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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
72 stars 40 forks source link

Encounter an Error while sorting reads #395

Closed wpearman1996 closed 4 years ago

wpearman1996 commented 4 years ago

Hi there, I just created a new miniconda environment and installed ipyrad. I ran the following command: ipyrad -p params-isopod.txt -s 123456 -f And had the following output:

Warning: technical replicates (same name) present.

 -------------------------------------------------------------
  ipyrad [v.0.9.40]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  Parallel connection | gru: 56 cores

  Step 1: Demultiplexing fastq data to Samples
  Warning: technical replicates (same name) present.
  [####################] 100% 0:17:14 | chunking large files
  [#########           ]  46% 0:43:26 | sorting reads
  Encountered an Error.
  Message: UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb8 in position 1: invalid start byte
Error: ipcluster shutdown and must be restarted

^CTraceback (most recent call last):
  File "/home/william/miniconda3/bin/ipyrad", line 10, in <module>
    sys.exit(main())
  File "/home/william/miniconda3/lib/python3.7/site-packages/ipyrad/__main__.py", line 598, in main
    CLI()
  File "/home/william/miniconda3/lib/python3.7/site-packages/ipyrad/__main__.py", line 75, in __init__
    self.run()
  File "/home/william/miniconda3/lib/python3.7/site-packages/ipyrad/__main__.py", line 520, in run
    pool.wrap_run()
  File "/home/william/miniconda3/lib/python3.7/site-packages/ipyrad/core/Parallel.py", line 345, in wrap_run
    self.cleanup()
  File "/home/william/miniconda3/lib/python3.7/site-packages/ipyrad/core/Parallel.py", line 382, in cleanup
    self.ipyclient.shutdown(hub=True, block=False)
  File "/home/william/miniconda3/lib/python3.7/site-packages/ipyparallel/client/client.py", line 1312, in shutdown
    f.wait()
  File "/home/william/miniconda3/lib/python3.7/site-packages/ipyparallel/client/futures.py", line 28, in wait
    return self._evt.wait(timeout)
  File "/home/william/miniconda3/lib/python3.7/threading.py", line 552, in wait
    signaled = self._cond.wait(timeout)
  File "/home/william/miniconda3/lib/python3.7/threading.py", line 296, in wait
    waiter.acquire()
KeyboardInterrupt

I have attached my parameter file below. i am running ubuntu 16.04. Using a new miniconda installation following the instructions set out on the readthedocs page for ipyrad. params-isopod.txt

Any idea what's going wrong? I'm not sure where to start looking to find the file with the error, let alone how to fix this.

wpearman1996 commented 4 years ago

I've repeated the same command a few times, including the -d for debug, it always occurs at the same point. but doesn't generate a log file - so can't get more details.

isaacovercast commented 4 years ago

It looks like a bad character in the raw data file. Tricky to debug remotely. Can you wetransfer me the raw data file? It would be simplest if I could look at the data.

isaacovercast commented 4 years ago

If it helps, the bad unicode character is: ¸ (it's not a comma). My guess is if there's one there will be many more. It might help to know if this is in the read name, the sequence string, or the quality string. This step has been bulletproof for a long time, so i'm guessing something is up with your data. Where did it come from? What sequencing instrument? Can you zcat | head -n 20 and paste in the first 20 lines so i can take a look?

wpearman1996 commented 4 years ago

Thanks! I managed to figure out what had happened - looks like one of the fastqs got corrupted at some point (maybe during decompression) - regardless, once i fixed that, it seemed to progress through fine.

isaacovercast commented 4 years ago

Cool, thanks for letting us know. Good luck with the rest of the assembly.

On Mon, Feb 17, 2020 at 9:48 PM wpearman1996 notifications@github.com wrote:

Closed #395 https://github.com/dereneaton/ipyrad/issues/395.

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/dereneaton/ipyrad/issues/395?email_source=notifications&email_token=ABNSXP6VVNSLDS2DYXVZEW3RDLZ2NA5CNFSM4KWL6KA2YY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOWV7KXTQ#event-3044977614, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNSXPZM7L4PGKOWKNWFNSTRDLZ2NANCNFSM4KWL6KAQ .

alexkrohn commented 2 years ago

Hi there. I'm also getting this error. Can you explain a bit more how you debugged it?

