hi!
I'm starting to analyze sequences and I see that this plugin can make the analysis much easier. I downloaded the manual and followed the steps but when indexing the reference genome I get an error so that
I guess that the problem is related to the installation of the bowtie2 but I am not able to solve it, I do not know if I have not installed it properly or in the right place. I am trying it in windows, although seeing that in Linux the .gz files can be used I am thinking about doing the analyzes in Linux. Anyway, do you know where is the problem, I know it is possibly easy to solve it, but I am not able to do it.
Thanks in advance.
Ester
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Anonymous
Anonymous
-
2018-06-15
sorry i did not paste the problem :
GRAVE: java.io.IOException: Cannot run program "bowtie2-build.exe": CreateProcess error=2, El sistema no puede encontrar el archivo especificado
....
....
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Based on the error log, it definitely looks like bowtie2 was not properly installed. The Eclipse+Plugin package (https://sourceforge.net/projects/ngsep/files/Eclipse%2BPlugin/) contains a installer for bowtie2. The only problem with this option is that the version of bowtie2 is a bit old. However, it works fine. It could also be he case that the folder with the bowtie2 program is not correctly registered in the path. You can solve this adding the path to the bowtie2 executables in the Path variable. Instructions to do this wih java are available in the user manual of NGSEP. We are also working on our own read aligner to make this process better in the future.
Let me know how things go
Jorge
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Anonymous
Anonymous
-
2018-06-16
Hi Jorge!
Thanks for your reply!!:)
I will try this and let you know if it works. Thanks again!!!
Ester
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If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Anonymous
Anonymous
-
2020-01-28
faceing same problem java.io.IOException: Cannot run program "bowtie2": error=2, No such file or directory while working with MacOS, I tried to add bowtie2 manually but it seems not working, can you please help me to sort out the issue?
Babar
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thanks for your interest in NGSEP. To solve your issue, first open a terminal and double check that bowtie2 is porperly installed by typing bowtie2. If you see the program options, in Mac sometimes bowtie2 is correctly installed but it is not visible from Eclipse until you restart the computer, so please also try that. In the worst case, you can use the command line to map your reads. You can follow our command line Tutorial (and QuickStart if you have a lot of samples) if you need help to do that. Once you have sorted bam files, everything should work fine.
Let me know how things go.
Jorge
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Anonymous
Anonymous
-
2021-05-09
I have a problem with read mapping as well. When I select the folder containing the fastq.gz files and I right-click I am presented with a menu showing the De novo GBS. I select that and fill the information in the following windows then I launch the analysis but the terminal console stalls indefinitely after issuing the following lines:
Gtk-Message: 09:32:26.897: GtkDialog mapped without a transient parent. This is discouraged.
Saved genome: ngsep.genome.ReferenceGenome@b003a41
java.nio.file.AccessDeniedException: /home/users/filippo_Aligner.log.lck
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
at java.base/sun.nio.fs.UnixFileSystemProvider.newFileChannel(UnixFileSystemProvider.java:182)
at java.base/java.nio.channels.FileChannel.open(FileChannel.java:292)
at java.base/java.nio.channels.FileChannel.open(FileChannel.java:345)
at java.logging/java.util.logging.FileHandler.openFiles(FileHandler.java:511)
at java.logging/java.util.logging.FileHandler.<init>(FileHandler.java:307)
at ngsepfx.controller.AnalysisAreaController.createLogHandler(AnalysisAreaController.java:277)
at ngsepfx.controller.ReadsAlignerController.processAlignmentsFile(ReadsAlignerController.java:273)
at ngsepfx.controller.ReadsAlignerController$1.call(ReadsAlignerController.java:245)
at ngsepfx.controller.ReadsAlignerController$1.call(ReadsAlignerController.java:1)
at javafx.graphics/javafx.concurrent.Task$TaskCallable.call(Task.java:1425)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:835)</init>
Thanks for your interest in NGSEP. Although the message is not clear, at first sight, the problem seems to be that you do not have write permissions in the directory that you chose as output (/home/users/). Please make sure that you select as output directory a directory where you can write files. Regarding menu options, I am assuming you actually chose "Multiple Reads Aligner", although it is true that the first option is "De Novo GBS".
