Activity for NGSEP
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NGSEP released /GUIFX/NGSEPlinux_5.1.0.tar.gz
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Jorge Duitama posted a comment on discussion Frequently Asked Questions
As a follow up in this post, it took us a while, but now we have available an updated version of the manual for version 5.0.0
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Thanks for your interest in NGSEP. You are right. We have postponed for already a bit too much the update of the manual for the graphical interface. I hope to have this done within the next month. In the mean time, please let me know if you need help to run the functionalities of the software that you may need for your data.
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Anonymous posted a comment on discussion Frequently Asked Questions
Hello, I am using NGSEPlinux 5.0.0 (thanks for this great tool) and I am wondering whether an updated manual for this version exists. The current one is for v. 4.x from 2020. Best regards
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Sorry to hear this. We will try to reproduce the error in an ubuntu 22 and get back to you. In the mean time, for the experiment with version 22.0.1, if possible please share the edited run.sh, a screenshot of the NGSEPlinux folder and the message that you get (if any) when running the run.sh script from the command line. Best regards
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Anonymous posted a comment on discussion Frequently Asked Questions
Hi Jorge, Thank you so much for your program and for your quick support I tried using both 21.0.1 version and 17.0.9. Editing the java version to 21.0.1, running rush.sh does not open anything at all. Using 17.0.9 does open NGSEP, but unfortunately leads to the same initial GUI error when clicking explore :( Best wishes
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Thanks for your interest in NGSEP. The current GUI has been tested in Ubuntu 20 running java 11. It is not easy for me to test with Ubuntu 22 at this time, but I could test with Ubuntu 23. Although I did not get the same error, the behavior of the file explorer was also weird. In all operative systems, these errors are normally related to the version of JavaFX, which is the infrastructure behind the graphical interface. By default we are including in the package a rather old version of javaFX (version...
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Anonymous posted a comment on discussion Frequently Asked Questions
Hello, Quite new to NGSEP and the world of bioinformatics. Trying to run NGSEP GUI on linux (ubuntu 22.04 [Jammy Jellyfish]) and have continuously run into an issue whenever NGSEP's trying to open up another window of files (i.e. clicking 'Explorer' in an attempt to change root folder or when trying to browse for an input file; see attached files) Any help would be greatly appreciated thank you!
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Xavier Argout posted a comment on discussion Frequently Asked Questions
Dear Jorge, thank you for your advice. I sorted again the Bowtie2 sam files with Picard tools and MultisampleVariantsDetector now works!!! Problem solved! Thank you, Xavier
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Dear Xavier I checked more closely at the commands used to sort the alignments and I ran a few tests and it seems like the issue happened at the sorting step. It looks like the samtools view command is not preserving the header of bowtie2, and then the samtools sort could be removing the RG tag from the alignments. The net effect is that your alignments in the sorted bam are missing a tag like this: RG:Z:CCKM23-041 This tag is required by the MultisampleVariantsDetector (and as far as I remember...
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Dear Jorge, it is the same reference file I used for mapping and for NGSEP. Please find attached chr1.fa
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Dear Jorge, it is the same reference file I used for mapping and for NGSEP. Please find attach chr1.fa
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Dear Xavier The bam file looks fine. The only thing that I see is that the name of the reference file used for mapping is Theobroma_cacao_criollo_chr.v2.0.fna and the name of the file used for variant calling is Theobromacacaocriollochr.v2.0.fna. Please use samtools faidx to verify if the two files have the exact same genome (including chromosome names) as follows: samtools faidx Theobroma_cacao_criollo_chr.v2.0.fna samtools faidx Theobromacacaocriollochr.v2.0.fna If they are the same, please share...
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Dear Jorge, thank you for your prompt answer. Yes it was a typo in my message, sorry. Mapping was done with Bowtie2 (in paired mode) and Bam files were generated with samtools : command line : samtools view -u CCKM23-041.header.sam | samtools sort -o CCKM23-041.sorted.bam Attached is the result of your command . Thanks again for your help. Xavier
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Dear Xavier Thanks for your interest in NGSEP. The command has a typo because the asterisk should go before sorted.bam (it should be *sorted.bam), but I guess it is just a typo. Based on the log everything looks fine. Please share some information on how did you generate the BAM files. Make sure that the reference used in the MultisampleVariantsDetector is the exact same reference used to align reads. If possible, please send me the result of the following command samtools view -h CCKM23-041.sorted.bam...
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Dear NGSEP team, I have just experienced a problem with the MultisampleVariantsDetector module. The analysis of 95 sorted bam samples with header seemed to run fine and finished with the message "INFO: Multisample Variants Detector Completed". The generated VCF file contained only the header lines, but no data lines with information about the SNP markers. The command line I used was java -jar NGSEPcore4.3.2.jar MultisampleVariantsDetector -r Theobromacacaocriollochr.v2.0.fna -maxAlnsPerStartPos 1000...