This occurred for me on the building clusters part of Step 3. (The fifth time Step 3 has failed for various reasons after 6 days of computing 😿 )

@isaacovercast how did you find that the ¸ symbol was the culprit?

@wpearman1996 how did you determine a FASTQ was corrupted?

isaacovercast commented 2 years ago

@alexkrohn Can you post the full output of the ipyrad run from the command line so I can see all the error text and the progress in step 3?

If you made it through step 2, then it's probably a different problem. A corrupt fastq file would have been identified during step 2.

alexkrohn commented 2 years ago

Screen Shot 2022-01-10 at 9 31 10 AM

Checked hard drive space (2.1 T still remaining), and verified that no samples are ready for step 4. Apologies for the cutoff screenshot -- the final line just says "Parallel connection closed" as usual. Nothing else after that.

isaacovercast commented 2 years ago

Well the symbol it doesn't like is the 'degree symbol': https://www.compart.com/en/unicode/U+00B0, but that doesn't really help because it feels like a corrupt file, no reason a random degree symbol would sneak in there somehow. Can you show me the contents of your project directory and also the _clust directory inside the project directory? Use ls -ltr. The output could be extensive, but that's fine. If you can copy/paste rather than screenshot that would be great too.

alexkrohn commented 2 years ago

Project directory: 

total 373
drwxrwxrwx 1 root  24576 Dec 22 11:12 raw/
-rwxrwxrwx 1 root   3215 Dec 27 12:16 params-just-alabam-and-beyeri.txt*
-rwxrwxrwx 1 root    326 Dec 27 12:17 notes.txt*
-rwxrwxrwx 1 root    944 Dec 27 12:55 app-cottontails-3rad_s1_demultiplex_stats.txt*
drwxrwxrwx 1 root  20480 Dec 27 17:10 app-cottontails-3rad_edits/
-rwxrwxrwx 1 root 175502 Dec 27 17:10 app-cottontails-3rad.json*
drwxrwxrwx 1 root  36864 Jan  3 04:55 app-cottontails-3rad_clust_0.85/
drwxrwxrwx 1 root 114688 Jan 10 05:10 app-cottontails-3rad-tmpalign/

