rdpstaff/ecofunprimer

primer design pipeline

ecofunprimer's Issues

Hardcoded path for entropy file

I know this work is still in development, therefore I also would like to report a bug. I am interested in the file with entropy values and I noticed that the path for that file is hardcoded to a home directory: https://github.com/rdpstaff/EcoFunPrimer/blob/master/src/edu/msu/cme/rdp/primerdesign/utils/OligosInfoGrapher.java#L41 Therefore in my local installation it is not working.

EcoFunPrimer/Dr. Rosen's lab

~/RDPTools/PrimerDesign/dist$ ls
PrimerDesign.jar
RDPTools/PrimerDesign/dist$ pwd
~/RDPTools/PrimerDesign/dist$ cd
$ java -Xmx8g -jar /home/eesi/RDPTools/PrimerDesign/dist/PrimerDesign.jar --help
usage: java -jar PrimerDesign.jar [--help] (-i|--input)
Shows all the files
$ java -Xmx8g -jar /home/eesi/RDPTools/PrimerDesign/dist/PrimerDesign.jar -subcommand screen -input Desktop/62518burkholderiales_coae_2_extended.fa -GraphOutput Desktop/ -oligoMinSize 15 -oligoMaxSize 30 -tempMin 55 -tempMax 63 -hairMax 35 -homoMax 35 -os mac -NoTEndFilter t -NoPoly3GCFilter t -PolyRunFilter 4 -GCFilterMin 0.45 -GCFi
python: can't open file '/home/eesi/RDPTools/PrimerDesign/dist/primer3/primersplot.py': [Errno 2] No such file or directory
End compile data points: 25/06/18 15:24:41

primersplot.py': [Errno 2] No such file or directory
Where is this file? Why it cannot locate it?

Primer design Java Runtime error

eesi@dhantha-CG1330:~/Desktop$ java -jar /home/eesi/RDPTools/PrimerDesign/dist/PrimerDesign.jar -subcommand select -input /home/eesi/Desktop/reduced.mfa -SlidingScale true -productLengthMin 150 -productLengthMax 500 -oligoMinSize 15 -oligoMaxSize 30 -maxMismatches 0 -tempMin 55 -tempMax 63 -hairMax 35 -homoMax 35 -isTreeWeightNeeded f -os mac -output outputfile -assayMax 30 -degenMax 1 -NoTEndFilter t -NoPoly3GCFilter t -PolyRunFilter 4 -GCFilterMin 0.45 -GCFilterMax 0.7 -sodiumConc 50.0 -magnesConc 1.5

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x00007fabba8b852f, pid=11535, tid=0x00007fabbb433700

JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)

Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode linux-amd64 compressed oops)

Problematic frame:

C [libc.so.6+0x8252f]

Can you help us with this?

build.xml:86 build failed

“”“download-ivy:
[mkdir] Created dir: /root/.ant/lib
[get] Getting: http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar
[get] To: /root/.ant/lib/ivy.jar
[get] Error getting http://repo2.maven.org/maven2/org/apache/ivy/ivy/2.1.0-rc2/ivy-2.1.0-rc2.jar to /root/.ant/lib/ivy.jar

BUILD FAILED
/home/aiqubo/MetaFunPrimer/MetaFunPrimer/RDPTools/PrimerDesign/build.xml:86: java.net.UnknownHostException: repo2.maven.org
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:607)
at java.net.Socket.connect(Socket.java:556)
at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
at sun.net.www.http.HttpClient.(HttpClient.java:242)
at sun.net.www.http.HttpClient.New(HttpClient.java:339)
at sun.net.www.http.HttpClient.New(HttpClient.java:357)
at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1226)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1162)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1056)
at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:990)
at org.apache.tools.ant.taskdefs.Get$GetThread.openConnection(Get.java:712)
at org.apache.tools.ant.taskdefs.Get$GetThread.get(Get.java:626)
at org.apache.tools.ant.taskdefs.Get$GetThread.run(Get.java:616)
”“”
java version "1.7.0_251"

Can you help us with this?

PrimerDesign.jar not being created

Hello
Following the instructions for installing EcoFunPrimer and RDPTools, the PrimerDesign.jar is not being created in the PrimerDesign/dist folder as is described in the instructions.

A jar file called EcoFunPrimer.jar is installed in the PrimerDesign/dist folder and libPrimer3.so file with a lib directory.

Separately, installing MetaFunPrimer, a PrimerDesign.jar is created inside the MetaFunPrimer/src directory, not the RDPTools/PrimerDesign/dist directory, so I could test the instruction: java -Xmx8g -jar /path/to/PrimerDesign.jar [--help].

The output is

ERROR: Program needs os type, used default: mac
ERROR: Program needs output file directory to start
ERROR: Program needs sequence input fasta file to start
Exception in thread "main" java.lang.NullPointerException
at edu.msu.cme.rdp.readseq.utils.SeqUtils.guessFileFormat(SeqUtils.java:326)
at edu.msu.cme.rdp.readseq.utils.SeqUtils.getSeqReaderCore(SeqUtils.java:261)
at edu.msu.cme.rdp.readseq.readers.SequenceReader.(SequenceReader.java:38)
at edu.msu.cme.rdp.readseq.readers.SequenceReader.readFully(SequenceReader.java:75)
at edu.msu.cme.rdp.primerdesign.selectprimers.SelectPrimerPipeline.main(SelectPrimerPipeline.java:68)
at edu.msu.cme.rdp.primerdesign.selectprimers.PrimerDesign.main(PrimerDesign.java:233)

In contract, the installed EcoFunPrimer.jar out put is

java -Xmx8g -jar EcoFunPrimer.jar [--help]
USAGE: java -jar EcoFunPrimer.jar
screen - Screen for primer regions with for the best coverage at each position
select - Select primer pairs using slidescale or user defined fwd and rev primer positions