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Dear NGSEP team, I just experience a problem with the MultisampleVariantsDetector module. Analysis done on 95 sorted bam samples with header seemed to run without problem and finished with a "INFO: Multisample Variants Detector Completed" message. The generated VCF file just contained the head lines but no data lines containing information about the SNP markers. The command line I used was this one : java -jar NGSEPcore4.3.2.jar MultisampleVariantsDetector -r Theobromacacaocriollochr.v2.0.fna -maxAlnsPerStartPos...
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Hi Diego About the reads aligner, the reads aligner is actually working better at this moment with long reads. Make sure to tell the software that you have ONT reads using the option -p. The software will use this option to choose the algorithm based on minimizers. If the reads have high error rates you can reduce the k-mer length with the option -k to something like 15. About variants detection, we usually do not perform filtering of variants or genotype calls at the discovery and genotyping stages....
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Hi Diego 1. The reads aligner is actually working better at this moment with long reads. Make sure to tell the software that you have ONT reads using the option -p. If the reads have high error rates you can reduce the k-mer length with the option -k to something like 15. We usually do not perform filtering of variants or genotype calls at the discovery and genotyping stages. The goal of MultisampleVariantsDetector is to obtain a raw genomic variation database with as much as you can get from the...
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Diego Almansa-Villa posted a comment on discussion Frequently Asked Questions
I have two unrelated questions regarding the operation of two modules for separate projects: 1- Does the "ReadsAligner" module work for mapping long reads (ONT) to a reference genome? Or does it only work with short reads? 2- I am using the "MultisampleVariantsDetector" module and would like to know which parameters I should adjust to call variants with a minimum of 5 reads of depth, and at least 15% of them being the reference allele. I appreciate your attention. Best regards, Diego
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Hi Diego Great, I checked the log and the problem is that you set a kmer length of 45bp and the current implementation only can take kmer lengths up to 31 bp. Unfortunatey, because of the threading, it keeps trying to process reads and at the end it fails because it finds zero edges. A k-mer length of 31 should be more than enough to assemble bacterial samples.
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I am conducting tests with different datasets, and this particular one corresponds to Escherichia coli (4.5 Mb) with 47,910 PacBio reads. https://drive.google.com/file/d/1ZQPnF4_gD51R3VCfhhBIZP1tMCuFiTNU/view?usp=sharing I tried to attach the file directly, but it didn't work, so I'll provide a link to Google Drive instead.
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Hi Diego Thanks for your interest in NGSEP. Looking at the code, it seems like the software is getting trouble to identify edges. Please share the log of the process and perhaps some information on the number of reads, technology and expected genome size, to track the error.
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Hello, I have been trying to test different Kmer sizes for the assembly of long reads using NGSEP Assembler, but when I try to execute sizes other than 15, it generates the following error: 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)...
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Thanks, it works for me!
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Hi Diego Thanks for your interest in NGSEP. As a user, you do not need to recompile the software. I recommend you to download and run the official version 4.3.1. For this, you just need the file NGSEPcore_4.3.1.jar, available either as part of the source code or directly in the files folder. You can download the live development cloning the git repository and build the version 4.3.2, but I must warn you that this version can have errors because we have not performed a full test run on this version....
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Anonymous posted a comment on discussion Frequently Asked Questions
Hi! I am trying to use your software for analysis and assembly purposes, but I encountered an error while attempting to compile the code. I obtained the code using the command: git clone https://github.com/NGSEP/NGSEPcore.git Later, when I tried to compile it using the command "make all", the terminal displayed the following error messages: rm -f NGSEPcore_4.3.2.jar rm -rf bin mkdir bin javac -cp lib/jsci-core.jar:lib/htsjdk-2.22.jar -d bin src/ngsep/.java src/ngsep//.java src/ngsep///.java src/ngsep/clustering/DistanceClusteringService.java:21:...
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Hi! I am trying to use your software for analysis and assembly purposes, but I encountered an error while attempting to compile the code. I obtained the code using the command: git clone https://github.com/NGSEP/NGSEPcore.git Later, when I tried to compile it using the command "make all", the terminal displayed the following error messages: rm -f NGSEPcore_4.3.2.jar rm -rf bin mkdir bin javac -cp lib/jsci-core.jar:lib/htsjdk-2.22.jar -d bin src/ngsep/.java src/ngsep//.java src/ngsep///.java src/ngsep/clustering/DistanceClusteringService.java:21:...
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Hi Thanks for your interest in NGSEP. The file NGSEPcore_4.3.1.jar is not expected to be executed with double click because it corresponds to the command line interface. If you wish to run the software from the command line, you can take a look to our training resources starting with the tutorial available here: https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt/download If you wish to run the graphical interface, you need to download the JavaFX distribution for MAC from here: https://sourceforge.net/projects/ngsep/files/GUIFX/NGSEPmac_4.3.1.tar.gz/download...
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Anonymous posted a comment on discussion Frequently Asked Questions
Hi, I'm getting a problem when running NGSEP on mac. When clicking on the NGSEPcore_4.3.1.jar file, the jar launcher does not start. When I run the code on the shell file in my terminal I get the next error: * Error: Could not find or load main class ngsepfx.Main * Caused by: java.lang.ClassNotFoundException: ngsepfx.Main Like to know how can I fix it. Thanks!
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