About bowtie2, since version 4, NGSEP does not require an installation of bowtie2 or any other reads aligner because now we include in NGSEP our own implementation of an FM-index based reads aligner for short reads. If you still prefer to use one of the classical aligners, you can run it separately and then sort read alignments and perform variants detection using NGSEP.
Let me know how things go.
Jorge
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Anonymous
Anonymous
-
2021-05-30
Dear Jorge,
first of all thanks for your reply. It took some time to run tests with the system administrator of the server (CentOS 7)where I am running NGSEP. He says that the software issues an error message since it tries to access a forbidden directory as you can read from the following message:
ES2 Prism: Error - GLX extension is not supported
GLX version 1.3 or higher is required
Gtk-Message: 18:44:37.863: GtkDialog mapped without a transient parent. This is discouraged.
java.nio.file.AccessDeniedException: /home/users/filippo.log.lck
In fact, it tries to generate a .log.lck file in the upper directory /home/users/ and not into mine: /home/users/filippo.geuna/
Is it possible to fix that?
Kind regards,
Filippo
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It is a bit weird that the software is trying to write in that directory. My only guess is that the output folder of the process is being set in that directory. Could you please share with me a print screen of the NGSEP window before submitting the process?. I could try to reproduce the error based on that information.
Best regards
Jorge
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Anonymous
Anonymous
-
2021-05-12
Hello,
I cannot get tNGSEP gui running on a Linux CentOS7 machine. (see error messages) below. I believe that I have installed the latest java / jdk versions (see at the end), but i got stuck at this point.
Could you please advice me how to the the gui running?
Best,
java -jar NGSEPfx_4.1.0.jar
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.UnsupportedClassVersionError: ngsepfx/Main has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:756)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:468)
at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:601)
Based on the error,it seems like you have different versions of java installed but the version called by default is java 1.7. Please run "which java" and "java -version" to confirm the version of java that you are actually using. To make sure you run java 11, you can use the full path to the java executable, something like:
/path/to/java11/bin/java ...
Let me know how things go
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Anonymous
Anonymous
-
2021-05-17
Great, this worked!
I added the full path to openjdk-11 java in the 'run.sh' file of the NGSEPlinux package.
Thank you!
👍
1
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Anonymous
Anonymous
-
2021-10-01
Dear Jorge,
the problem I encounter when trying to create the Index of a large (10GB) genome is reported below:
-bash-4.2$ java -Xmx27g -jar NGSEPcore.jar GenomeIndexer -i /home/users/filippo.geuna/genomica/Data_Frumento_duro_Tateo_copy/Td_Svevo_v1.fa.gz -o /home/users/filippo.geuna/genomica/Data_Frumento_duro_Tateo_copy/Td_Svevo_v1_GenomeIndexer.fm.gz
Oct 01, 2021 12:06:41 PM ngsep.genome.GenomeIndexer createIndex
INFO: Loading genome from file /home/users/filippo.geuna/genomica/Data_Frumento_duro_Tateo_copy/Td_Svevo_v1.fa.gz
Oct 01, 2021 12:14:21 PM ngsep.genome.GenomeIndexer createIndex
INFO: Building index for genome in file /home/users/filippo.geuna/genomica/Data_Frumento_duro_Tateo_copy/Td_Svevo_v1.fa.gz
Oct 01, 2021 12:14:33 PM ngsep.sequences.FMIndex loadQualifiedSequences
INFO: Building index for 1 sequences. Internal sequence length: 585266722
Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at ngsep.NGSEPcore.main(NGSEPcore.java:66)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index 1040474172 out of bounds for length 972433211
at ngsep.sequences.DC3SuffixArrayGenerator.calculateRanks(DC3SuffixArrayGenerator.java:310)
at ngsep.sequences.DC3SuffixArrayGenerator.getSuffixArray(DC3SuffixArrayGenerator.java:153)
at ngsep.sequences.DC3SuffixArrayGenerator.getSuffixArray(DC3SuffixArrayGenerator.java:149)
at ngsep.sequences.DC3SuffixArrayGenerator.getSuffixArray(DC3SuffixArrayGenerator.java:149)
at ngsep.sequences.DC3SuffixArrayGenerator.<init>(DC3SuffixArrayGenerator.java:73)
at ngsep.sequences.FMIndexSingleSequence.calculate(FMIndexSingleSequence.java:128)
at ngsep.sequences.FMIndexSingleSequence.<init>(FMIndexSingleSequence.java:103)
