Canu - Revision history

Rf at 16:04, 17 November 2017

2017-11-17T16:04:43Z

2017-04-06T14:12:00Z

2017-04-06T14:04:57Z

2017-04-06T13:51:34Z

2017-04-06T13:50:45Z

2017-04-06T13:25:39Z

2017-03-23T13:04:24Z

2017-03-23T12:26:26Z

2017-03-15T18:13:36Z

2017-03-15T18:11:31Z

@@ Line 9: / Line 9: @@
 * trimming
 * unitig construction
 = Example Usage =

@@ Line 51: / Line 51: @@
   Finished stage 'merylConfigure', reset canuIteration.
   Finished stage 'merylCheck', reset canuIteration.
 * Preferably run <code>canu</code> on a hard disk, try not to use a Windows Network share. Spaces in folders or filenames will annoy it.
 = Example Output =

@@ Line 32: / Line 32: @@
   canu -p plar3 -d plar3 genomeSize=23.729m minReadLength=250 minOverlapLength=50 -nanopore-raw allr1.fastq.gz
-= Difficulties =
+= Running notes =
 * Preferably run <code>canu</code> on a hard disk, try not to use a Windows Network share. Spaces in folders or filenames will annoy it.

← Older revision		Revision as of 13:51, 6 April 2017
Line 34:		Line 34:
	= Difficulties =		= Difficulties =

−	* Preferably run canu on a hard disk, try not to use a Windows Network share. Spaces in folders or filenames will annoy it.	+	* Preferably run <code>canu</code> on a hard disk, try not to use a Windows Network share. Spaces in folders or filenames will annoy it.

@@ Line 11: / Line 11: @@
 = Example Usage =
 The following use Nick Loman's Ecoli data file which can be obtained via:
@@ Line 18: / Line 21: @@
 As you can see, this is a 2D data set. The downloaded file will be calle '''oxford.fasta'''.
-The recommended way to run '''canu''' for this is:
+The recommended way to run <code>canu</code> for this is:
   canu -p ecoli -d ecoli-oxford genomeSize=4.8m -nanopore-raw oxford.fasta

@@ Line 5: / Line 5: @@
 It comes from the Maryland Bioinformatics Laboratory, and is based on the Celera Assembler, whose code base is no longer maintained and was made open source in 2014.
-It has three high level componenet tasks:
+It has three high level component tasks:
 * correction
 * trimming
@@ Line 376: / Line 376: @@
 A bug has been posted to the development team [https://github.com/marbl/canu/issues/408 here].

← Older revision		Revision as of 13:04, 23 March 2017
Line 327:		Line 327:

	canu failed with 'failed to read estimated mer threshold from 'trimming/0-mercounts/plar3.ms22.estMerThresh.out''.		canu failed with 'failed to read estimated mer threshold from 'trimming/0-mercounts/plar3.ms22.estMerThresh.out''.
		+
		+	Points:
		+	* The stage where the program is affect by the bug is in reading '''mer threshold estimate'''. However this appears not to be ready as only a
		+	trimming/0-mercounts/plar3.ms22.estMerThresh.out.WORKING
		+
		+	file exists, albeit of zero size.
		+

← Older revision		Revision as of 12:26, 23 March 2017
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	Complete documentation at http://canu.readthedocs.org/en/latest/		Complete documentation at http://canu.readthedocs.org/en/latest/
		+
		+	= Running problems =
		+
		+	A bug has been posted to the development team [https://github.com/marbl/canu/issues/408 here].

← Older revision		Revision as of 18:13, 15 March 2017
Line 300:		Line 300:

	canu failed with 'gatekeeper store exists, but contains no reads'.		canu failed with 'gatekeeper store exists, but contains no reads'.
		+
		+	It some times says "don't panic" and other times:
		+
		+	-- Finished stage 'obt-gatekeeper', reset canuIteration.
		+	-- Finished stage 'merylConfigure', reset canuIteration.
		+	--
		+	-- Running jobs. First attempt out of 2.
		+	----------------------------------------
		+	-- Starting concurrent execution on Wed Mar 15 18:06:12 2017 with 843.099 GB free disk space (1 processes; 8 concurrently)
		+
		+	cd trimming/0-mercounts
		+	./meryl.sh 1 > ./meryl.000001.out 2>&1
		+
		+	-- Finished on Wed Mar 15 18:06:38 2017 (26 seconds) with 842.7 GB free disk space
		+	----------------------------------------
		+	-- Meryl finished successfully.
		+	-- Finished stage 'merylCheck', reset canuIteration.
		+	================================================================================
		+	Please panic. canu failed, and it shouldn't have.
		+
		+	Stack trace:
		+
		+	at /home/nutria/gitrepos/canu/Linux-amd64/bin/lib/canu/Execution.pm line 1475.
		+	canu::Execution::caFailure("failed to read estimated mer threshold from 'trimming/0-merco"..., undef) called at /home/nutria/gitrepos/canu/Linux-amd64/bin/lib/canu/Meryl.pm line 446
		+	canu::Meryl::merylProcess("plar3", "obt") called at /home/nutria/gitrepos/canu/Linux-amd64/bin/canu line 547
		+
		+	canu failed with 'failed to read estimated mer threshold from 'trimming/0-mercounts/plar3.ms22.estMerThresh.out''.

@@ Line 24: / Line 24: @@
 <ins>Explanation</ins>:
 * '''-p''', a prefix
 = Example Output =