Output of *_clust_0.85 directory

-rwxrwxrwx 1 root  181005150 Jan  6 15:07 SO399001.htemp*
-rwxrwxrwx 1 root  425084883 Jan  6 15:07 SO399001.utemp*
-rwxrwxrwx 1 root  425084883 Jan  6 15:08 SO399001.utemp.sort*
-rwxrwxrwx 1 root 1431502905 Jan  6 15:10 SO399001.clust.txt*
-rwxrwxrwx 1 root  175605354 Jan  6 15:20 SO421001.htemp*
-rwxrwxrwx 1 root  497848591 Jan  6 15:20 SO421001.utemp*
-rwxrwxrwx 1 root  497848591 Jan  6 15:21 SO421001.utemp.sort*
-rwxrwxrwx 1 root  176489915 Jan  6 15:22 SO385001.htemp*
-rwxrwxrwx 1 root  423020222 Jan  6 15:22 SO385001.utemp*
-rwxrwxrwx 1 root  423020222 Jan  6 15:24 SO385001.utemp.sort*
-rwxrwxrwx 1 root 1635180065 Jan  6 15:26 SO421001.clust.txt*
-rwxrwxrwx 1 root 1418059786 Jan  6 15:26 SO385001.clust.txt*
-rwxrwxrwx 1 root   44234104 Jan  6 17:28 SO397001.htemp*
-rwxrwxrwx 1 root   38716294 Jan  6 17:28 SO397001.utemp*
-rwxrwxrwx 1 root   38716294 Jan  6 17:29 SO397001.utemp.sort*
-rwxrwxrwx 1 root  163419113 Jan  6 17:29 SO397001.clust.txt*
-rwxrwxrwx 1 root  190572608 Jan  6 18:50 SO366001.htemp*
-rwxrwxrwx 1 root  407503231 Jan  6 18:50 SO366001.utemp*
-rwxrwxrwx 1 root  407503231 Jan  6 18:51 SO366001.utemp.sort*
-rwxrwxrwx 1 root 1373239426 Jan  6 18:53 SO366001.clust.txt*
-rwxrwxrwx 1 root  201261544 Jan  6 19:48 SO373001.htemp*
-rwxrwxrwx 1 root  519414840 Jan  6 19:48 SO373001.utemp*
-rwxrwxrwx 1 root  519414840 Jan  6 19:49 SO373001.utemp.sort*
-rwxrwxrwx 1 root 1706520652 Jan  6 19:51 SO373001.clust.txt*
-rwxrwxrwx 1 root  201731209 Jan  6 22:29 SO374001.htemp*
-rwxrwxrwx 1 root  522560275 Jan  6 22:29 SO374001.utemp*
-rwxrwxrwx 1 root  522560275 Jan  6 22:31 SO374001.utemp.sort*
-rwxrwxrwx 1 root 1715735111 Jan  6 22:33 SO374001.clust.txt*
-rwxrwxrwx 1 root  209260107 Jan  6 23:27 SO412001.htemp*
-rwxrwxrwx 1 root  411029567 Jan  6 23:27 SO412001.utemp*
-rwxrwxrwx 1 root  411029567 Jan  6 23:28 SO412001.utemp.sort*
-rwxrwxrwx 1 root 1409548155 Jan  6 23:30 SO412001.clust.txt*
-rwxrwxrwx 1 root   91704808 Jan  7 00:55 SO60001.htemp*
-rwxrwxrwx 1 root  216003671 Jan  7 00:55 SO60001.utemp*
-rwxrwxrwx 1 root  216003671 Jan  7 00:56 SO60001.utemp.sort*
-rwxrwxrwx 1 root  673013316 Jan  7 00:57 SO60001.clust.txt*
-rwxrwxrwx 1 root  202747472 Jan  7 01:17 SO379001.htemp*
-rwxrwxrwx 1 root  544225358 Jan  7 01:17 SO379001.utemp*
-rwxrwxrwx 1 root          0 Jan  7 01:17 SO379001.clust.txt*
-rwxrwxrwx 1 root  544225358 Jan  7 01:18 SO379001.utemp.sort*
-rwxrwxrwx 1 root  214754164 Jan  7 03:01 SO376001.htemp*
-rwxrwxrwx 1 root  501260356 Jan  7 03:01 SO376001.utemp*
-rwxrwxrwx 1 root  501260356 Jan  7 03:02 SO376001.utemp.sort*
-rwxrwxrwx 1 root 1681373052 Jan  7 03:04 SO376001.clust.txt*
