Recent changes to FAQ

WikiPage FAQ modified by Mathias Kuhring

Mathias Kuhring — Mon, 09 Jul 2012 16:06:35 -0000

--- v3
+++ v4
@@ -9,7 +9,7 @@
 Could not create the Java virtual machine.*
 
 **A 1:**
-The running scripts try to start the Java VM with 1 GB heap size (memory space) per default.
+The execution scripts try to start the Java VM with 1 GB heap size (memory space) per default and will terminate if not enough memory space is available.
 
 If necessary, it can be changed in the scripts. Open the scripts with a text editor and replace the heap size request "-Xms1024m -Xmx1024m" with values more suitable for the installed memory (e.g. decrease it: "-Xms512m -Xmx512m").  Note, it has to be less than the memory actually installed because Java can't allocate the whole memory for it self.

WikiPage FAQ modified by Mathias Kuhring

Mathias Kuhring — Thu, 05 Jul 2012 15:22:32 -0000

--- v2
+++ v3
@@ -1,8 +1,5 @@
 Frequently Asked Questions
 ==========================
-
-Execution Problems
-------------------
 
 **Q 1:**
 Following error message prevents execution:
@@ -16,6 +13,7 @@
 
 If necessary, it can be changed in the scripts. Open the scripts with a text editor and replace the heap size request "-Xms1024m -Xmx1024m" with values more suitable for the installed memory (e.g. decrease it: "-Xms512m -Xmx512m").  Note, it has to be less than the memory actually installed because Java can't allocate the whole memory for it self.
 
+---
 
 **Q 2:**
 An error message similar to the following interrupts execution:
@@ -29,3 +27,49 @@
 This probably happens because the size of imported data (PSMs, gene annotations, etc.) exceeds the available Java heap size. If more physical memory is available than acutally used, the heap size can be increased. 
 
 Please consider answer 1 for how to alter the heap size.
+
+---
+
+**Q 3:**
+What is the assembly version of the gene annotations, amino acid sequences and genome  downloaded with the download tool?
+
+**A 3:**
+
+Organism | Assembly
+---------|---------
+Caenorhabditis elegans | ce10
+Danio rerio (Zebrafish) | danRer6
+Drosophila melanogaster (Fruit fly) | dm3
+Gallus gallus (Chicken) | galGal3
+Homo sapiens (Human) | hg19
+Mus musculus (Mouse) | mm10
+Rattus norvegicus (Rat) | rn4
+Saccharomyces cerevisiae (Yeast) | sacCer3
+
+---
+
+**Q 4:**
+The upload to the USCS Genome Browser aborts with following error message:
+
+*... Error line ? of custom track: chromEnd larger than chrom chr? size ..."*
+
+**A 4:**
+The coordinates of the mapped PSMs exceeds the possible range of the selected genome.
+
+Make sure "clade", "genome" and "assembly" matches the organism and version used for mapping with iPiG.
+
+For assembly versions please consider answer 3, if the data were retrieved with the download tool.
+
+---
+
+**Q 5:**
+The upload to the USCS Genome Browser aborts with following error message:
+
+*Unrecognized format line ? of custom track: ... (note: chrom names are case sensitive)*
+
+**A 5:**
+Probably, the chromosome indicated by the PSM is not available in the selected genome.
+
+Make sure "clade", "genome" and "assembly" matches the organism and version used for mapping with iPiG.
+
+For assembly versions please consider answer 3, if the data were retrieved with the download tool.

WikiPage FAQ modified by Mathias Kuhring

Mathias Kuhring — Thu, 05 Jul 2012 14:32:34 -0000

--- v1
+++ v2
@@ -4,28 +4,28 @@
 Execution Problems
 ------------------
 
-Q 1:
+**Q 1:**
 Following error message prevents execution:
 
-Error occurred during initialization of VM
-Could not reserve enough space for object heap
-Could not create the Java virtual machine.
+*Error occurred during initialization of VM

+Could not reserve enough space for object heap

+Could not create the Java virtual machine.*
 
-A 1:
+**A 1:**
 The running scripts try to start the Java VM with 1 GB heap size (memory space) per default.
 
 If necessary, it can be changed in the scripts. Open the scripts with a text editor and replace the heap size request "-Xms1024m -Xmx1024m" with values more suitable for the installed memory (e.g. decrease it: "-Xms512m -Xmx512m").  Note, it has to be less than the memory actually installed because Java can't allocate the whole memory for it self.
 
 
-Q 2:
+**Q 2:**
 An error message similar to the following interrupts execution:
 
-Exception in thread "Thread-4" java.lang.OutOfMemoryError: Java heap space
-	...
-	at de.rki.ng4.ipig.Ipig.run(Ipig.java:97)
-	at de.rki.ng4.ipig.gui.IpigGui$Mapper.run(IpigGui.java:632)
+*Exception in thread "Thread-4" java.lang.OutOfMemoryError: Java heap space

+	...

+	at de.rki.ng4.ipig.Ipig.run(Ipig.java:97)

+	at de.rki.ng4.ipig.gui.IpigGui$Mapper.run(IpigGui.java:632)*
 
-A 2:
+**A 2:**
 This probably happens because the size of imported data (PSMs, gene annotations, etc.) exceeds the available Java heap size. If more physical memory is available than acutally used, the heap size can be increased. 
 
 Please consider answer 1 for how to alter the heap size.

WikiPage FAQ modified by Mathias Kuhring

Mathias Kuhring — Thu, 05 Jul 2012 14:28:13 -0000

Frequently Asked Questions ========================== Execution Problems ------------------ Q 1: Following error message prevents execution: Error occurred during initialization of VM Could not reserve enough space for object heap Could not create the Java virtual machine. A 1: The running scripts try to start the Java VM with 1 GB heap size (memory space) per default. If necessary, it can be changed in the scripts. Open the scripts with a text editor and replace the heap size request "-Xms1024m -Xmx1024m" with values more suitable for the installed memory (e.g. decrease it: "-Xms512m -Xmx512m"). Note, it has to be less than the memory actually installed because Java can't allocate the whole memory for it self. Q 2: An error message similar to the following interrupts execution: Exception in thread "Thread-4" java.lang.OutOfMemoryError: Java heap space ... at de.rki.ng4.ipig.Ipig.run(Ipig.java:97) at de.rki.ng4.ipig.gui.IpigGui$Mapper.run(IpigGui.java:632) A 2: This probably happens because the size of imported data (PSMs, gene annotations, etc.) exceeds the available Java heap size. If more physical memory is available than acutally used, the heap size can be increased. Please consider answer 1 for how to alter the heap size.