at ngsep.sequences.FMIndexSingleSequence.<init>(FMIndexSingleSequence.java:97)
at ngsep.sequences.FMIndex.loadQualifiedSequences(FMIndex.java:78)
at ngsep.genome.ReferenceGenomeFMIndex.<init>(ReferenceGenomeFMIndex.java:51)
at ngsep.genome.GenomeIndexer.createIndex(GenomeIndexer.java:93)
at ngsep.genome.GenomeIndexer.run(GenomeIndexer.java:85)
at ngsep.genome.GenomeIndexer.main(GenomeIndexer.java:79)
... 5 more</init></init></init></init>
I issued the command both without extra assigned RAM (java -jar) and with it ( java -Xmx27g -jar) but the program stalls after about 10 minutes at the same point issuing the following message (as you can read above):
This definitely looks like an error trying to index genomes with large chromosomes. We will try to reproduce and fix the error for the next release. In the mean time, please find attached an updated version of the script that we used to include in NGSEP3 to map reads with bowtie2, including the options to register properly the needed RG tags. Although ideally we would like people to start using our reads aligner, we also want to remain interoperable with sorted bam files generated with bowtie2 and bwa. This script is now available in the training folder and will be available in future versions. Anyways, I hope to have this issue fixed for the next version, so that you guys can try our reads aligner.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Anonymous
Anonymous
-
2021-10-01
Hello Jorge,
thanks for your prompt reply and for the script you provided. One question again: this script does not make an index, is it right? Can I run it without any previously made index?
Regards
Filippo
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
You are right. The script does not make an index because it is made to be executed sample by sample. You can build a new index just one time or use a previously made index.
Best regards
Jorge
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Anonymous
Anonymous
-
2021-10-05
OK Jorge,
thanks a lot again.
Filippo
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
hi!
I'm starting to analyze sequences and I see that this plugin can make the analysis much easier. I downloaded the manual and followed the steps but when indexing the reference genome I get an error so that
I guess that the problem is related to the installation of the bowtie2 but I am not able to solve it, I do not know if I have not installed it properly or in the right place. I am trying it in windows, although seeing that in Linux the .gz files can be used I am thinking about doing the analyzes in Linux. Anyway, do you know where is the problem, I know it is possibly easy to solve it, but I am not able to do it.
Thanks in advance.
Ester
sorry i did not paste the problem :
GRAVE: java.io.IOException: Cannot run program "bowtie2-build.exe": CreateProcess error=2, El sistema no puede encontrar el archivo especificado
....
....
Hi Ester
Based on the error log, it definitely looks like bowtie2 was not properly installed. The Eclipse+Plugin package (https://sourceforge.net/projects/ngsep/files/Eclipse%2BPlugin/) contains a installer for bowtie2. The only problem with this option is that the version of bowtie2 is a bit old. However, it works fine. It could also be he case that the folder with the bowtie2 program is not correctly registered in the path. You can solve this adding the path to the bowtie2 executables in the Path variable. Instructions to do this wih java are available in the user manual of NGSEP. We are also working on our own read aligner to make this process better in the future.
Let me know how things go
Jorge
Hi Jorge!
Thanks for your reply!!:)
I will try this and let you know if it works. Thanks again!!!
Ester
No problem. Let me know how things go.
Jorge
faceing same problem java.io.IOException: Cannot run program "bowtie2": error=2, No such file or directory while working with MacOS, I tried to add bowtie2 manually but it seems not working, can you please help me to sort out the issue?
Babar
Hi Babar
Thanks for your interest in NGSEP. To solve your issue, first open a terminal and double check that bowtie2 is porperly installed by typing bowtie2. If you see the program options, in Mac sometimes bowtie2 is correctly installed but it is not visible from Eclipse until you restart the computer, so please also try that. In the worst case, you can use the command line to map your reads. You can follow our command line Tutorial (and QuickStart if you have a lot of samples) if you need help to do that. Once you have sorted bam files, everything should work fine.
Let me know how things go.