-rwxrwxrwx 1 root  220358361 Jan  7 06:15 SO394001.htemp*
-rwxrwxrwx 1 root  511417603 Jan  7 06:15 SO394001.utemp*
-rwxrwxrwx 1 root  511417603 Jan  7 06:16 SO394001.utemp.sort*
-rwxrwxrwx 1 root 1704495339 Jan  7 06:19 SO394001.clust.txt*
-rwxrwxrwx 1 root  151502736 Jan  7 17:07 SO423001.htemp*
-rwxrwxrwx 1 root  398915299 Jan  7 17:07 SO423001.utemp*
-rwxrwxrwx 1 root  398915299 Jan  7 17:08 SO423001.utemp.sort*
-rwxrwxrwx 1 root 1335436568 Jan  7 17:10 SO423001.clust.txt*
-rwxrwxrwx 1 root  176841320 Jan  7 21:34 SO382001.htemp*
-rwxrwxrwx 1 root  437708084 Jan  7 21:34 SO382001.utemp*
-rwxrwxrwx 1 root  437708084 Jan  7 21:36 SO382001.utemp.sort*
-rwxrwxrwx 1 root 1457190078 Jan  7 21:38 SO382001.clust.txt*
-rwxrwxrwx 1 root  165763728 Jan  7 23:46 SO422001.htemp*
-rwxrwxrwx 1 root  392709326 Jan  7 23:46 SO422001.utemp*
-rwxrwxrwx 1 root  392709326 Jan  7 23:46 SO422001.utemp.sort*
-rwxrwxrwx 1 root 1331529778 Jan  7 23:48 SO422001.clust.txt*
-rwxrwxrwx 1 root  138206818 Jan  8 00:45 SO424001.htemp*
-rwxrwxrwx 1 root  375380308 Jan  8 00:45 SO424001.utemp*
-rwxrwxrwx 1 root  375380308 Jan  8 00:45 SO424001.utemp*
-rwxrwxrwx 1 root  375380308 Jan  8 00:47 SO424001.utemp.sort*
-rwxrwxrwx 1 root 1253962742 Jan  8 00:48 SO424001.clust.txt*
-rwxrwxrwx 1 root  178126936 Jan  8 00:58 SO409001.htemp*
-rwxrwxrwx 1 root  404925627 Jan  8 00:58 SO409001.utemp*
-rwxrwxrwx 1 root  404925627 Jan  8 00:59 SO409001.utemp.sort*
-rwxrwxrwx 1 root 1368696224 Jan  8 01:01 SO409001.clust.txt*
-rwxrwxrwx 1 root  100550868 Jan  8 03:24 SO54b001.htemp*
-rwxrwxrwx 1 root  223613723 Jan  8 03:24 SO54b001.utemp*
-rwxrwxrwx 1 root  223613723 Jan  8 03:25 SO54b001.utemp.sort*
-rwxrwxrwx 1 root  718446225 Jan  8 03:26 SO54b001.clust.txt*
-rwxrwxrwx 1 root  175072200 Jan  8 04:11 SO410001.htemp*
-rwxrwxrwx 1 root  393183303 Jan  8 04:11 SO410001.utemp*
-rwxrwxrwx 1 root  393183303 Jan  8 04:12 SO410001.utemp.sort*
-rwxrwxrwx 1 root 1346808094 Jan  8 04:14 SO410001.clust.txt*
-rwxrwxrwx 1 root  166027232 Jan  8 05:12 SO391001.htemp*
-rwxrwxrwx 1 root  400632795 Jan  8 05:12 SO391001.utemp*
-rwxrwxrwx 1 root  400632795 Jan  8 05:13 SO391001.utemp.sort*
-rwxrwxrwx 1 root 1354362846 Jan  8 05:15 SO391001.clust.txt*
-rwxrwxrwx 1 root  196083467 Jan  8 05:52 SO419001.htemp*
-rwxrwxrwx 1 root  430277427 Jan  8 05:52 SO419001.utemp*
-rwxrwxrwx 1 root  430277427 Jan  8 05:53 SO419001.utemp.sort*
-rwxrwxrwx 1 root 1471481590 Jan  8 05:55 SO419001.clust.txt*
-rwxrwxrwx 1 root  195216846 Jan  8 09:12 SO413001.htemp*
-rwxrwxrwx 1 root  358599323 Jan  8 09:12 SO413001.utemp*
-rwxrwxrwx 1 root  358599323 Jan  8 09:13 SO413001.utemp.sort*
