drigodwin

2016-10-18 12:13:58
Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.80-b11 mixed mode):

"sftp reader" daemon prio=5 tid=0x00007ff264d97000 nid=0x5e8c3 in Object.wait() [0x00007000070e6000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	- waiting on <0x00000007f22ba960> (a net.schmizz.sshj.common.Buffer$PlainBuffer)
	at java.lang.Object.wait(Object.java:503)
	at net.schmizz.sshj.connection.channel.ChannelInputStream.read(ChannelInputStream.java:128)
	- locked <0x00000007f22ba960> (a net.schmizz.sshj.common.Buffer$PlainBuffer)

drigodwin

2016-10-18 12:41:39
Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.80-b11 mixed mode):

"reader" daemon prio=5 tid=0x00007ff2661cc000 nid=0x16037 runnable [0x000070000e642000]
   java.lang.Thread.State: RUNNABLE
	at net.schmizz.sshj.transport.Reader.run(Reader.java:63)

"Thread-296327" daemon prio=5 tid=0x00007ff26623e800 nid=0x85377 in Object.wait() [0x000070000db21000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)

drigodwin

2016-10-18 10:27:56,341 DEBUG 102 j.headers [er-LsPYHwKd-1111] >> GET https://cloudsoft2-lon.openstack.blueboxgrid.com:8774/v2/a0ade3ca76784719845363979dc1014e/os-security-groups HTTP/1.1
2016-10-18 10:27:56,341 DEBUG 102 j.headers [er-LsPYHwKd-1111] >> Accept: application/json
2016-10-18 10:27:56,341 DEBUG 102 j.headers [er-LsPYHwKd-1111] >> X-Auth-Token: 428b4d663e4943cdb13348ebe2dd169a
2016-10-18 10:28:02,322 DEBUG 102 j.headers [er-LsPYHwKd-1111] << HTTP/1.1 200 OK
2016-10-18 10:28:02,322 DEBUG 102 j.headers [er-LsPYHwKd-1111] << Date: Tue, 18 Oct 2016 09:28:02 GMT
2016-10-18 10:28:02,322 DEBUG 102 j.headers [er-LsPYHwKd-1111] << Connection: close
2016-10-18 10:28:02,322 DEBUG 102 j.headers [er-LsPYHwKd-1111] << X-Compute-Request-Id: req-7489d376-9d69-4618-99ea-0b2bee13c589
2016-10-18 10:28:02,323 DEBUG 102 j.headers [er-LsPYHwKd-1111] << Content-Type: application/json
2016-10-18 10:28:02,323 DEBUG 102 j.headers [er-LsPYHwKd-1111] << Content-Length: 164061
2016-10-18 10:28:02,377 DEBUG 102 j.wire [er-LsPY

drigodwin

${r"sudo sed -i.bak '/^nameserver /{h;s/.*/nameserver 8\.8\.8\.8/};${x;/^$/{s//nameserver 8\.8\.8\.8/;H};x}' /etc/resolv.conf"}

drigodwin

This is an empty test file

drigodwin

                          Status  esc.bam
1                       Assigned  7750622
2            Unassigned_Unmapped        0
3      Unassigned_MappingQuality        0
4             Unassigned_Chimera        0
5      Unassigned_FragmentLength        0
6           Unassigned_Duplicate        0
7        Unassigned_MultiMapping 21821282
8           Unassigned_Secondary        0

drigodwin

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P esc.bam                                        ||
||                                                                            ||
||      Dir for temp files : .                                                ||
||                 Threads : 1                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||         Strand specific : no                                               ||

drigodwin

fc <- featureCounts(file="esc.bam",annot.ext="../../../genomes/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/Mus_musculus.NCBIM37.58.gtf",isGTFAnnotationFile = TRUE,GTF.featureType = "CDS",GTF.attrType = "gene_id")
write.table(x=data.frame(fc$annotation[,c("GeneID","Length")],fc$counts,stringsAsFactors=FALSE),file="counts.txt",quote=FALSE,sep="\t",row.names=FALSE)

drigodwin

tpm <- function(counts, lengths) {
  rate <- counts / lengths
  rate / sum(rate) * 1e6
}

ftr.cnt <- read.table("counts.txt", sep="\t", stringsAsFactors=FALSE,
  header=TRUE)
library(dplyr)
library(tidyr)

drigodwin

hello world