43GiB/51GiB(85%) CN:5 DL:10MiB ETA:12m6s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:42:59 2023 ***

[#2b99bd 44GiB/51GiB(86%) CN:5 DL:8.9MiB ETA:13m5s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:44:00 2023 ***

[#2b99bd 45GiB/51GiB(87%) CN:5 DL:10MiB ETA:9m55s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:45:00 2023 ***

[#2b99bd 45GiB/51GiB(88%) CN:5 DL:10MiB ETA:9m35s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:46:01 2023 ***

[#2b99bd 46GiB/51GiB(89%) CN:5 DL:7.2MiB ETA:12m25s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:47:01 2023 ***

[#2b99bd 46GiB/51GiB(90%) CN:5 DL:6.6MiB ETA:12m19s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:48:01 2023 ***

[#2b99bd 47GiB/51GiB(91%) CN:5 DL:6.7MiB ETA:11m4s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:49:02 2023 ***

[#2b99bd 47GiB/51GiB(92%) CN:5 DL:9.1MiB ETA:7m12s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:50:03 2023 ***

[#2b99bd 47GiB/51GiB(93%) CN:5 DL:7.1MiB ETA:8m7s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:51:03 2023 ***

[#2b99bd 48GiB/51GiB(94%) CN:5 DL:5.8MiB ETA:8m46s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:52:03 2023 ***

[#2b99bd 48GiB/51GiB(94%) CN:5 DL:7.7MiB ETA:5m45s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:53:04 2023 ***

[#2b99bd 49GiB/51GiB(95%) CN:5 DL:7.2MiB ETA:5m15s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:54:05 2023 ***

[#2b99bd 49GiB/51GiB(96%) CN:5 DL:3.6MiB ETA:8m57s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:55:11 2023 ***

[#2b99bd 49GiB/51GiB(96%) CN:5 DL:0B] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:56:12 2023 ***

[#2b99bd 50GiB/51GiB(97%) CN:5 DL:5.6MiB ETA:3m55s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:57:12 2023 ***

[#2b99bd 50GiB/51GiB(98%) CN:5 DL:6.4MiB ETA:2m35s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:58:12 2023 ***

[#2b99bd 50GiB/51GiB(98%) CN:5 DL:6.2MiB ETA:1m38s] FILE: tmp/3290078511923703767/gtdb.tar.gz

*** Download Progress Summary as of Wed Sep 27 14:59:13 2023 ***

[#2b99bd 51GiB/51GiB(99%) CN:5 DL:5.6MiB ETA:46s] FILE: tmp/3290078511923703767/gtdb.tar.gz

[#2b99bd 51GiB/51GiB(99%) CN:1 DL:6.6MiB]
09/27 14:59:56 [NOTICE] Download complete: tmp/3290078511923703767/gtdb.tar.gz

Download Results: gid |stat|avg speed |path/URI ======+====+===========+======================================================= 2b99bd|OK | 8.9MiB/s|tmp/3290078511923703767/gtdb.tar.gz

Status Legend: (OK):download completed.

09/27 14:59:57 [NOTICE] Downloading 1 item(s)

09/27 14:59:57 [NOTICE] Allocating disk space. Use --file-allocation=none to disable it. See --file-allocation option in man page for more details. [#8eef3f 51MiB/54MiB(95%) CN:1 DL:4.9MiB]
09/27 15:00:10 [NOTICE] Download complete: tmp/3290078511923703767/bac120_taxonomy.tsv

Download Results: gid |stat|avg speed |path/URI ======+====+===========+======================================================= 8eef3f|OK | 4.2MiB/s|tmp/3290078511923703767/bac120_taxonomy.tsv

Status Legend: (OK):download completed.