-rwxrwxrwx 1 root 1200570486 Jan  8 09:15 SO413001.clust.txt*
-rwxrwxrwx 1 root  193890289 Jan  8 12:22 SO416001.htemp*
-rwxrwxrwx 1 root  410204910 Jan  8 12:22 SO416001.utemp*
-rwxrwxrwx 1 root  410204910 Jan  8 12:23 SO416001.utemp.sort*
-rwxrwxrwx 1 root 1388850589 Jan  8 12:25 SO416001.clust.txt*
-rwxrwxrwx 1 root  174533040 Jan  9 00:24 SO370001.htemp*
-rwxrwxrwx 1 root  365363188 Jan  9 00:24 SO370001.utemp*
-rwxrwxrwx 1 root  365363188 Jan  9 00:25 SO370001.utemp.sort*
-rwxrwxrwx 1 root 1233376799 Jan  9 00:27 SO370001.clust.txt*
-rwxrwxrwx 1 root  166380794 Jan  9 01:32 SO411001.htemp*
-rwxrwxrwx 1 root  362408253 Jan  9 01:32 SO411001.utemp*
-rwxrwxrwx 1 root  362408253 Jan  9 01:32 SO411001.utemp.sort*
-rwxrwxrwx 1 root 1240926934 Jan  9 01:34 SO411001.clust.txt*
-rwxrwxrwx 1 root  158299361 Jan  9 02:33 SO402001.htemp*
-rwxrwxrwx 1 root  334689603 Jan  9 02:33 SO402001.utemp*
-rwxrwxrwx 1 root  334689603 Jan  9 02:34 SO402001.utemp.sort*
-rwxrwxrwx 1 root 1138904919 Jan  9 02:36 SO402001.clust.txt*
-rwxrwxrwx 1 root  153894827 Jan  9 03:10 SO360001.htemp*
-rwxrwxrwx 1 root  320557898 Jan  9 03:10 SO360001.utemp*
-rwxrwxrwx 1 root  320557898 Jan  9 03:11 SO360001.utemp.sort*
-rwxrwxrwx 1 root 1099591585 Jan  9 03:12 SO360001.clust.txt*
-rwxrwxrwx 1 root  159451560 Jan  9 04:50 SO407001.htemp*
-rwxrwxrwx 1 root  324098732 Jan  9 04:50 SO407001.utemp*
-rwxrwxrwx 1 root  324098732 Jan  9 04:51 SO407001.utemp.sort*
-rwxrwxrwx 1 root 1123371976 Jan  9 04:53 SO407001.clust.txt*
-rwxrwxrwx 1 root  177112162 Jan  9 05:20 SO420001.htemp*
-rwxrwxrwx 1 root  375993804 Jan  9 05:20 SO420001.utemp*
-rwxrwxrwx 1 root  375993804 Jan  9 05:21 SO420001.utemp.sort*
-rwxrwxrwx 1 root 1278434476 Jan  9 05:23 SO420001.clust.txt*
-rwxrwxrwx 1 root  168894917 Jan  9 06:20 SO414001.htemp*
-rwxrwxrwx 1 root  350771595 Jan  9 06:20 SO414001.utemp*
-rwxrwxrwx 1 root  350771595 Jan  9 06:21 SO414001.utemp.sort*
-rwxrwxrwx 1 root 1207750347 Jan  9 06:23 SO414001.clust.txt*
-rwxrwxrwx 1 root  158277351 Jan  9 11:59 SO408001.htemp*
-rwxrwxrwx 1 root  317551665 Jan  9 11:59 SO408001.utemp*
-rwxrwxrwx 1 root  317551665 Jan  9 11:59 SO408001.utemp.sort*
-rwxrwxrwx 1 root 1100018867 Jan  9 12:01 SO408001.clust.txt*
-rwxrwxrwx 1 root   99263248 Jan  9 12:56 SO93001.htemp*
-rwxrwxrwx 1 root  224987151 Jan  9 12:56 SO93001.utemp*
-rwxrwxrwx 1 root  224987151 Jan  9 12:56 SO93001.utemp.sort*
-rwxrwxrwx 1 root  714856115 Jan  9 12:58 SO93001.clust.txt*
-rwxrwxrwx 1 root  197284965 Jan  9 15:08 SO417001.htemp*
-rwxrwxrwx 1 root  361786935 Jan  9 15:08 SO417001.utemp*
-rwxrwxrwx 1 root  361786935 Jan  9 15:09 SO417001.utemp.sort*
-rwxrwxrwx 1 root 1263650069 Jan  9 15:11 SO417001.clust.txt*
