MayurDivate
commented
3 years ago Dear @MargheritaSq
"I considerd hg19 as reference genome and only chrM"For alignment of sample data, you must include chromosomes other than ChrM. ChrM filtering is optional.
Mayur
MargheritaSq
Hi!
I am following the GUAVA manual analyzing the Sample Data (DMSO_Rep1_R1.fastq and DMSO_Rep1_R2.fastq) and everything worked perfectly fine until the Picard step. In my output folder I have the Adpater and Fastqc results but after bowtie2 finished to work I did not get and bowtie directory containing its results. I do not know if it is ok or not. Anyway for the analysis I considerd hg19 as reference genome and only chrM, as described in the manual. I had left all the other parameter sto the default values. Could you help me?
Thanks!
Down here I report GUAVA complete output:
(GUAVAenvpy2.7) MargherariosAir:GUAVA-1 margheritas$ java -jar GUAVA.jar GUAVA version 1 Operating System of machine :Mac OS X cutadapt: Working! bowtie: Working! bowtie2: Working! fastqc: Working! samtools: Working! macs2: Working! Picard: Working! bedtools: Working! bedGraphToBigWig: Working! igv: Working! Adapter trimming...Done fastq QC... Alignment... Please wait while bowtie2 alignment is finished..Done! ---- Alignment filtering ------ Remove duplicates... Cannot run program "picard" (in directory "/Users/margheritas/MyPythonEnv/GUAVA-1/Result_sample_data_DMSO_rep1/DMSO_Rep1_R1_OUTPUT"): error=2, No such file or directory Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at umac.guava.Tool.writeLog(Tool.java:89) at umac.guava.AnalysisWorkflow.getDuplicateFilteredBAM(AnalysisWorkflow.java:707) at umac.guava.AnalysisWorkflow.runAlignmentFiltering(AnalysisWorkflow.java:556) at umac.guava.AnalysisWorkflow.startGUIGuavaAnalysis(AnalysisWorkflow.java:166) at umac.guava.MainJFrame.startJButtonActionPerformed(MainJFrame.java:837) at umac.guava.MainJFrame.access$700(MainJFrame.java:27) at umac.guava.MainJFrame$8.actionPerformed(MainJFrame.java:267) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) at java.awt.Component.processMouseEvent(Component.java:6539) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6304) at java.awt.Container.processEvent(Container.java:2239) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2297) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476) at java.awt.Container.dispatchEventImpl(Container.java:2283) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84) at java.awt.EventQueue$4.run(EventQueue.java:733) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:730) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)