09/27 15:00:10 [NOTICE] Downloading 1 item(s) [#c371fe 880KiB/1.0MiB(81%) CN:1 DL:268KiB]
09/27 15:00:15 [NOTICE] Download complete: tmp/3290078511923703767/ar53_taxonomy.tsv

Download Results: gid |stat|avg speed |path/URI ======+====+===========+======================================================= c371fe|OK | 273KiB/s|tmp/3290078511923703767/ar53_taxonomy.tsv

Status Legend: (OK):download completed. tar2db tmp/3290078511923703767/gtdb.tar.gz tmp/3290078511923703767/tardb --tar-include faa$ --threads 64 -v 3

Time for merging to tardb: 0h 0m 0s 62ms Time for merging to tardb.lookup: 0h 0m 0s 77ms Time for processing: 0h 1m 8s 163ms createdb tmp/3290078511923703767/tardb gtdb --compressed 0 -v 3

Converting sequences

Time for merging to gtdb_h: 0h 0m 0s 32ms Time for merging to gtdb: 0h 0m 0s 34ms Database type: Nucleotide The input files have no entry: - tmp/3290078511923703767/tardb Please check your input files. Only files in fasta/fastq[.gz|bz2] are supported Error: createdb died

Context

NA

Your Environment

mmseqs2 release 14-7e284 installed via conda on RHEL8

g0ddengr avatar Sep 27 '23 19:09 g0ddengr

The issue is fixed in git, but not part of a release yet.

You can download precompiled binaries from https://mmseqs.com/latest that contains the fix or compile MMseqs2 from source.

milot-mirdita avatar Sep 29 '23 15:09 milot-mirdita

Hi,

I followed this thread and used the latest binary to run the following code, issues with GTDB.lookup. Downloading data from GTDB appeared to be fine.

# command:
mmseqs databases UniProtKB/Swiss-Prot "$OUT_DIR"/uniprotkb_swissprot "$TMP_DIR" --threads 128 --remove-tmp-files

# output directory:
-rw-r--r--  1 gnii0001 pc77         0 Jan 27 16:54 GTDB
-rw-r--r--  1 gnii0001 pc77         4 Jan 27 16:54 GTDB.dbtype
-rw-r--r--  1 gnii0001 pc77         0 Jan 27 16:54 GTDB_h
-rw-r--r--  1 gnii0001 pc77         4 Jan 27 16:54 GTDB_h.dbtype
-rw-r--r--  1 gnii0001 pc77         0 Jan 27 16:54 GTDB_h.index
-rw-r--r--  1 gnii0001 pc77         0 Jan 27 16:54 GTDB.index
-rw-r--r--  1 gnii0001 pc77         0 Jan 27 17:33 GTDB_mapping
-rw-r--r--  1 gnii0001 pc77         0 Jan 27 16:54 GTDB.source
-rw-r--r--  1 gnii0001 pc77  25771406 Jan 27 17:33 GTDB_taxonomy

# slurm error
awk: cmd. line:1: fatal: cannot open file `/home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/GTDB.lookup' for reading: No such file or directory

# slurm standard output:
....
Download Results:
gid   |stat|avg speed  |path/URI
======+====+===========+=======================================================
94ce2b|OK  |    88MiB/s|/home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/tmp/13846894499670505008/bac120_taxonomy.tsv

Status Legend:
(OK):download completed.

01/27 17:33:08 [NOTICE] Downloading 1 item(s)

01/27 17:33:09 [NOTICE] Download complete: /home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/tmp/13846894499670505008/ar53_taxonomy.tsv

Download Results:
gid   |stat|avg speed  |path/URI
======+====+===========+=======================================================
13f000|OK  |   6.3MiB/s|/home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/tmp/13846894499670505008/ar53_taxonomy.tsv

Status Legend:
(OK):download completed.
Create directory /home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/tmp/13846894499670505008/taxdb
createtaxdb /home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/GTDB /home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/tmp/13846894499670505008/taxdb --ncbi-tax-dump /home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/tmp/13846894499670505008/taxonomy --tax-mapping-file /home/gnii0001/pc77/scratch_nobackup/Database/mmseqs_formatted/tmp/13846894499670505008/taxonomy/mapping_genomes --tax-mapping-mode 1 --threads 128 -v 3 

Loading nodes file ... Done, got 113318 nodes
Loading merged file ... Done, added 0 merged nodes.
Loading names file ... Done
Init RMQ ...Done
Error: createtaxdb died

Any tips? Thanks.

ganiatgithub avatar Jan 27 '24 07:01 ganiatgithub