-rwxrwxrwx 1 root  190649860 Jan  9 17:34 SO418001.htemp*
-rwxrwxrwx 1 root  317578465 Jan  9 17:34 SO418001.utemp*
-rwxrwxrwx 1 root  317578465 Jan  9 17:35 SO418001.utemp.sort*
-rwxrwxrwx 1 root 1113573723 Jan  9 17:37 SO418001.clust.txt*
-rwxrwxrwx 1 root  135174346 Jan  9 22:15 SO363001.htemp*
-rwxrwxrwx 1 root  224730850 Jan  9 22:15 SO363001.utemp*
-rwxrwxrwx 1 root  224730850 Jan  9 22:15 SO363001.utemp.sort*
-rwxrwxrwx 1 root  790262161 Jan  9 22:16 SO363001.clust.txt*
-rwxrwxrwx 1 root  130198798 Jan  9 22:48 SO53001.htemp*
-rwxrwxrwx 1 root  288121348 Jan  9 22:48 SO53001.utemp*
-rwxrwxrwx 1 root  288121348 Jan  9 22:48 SO53001.utemp.sort*
-rwxrwxrwx 1 root  917773987 Jan  9 22:49 SO53001.clust.txt*
-rwxrwxrwx 1 root  141848990 Jan  9 23:05 SO227001.htemp*
-rwxrwxrwx 1 root  193213307 Jan  9 23:05 SO227001.utemp*
-rwxrwxrwx 1 root  193213307 Jan  9 23:06 SO227001.utemp.sort*
-rwxrwxrwx 1 root  703922653 Jan  9 23:07 SO227001.clust.txt*
-rwxrwxrwx 1 root  157369606 Jan  9 23:34 SO415001.htemp*
-rwxrwxrwx 1 root  313773552 Jan  9 23:34 SO415001.utemp*
-rwxrwxrwx 1 root  313773552 Jan  9 23:35 SO415001.utemp.sort*
-rwxrwxrwx 1 root 1078452034 Jan  9 23:36 SO415001.clust.txt*
-rwxrwxrwx 1 root  156825342 Jan 10 00:28 SO228T001.htemp*
-rwxrwxrwx 1 root  298999594 Jan 10 00:28 SO228T001.utemp*
-rwxrwxrwx 1 root  298999594 Jan 10 00:29 SO228T001.utemp.sort*
-rwxrwxrwx 1 root 1025189535 Jan 10 00:30 SO228T001.clust.txt*
-rwxrwxrwx 1 root  115683109 Jan 10 00:32 SO90001.htemp*
-rwxrwxrwx 1 root  257009824 Jan 10 00:32 SO90001.utemp*
-rwxrwxrwx 1 root  257009824 Jan 10 00:32 SO90001.utemp.sort*
-rwxrwxrwx 1 root  806771887 Jan 10 00:33 SO90001.clust.txt*
-rwxrwxrwx 1 root  122045532 Jan 10 02:22 SO96001.htemp*
-rwxrwxrwx 1 root  270200766 Jan 10 02:22 SO96001.utemp*
-rwxrwxrwx 1 root  270200766 Jan 10 02:23 SO96001.utemp.sort*
-rwxrwxrwx 1 root  862465352 Jan 10 02:25 SO96001.clust.txt*
-rwxrwxrwx 1 root  108212242 Jan 10 04:45 SO54a001.htemp*
-rwxrwxrwx 1 root  229932536 Jan 10 04:45 SO54a001.utemp*
-rwxrwxrwx 1 root  229932536 Jan 10 04:45 SO54a001.utemp.sort*
-rwxrwxrwx 1 root  735767141 Jan 10 04:46 SO54a001.clust.txt*
-rwxrwxrwx 1 root  123293746 Jan 10 05:08 SO89001.htemp*
-rwxrwxrwx 1 root  245313614 Jan 10 05:08 SO89001.utemp*
-rwxrwxrwx 1 root  245313614 Jan 10 05:08 SO89001.utemp.sort*
-rwxrwxrwx 1 root  789319540 Jan 10 05:09 SO89001.clust.txt*
-rwxrwxrwx 1 root  173853086 Jan 10 05:23 SO231T001.htemp*
-rwxrwxrwx 1 root  281309225 Jan 10 05:23 SO231T001.utemp*
-rwxrwxrwx 1 root  281309225 Jan 10 05:23 SO231T001.utemp.sort*
-rwxrwxrwx 1 root  977243497 Jan 10 05:25 SO231T001.clust.txt*
isaacovercast commented 2 years ago