Jorge
I have a problem with read mapping as well. When I select the folder containing the fastq.gz files and I right-click I am presented with a menu showing the De novo GBS. I select that and fill the information in the following windows then I launch the analysis but the terminal console stalls indefinitely after issuing the following lines:
Gtk-Message: 09:32:26.897: GtkDialog mapped without a transient parent. This is discouraged.
Saved genome: ngsep.genome.ReferenceGenome@b003a41
java.nio.file.AccessDeniedException: /home/users/filippo_Aligner.log.lck
at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:90)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111)
at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116)
at java.base/sun.nio.fs.UnixFileSystemProvider.newFileChannel(UnixFileSystemProvider.java:182)
at java.base/java.nio.channels.FileChannel.open(FileChannel.java:292)
at java.base/java.nio.channels.FileChannel.open(FileChannel.java:345)
at java.logging/java.util.logging.FileHandler.openFiles(FileHandler.java:511)
at java.logging/java.util.logging.FileHandler.<init>(FileHandler.java:307)
at ngsepfx.controller.AnalysisAreaController.createLogHandler(AnalysisAreaController.java:277)
at ngsepfx.controller.ReadsAlignerController.processAlignmentsFile(ReadsAlignerController.java:273)
at ngsepfx.controller.ReadsAlignerController$1.call(ReadsAlignerController.java:245)
at ngsepfx.controller.ReadsAlignerController$1.call(ReadsAlignerController.java:1)
at javafx.graphics/javafx.concurrent.Task$TaskCallable.call(Task.java:1425)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:835)</init>
Hi Filippo
Thanks for your interest in NGSEP. Although the message is not clear, at first sight, the problem seems to be that you do not have write permissions in the directory that you chose as output (/home/users/). Please make sure that you select as output directory a directory where you can write files. Regarding menu options, I am assuming you actually chose "Multiple Reads Aligner", although it is true that the first option is "De Novo GBS".
About bowtie2, since version 4, NGSEP does not require an installation of bowtie2 or any other reads aligner because now we include in NGSEP our own implementation of an FM-index based reads aligner for short reads. If you still prefer to use one of the classical aligners, you can run it separately and then sort read alignments and perform variants detection using NGSEP.
Let me know how things go.
Jorge
Dear Jorge,
first of all thanks for your reply. It took some time to run tests with the system administrator of the server (CentOS 7)where I am running NGSEP. He says that the software issues an error message since it tries to access a forbidden directory as you can read from the following message:
ES2 Prism: Error - GLX extension is not supported
GLX version 1.3 or higher is required
Gtk-Message: 18:44:37.863: GtkDialog mapped without a transient parent. This is discouraged.
java.nio.file.AccessDeniedException: /home/users/filippo.log.lck
In fact, it tries to generate a .log.lck file in the upper directory /home/users/ and not into mine: /home/users/filippo.geuna/
Is it possible to fix that?
Kind regards,
Filippo
Dear Fillipo
It is a bit weird that the software is trying to write in that directory. My only guess is that the output folder of the process is being set in that directory. Could you please share with me a print screen of the NGSEP window before submitting the process?. I could try to reproduce the error based on that information.
Best regards
Jorge
Hello,
I cannot get tNGSEP gui running on a Linux CentOS7 machine. (see error messages) below. I believe that I have installed the latest java / jdk versions (see at the end), but i got stuck at this point.
Could you please advice me how to the the gui running?
Best,
java -jar NGSEPfx_4.1.0.jar
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.UnsupportedClassVersionError: ngsepfx/Main has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:756)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:468)
at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:601)
java-1.7.0-openjdk-headless.x86_64 1:1.7.0.261-2.6.22.2.el7_8 @updates
java-1.8.0-openjdk.x86_64 1:1.8.0.292.b10-1.el7_9 @updates
java-1.8.0-openjdk-devel.x86_64 1:1.8.0.292.b10-1.el7_9 @updates
java-1.8.0-openjdk-headless.x86_64 1:1.8.0.292.b10-1.el7_9 @updates
java-11-openjdk.x86_64 1:11.0.11.0.9-1.el7_9 @updates
java-11-openjdk-devel.x86_64 1:11.0.11.0.9-1.el7_9 @updates
java-11-openjdk-headless.x86_64 1:11.0.11.0.9-1.el7_9 @updates
Hi
Based on the error,it seems like you have different versions of java installed but the version called by default is java 1.7. Please run "which java" and "java -version" to confirm the version of java that you are actually using. To make sure you run java 11, you can use the full path to the java executable, something like:
/path/to/java11/bin/java ...
