BUSCO - Revision history

Rf at 15:25, 31 January 2017

2017-01-31T15:25:36Z

2017-01-31T15:24:52Z

2017-01-31T14:29:39Z

2017-01-31T14:28:43Z

2017-01-31T14:19:34Z

2016-08-01T12:12:09Z

2016-08-01T12:07:35Z

2016-07-27T16:16:19Z

2016-07-27T16:16:02Z

2016-07-27T16:06:01Z

@@ Line 48: / Line 48: @@
 After loading the module, the template is as follows:
-  BUSCO -o NAME -in ASSEMBLY -l LINEAGE -m genome
+  BUSCO.py -o NAME -in ASSEMBLY -l LINEAGE -m genome
 <ins>Explanation</ins>:
@@ Line 58: / Line 58: @@
 So, a typical command on a bacteria assembly would run like this:
-  BUSCO -in scaffolds.fasta -o busc0 -l $BACTERIA_LIN -m genome
+  BUSCO.py -in scaffolds.fasta -o busc0 -l $BACTERIA_LIN -m genome
 == typical usage queue job script ==
@@ Line 79: / Line 79: @@
   fi
   module load BUSCO
-  BUSCO -in $1 -o $2 -c $NSLOTS -l $BACTERIA_LIN -m genome
+  BUSCO.py -in $1 -o $2 -c $NSLOTS -l $BACTERIA_LIN -m genome
 '''NOTE''' the usage of the '''-c''' (CPUs) option here, it specified how many CPUs/process/threads BUSCO will run with, alllowing parallelisation and faster processing. Its value is '''$NSLOTS''' with rfere to the '''-pe multi 4''' line appearing higher up. i.e. BUSCO will run with 4 parallel threads in this case.

@@ Line 32: / Line 32: @@
 is enough, as all BUSCO's dependencies (python/3.4, augustus/3.2.2, hmmer/3.1b2, EMBOSS/6.6.0) will also be loaded at the same time.
-The main BUSCO executable is a python script called
+The main BUSCO executable is a python script called. Becuase of the loaded modules this should run under python3.4 which is the recommended version of python for Busco.
-However, there is a symlink to this called BUSCO, so the program can equally well be launched with a simple
+  BUSCO.py
 ==modes==

@@ Line 11: / Line 11: @@
 "Write access to the Augustus installation directory is necessary for retraining the gene finder", so retraining is probably best carried out by the sysadmin under "root" user.
-BUSCO is primarily a python application and though it can, apparently, work with version 2 of python, version 3 is recommended.
+BUSCO is primarily a python application and though it can - apparently - work with version 2 of python, it is version 3 that is recommended and implemented on marvin.
 The broad BUSCO process is as follows:

@@ Line 1: / Line 1: @@
 = Introduction =
-BUSCO, like Cegma, is a special tool for the field of "completeness assessment". This concerns genome assemblies, particularly ones generated de-novo, when by concentrating on a core set of genes, one can estimate how complete the assembly is by the number of the these core geens that the assembly has managed to recover.
+BUSCO, like Cegma, is a special tool for the field of "completeness assessment". This concerns genome assemblies, particularly ones generated de-novo, when by concentrating on a core set of genes, one can estimate how complete the assembly is by the number of the these core genes that the assembly has managed to recover.
 BUSCO actually stands for "Benchmarking Universal Single-Copy Orthologs" and labels itself as a quality measure of the assembly. Busco also means "I search" in the Spanish, Galician and Portuguese languages, in which the authors find satisfaction, as the broad goal of the tool is one of a quest for quality.

@@ Line 96: / Line 96: @@
 == writeable augustus directory==
-There is a certain error, which, because it only refers to the retaining operation, can be safely ignored (unless when wanting to retrain of course)
+There is a certain error, which, because it only refers to the re-training operation, can be safely ignored (unless when wanting to undertake re-training of course)
   Error: Cannot write to Augustus directory, please make sure you have write permissions to /usr/local/Modules/modulefiles/tools/augustus/3.2.2/config
-This was corrected by creating a world writeable directory in shelf (scratch) filesystem
+This was corrected by creating a world writeable directory in shelf (scratch) filesystem.

@@ Line 83: / Line 83: @@
   BUSCO -in $1 -o $2 -c $NSLOTS -l $BACTERIA_LIN -m genome
-If we named this script, say, runbuscbact.sh, then we could sunr it like to, not forgetting to give the input assebmly file (with the path to the directory in which it may be found, and our chosen output folder name which will be prefixed with '''run_'''.
+If we named this script, say, '''runbuscbact.sh''', then we could run it like so (not forgetting to give the input assembly file, with the path to the directory in which it may be found, and our chosen output folder name which will be prefixed with '''run_'''):
   qsub runbuscbact.sh 504302_trimmoed2/scaffolds.fasta out0

@@ Line 85: / Line 85: @@
 If we named this script, say, runbuscbact.sh, then we could sunr it like to, not forgetting to give the input assebmly file (with the path to the directory in which it may be found, and our chosen output folder name which will be prefixed with '''run_'''.
-  qsub runbuscbact.sh 504302_trimmoed2/scaffolds.fasta hideous0
+  qsub runbuscbact.sh 504302_trimmoed2/scaffolds.fasta out0
 = Potential errors =

← Older revision		Revision as of 16:06, 27 July 2016
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	Error: Cannot write to Augustus directory, please make sure you have write permissions to /usr/local/Modules/modulefiles/tools/augustus/3.2.2/config		Error: Cannot write to Augustus directory, please make sure you have write permissions to /usr/local/Modules/modulefiles/tools/augustus/3.2.2/config
		+
		+	This was corrected by creating a world writeable directory in shelf (scratch) filesystem