Can I see this too ls -ltr app-cottontails-3rad-tmpalign?

isaacovercast commented 2 years ago

Here's a clue, zero sized cluster file:

-rwxrwxrwx 1 root  202747472 Jan  7 01:17 SO379001.htemp*
-rwxrwxrwx 1 root  544225358 Jan  7 01:17 SO379001.utemp*
-rwxrwxrwx 1 root          0 Jan  7 01:17 SO379001.clust.txt*

Can you wetransfer me the htemp and utemp files for that sample (S0379001)?

isaacovercast commented 2 years ago

Also, there should be a file called S0379001_derep.fa in the tmpalign directory, so if I can get that file too (wetransfer) that would be great.

alexkrohn commented 2 years ago

Sent the wetransfer files to your gmail.

I noticed that zero sized file too. I looked back through the edits folder and tried to grep the degree sign for any SO379001 files, but couldn't find any lines that had a degree sign in them...

Here's the tmpalign folder:

total 1067566384
-rwxrwxrwx 1 root root  5381950071 Jan  4 01:57 SO413001_nonmerged_R2_.fastq
-rwxrwxrwx 1 root root  5415510323 Jan  4 01:57 SO413001_nonmerged_R1_.fastq
-rwxrwxrwx 1 root root  6642132519 Jan  4 02:52 SO416001_nonmerged_R2_.fastq
-rwxrwxrwx 1 root root  6684697709 Jan  4 02:52 SO416001_nonmerged_R1_.fastq
-rwxrwxrwx 1 root root  6839050734 Jan  4 02:52 SO424001_nonmerged_R2_.fastq
-rwxrwxrwx 1 root root  6880310178 Jan  4 02:52 SO424001_nonmerged_R1_.fastq
-rwxrwxrwx 1 root root  7047153578 Jan  4 03:07 SO391001_nonmerged_R2_.fastq
-rwxrwxrwx 1 root root  7092074778 Jan  4 03:07 SO391001_nonmerged_R1_.fastq
-rwxrwxrwx 1 root root  7027608960 Jan  4 03:12 SO410001_nonmerged_R2_.fastq
-rwxrwxrwx 1 root root  7072014260 Jan  4 03:12 SO410001_nonmerged_R1_.fastq
-rwxrwxrwx 1 root root  6966597718 Jan  4 03:14 SO422001_nonmerged_R2_.fastq
-rwxrwxrwx 1 root root  7008333236 Jan  4 03:14 SO422001_nonmerged_R1_.fastq
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isaacovercast commented 2 years ago

Somehow the utemp.sort file is being compressed. I can do this (from inside clustmap.py.build_clusters()):

    with open(usort, 'rt') as insort:
        # iterator, seed null, seqlist null
        isort = iter(insort)
        print(next(isort))

And I get the exact error message:

UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb0 in position 1: invalid start byte

We are sorting the .utemp file with the system default sort command, like this:

cmd = ["sort", "-k", "2", uhandle, "-o", usort]
proc = sps.Popen(cmd, close_fds=True)
proc.communicate()[0]

So it looks like, for whatever reason, the system default sort command is compressing the output by default. GNU sort does have a compression option (man sort) --compress-program=PROG, but we do not use this. Perhaps the system default sort isn't GNU? You can check with sort --version, mine is sort (GNU coreutils) 8.25.

isaacovercast commented 2 years ago

Indeed the first few bytes in hex are 00b0:

$ xxd SO379001.utemp.sort | head -n 1
00000000: 00b0 b63a 25bd e813 e1ca 64e3 3f76 dddb  ...:%.....d.?v..
alexkrohn commented 2 years ago

Very weird! My sort version is identical to yours. And, only SO379001 is listed as a data file when I do file app-cottontails-3rad_clust_0.85/*sort. All the other individuals are ASCII text.

alexkrohn commented 2 years ago

Maybe it was a mistake based on cosmic radiation or running out of RAM? It sounds like the best solution would just be to try step 3 over again and let you know in 6 days if it happens again 😅

isaacovercast commented 2 years ago

Weird! The utemp and utemp.sort files are identical size:

$ ls -l
total 3173496
-rw-r--r-- 1 isaac isaac 1958440910 Jan 10 12:30 SO379001_derep.fa
-rw-r--r-- 1 isaac isaac  202747472 Jan 10 11:59 SO379001.htemp
-rw-r--r-- 1 isaac isaac  544225358 Jan 10 11:59 SO379001.utemp
-rw-r--r-- 1 isaac isaac  544225358 Jan 10 11:59 SO379001.utemp.sort

But they are _definitely different, which is insane.

$ strings SO379001.utemp.sort | grep size | wc -l
5658139
$ grep size SO379001.utemp | wc -l
120417

All of the data inside the munged sort file is unique as well

$ strings SO379001.utemp.sort | grep size | uniq | wc -l
5658139

What the heck?

isaacovercast commented 2 years ago

It definitely sounds like a gremlin of some kind. Sorry it's such a hack and takes so long to run, I really wish there was checkpointing on step 3. I'll keep thinking about it, but yeah, if you can run it again I'd be curious to see if it fails in the same way. I would rm -rf the tmpalign folder, for good measure. It could also be a holdover bug of some kind from a previous failed run, and the tmpalign directory doesn't get cleaned up automatically in a crash. Good luck.

alexkrohn commented 2 years ago

Gremlins! And so far from Halloween!!

Thanks for your digging. I'll re-run it and let you know if the error persists.