Let me know how things go
Great, this worked!
I added the full path to openjdk-11 java in the 'run.sh' file of the NGSEPlinux package.
Thank you!
Dear Jorge,
the problem I encounter when trying to create the Index of a large (10GB) genome is reported below:
-bash-4.2$ java -Xmx27g -jar NGSEPcore.jar GenomeIndexer -i /home/users/filippo.geuna/genomica/Data_Frumento_duro_Tateo_copy/Td_Svevo_v1.fa.gz -o /home/users/filippo.geuna/genomica/Data_Frumento_duro_Tateo_copy/Td_Svevo_v1_GenomeIndexer.fm.gz
Oct 01, 2021 12:06:41 PM ngsep.genome.GenomeIndexer createIndex
INFO: Loading genome from file /home/users/filippo.geuna/genomica/Data_Frumento_duro_Tateo_copy/Td_Svevo_v1.fa.gz
Oct 01, 2021 12:14:21 PM ngsep.genome.GenomeIndexer createIndex
INFO: Building index for genome in file /home/users/filippo.geuna/genomica/Data_Frumento_duro_Tateo_copy/Td_Svevo_v1.fa.gz
Oct 01, 2021 12:14:33 PM ngsep.sequences.FMIndex loadQualifiedSequences
INFO: Building index for 1 sequences. Internal sequence length: 585266722
Exception in thread "main" java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at ngsep.NGSEPcore.main(NGSEPcore.java:66)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Index 1040474172 out of bounds for length 972433211
at ngsep.sequences.DC3SuffixArrayGenerator.calculateRanks(DC3SuffixArrayGenerator.java:310)
at ngsep.sequences.DC3SuffixArrayGenerator.getSuffixArray(DC3SuffixArrayGenerator.java:153)
at ngsep.sequences.DC3SuffixArrayGenerator.getSuffixArray(DC3SuffixArrayGenerator.java:149)
at ngsep.sequences.DC3SuffixArrayGenerator.getSuffixArray(DC3SuffixArrayGenerator.java:149)
at ngsep.sequences.DC3SuffixArrayGenerator.<init>(DC3SuffixArrayGenerator.java:73)
at ngsep.sequences.FMIndexSingleSequence.calculate(FMIndexSingleSequence.java:128)
at ngsep.sequences.FMIndexSingleSequence.<init>(FMIndexSingleSequence.java:103)
at ngsep.sequences.FMIndexSingleSequence.<init>(FMIndexSingleSequence.java:97)
at ngsep.sequences.FMIndex.loadQualifiedSequences(FMIndex.java:78)
at ngsep.genome.ReferenceGenomeFMIndex.<init>(ReferenceGenomeFMIndex.java:51)
at ngsep.genome.GenomeIndexer.createIndex(GenomeIndexer.java:93)
at ngsep.genome.GenomeIndexer.run(GenomeIndexer.java:85)
at ngsep.genome.GenomeIndexer.main(GenomeIndexer.java:79)
... 5 more</init></init></init></init>
I issued the command both without extra assigned RAM (java -jar) and with it ( java -Xmx27g -jar) but the program stalls after about 10 minutes at the same point issuing the following message (as you can read above):
Dear Filippo
This definitely looks like an error trying to index genomes with large chromosomes. We will try to reproduce and fix the error for the next release. In the mean time, please find attached an updated version of the script that we used to include in NGSEP3 to map reads with bowtie2, including the options to register properly the needed RG tags. Although ideally we would like people to start using our reads aligner, we also want to remain interoperable with sorted bam files generated with bowtie2 and bwa. This script is now available in the training folder and will be available in future versions. Anyways, I hope to have this issue fixed for the next version, so that you guys can try our reads aligner.
Best regards
Jorge
Hello Jorge,
thanks for your prompt reply and for the script you provided. One question again: this script does not make an index, is it right? Can I run it without any previously made index?
Regards
Filippo
Hi Fillipo
You are right. The script does not make an index because it is made to be executed sample by sample. You can build a new index just one time or use a previously made index.
Best regards
Jorge
OK Jorge,
thanks a lot again.
Filippo