INTEGRATE Activity
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Activity for INTEGRATE
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Alexander Chang created ticket #9
Failure error
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Danqing Shen modified a comment on discussion General Discussion
I'm getting Aborted(core dumped) error when i'm trying to run Integrate-0.2.6 software on mRNASeq samples. Here is the script: Integrate fusion ./Mus_musculus.GRCm38.dna.primary_assembly.fa ./annot.VM24.txt ./bwts ./accepted_hits_sorted.bam ./unmapped.bam Here is the output: INTEGRATE version 0.2.6 Loading reference... 1 1 195471971 10 195471972 326166964 11 326166965 448249507 12 448249508 568378529 13 568378530 688800168 14 688800169 813702412 15 813702413 917746097 16 917746098 1015953865 17 1015953866...
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I'm getting Aborted(core dumped) error when i'm trying to run Integrate-0.2.6 software on mRNASeq samples. Here is the script: Integrate fusion ./Mus_musculus.GRCm38.dna.primary_assembly.fa ./annot.VM24.txt ./bwts ./accepted_hits_sorted.bam ./unmapped.bam Here is the output: INTEGRATE version 0.2.6 Loading reference... 1 1 195471971 10 195471972 326166964 11 326166965 448249507 12 448249508 568378529 13 568378530 688800168 14 688800169 813702412 15 813702413 917746097 16 917746098 1015953865 17 1015953866...
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I'm getting Aborted(core dumped) error when i'm trying to run Integrate-0.2.6 software on mRNASeq samples. Here is the script: Integrate fusion ./Mus_musculus.GRCm38.dna.primary_assembly.fa ./annot.VM24.txt ./bwts ./accepted_hits_sorted.bam ./unmapped.bam Here is the output: INTEGRATE version 0.2.6 Loading reference... 1 1 195471971 10 195471972 326166964 11 326166965 448249507 12 448249508 568378529 13 568378530 688800168 14 688800169 813702412 15 813702413 917746097 16 917746098 1015953865 17 1015953866...
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ian loveless posted a comment on discussion General Discussion
Is there a way of calculating TPM or RPKM for a given fusion, given the outputs from integrate? Thanks, Ian
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Bob posted a comment on ticket #8
I don't think so.Because the reference.fasta size in the test-data is small, I still get the same error.I doubt whether docker cannot be used. Could you help me test Integrate mkbwt with docker? Thanks!
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Jin posted a comment on ticket #8
Could it be that you haven't used enough memory?
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In addition, I also received the same error when using reference.fasta in the test-data.tar.gz. docker run jinwashu/integrate:0.2.6 Integrate mkbwt reference.fasta INTEGRATE version 0.2.6 Load ref Couldn't open file for reading: reference.fasta.
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Integrate mkbwt couldn't open ref.fa file for reading
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Please try our docker version at: https://hub.docker.com/r/jinwashu/integrate
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Stephane Plaisance created ticket #7
build fails
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Jin posted a comment on discussion General Discussion
There is an -mb option for both mkbwt and fusion. Try reduce the value to the length of the smallest contig you have.
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Hannah Charlton posted a comment on discussion General Discussion
Hi, I am trying to use the Integrate tool to investigate fusions in a a couple of non-model organisms. I could get the test data to run without any problem, so I think the installation of Integrate itself is okay. When I try and run Integrate mkbwt on my reference file devil.fa , it appears to run and load the reference file in fine: ../INTEGRATE$ ./Integrate mkbwt devil.fa INTEGRATE version 0.2.6 Load ref Chr1_supercontig_000000000 1 2180112 Chr1_supercontig_000000001 2180113 2553658 Chr1_supercontig_000000002...
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Hi Arnold, Please refer to https://github.com/ChrisMaherLab/INTEGRATE-Vis, which contains the detailed commands for generating annotation files, and addtional examples. As for the test case here, becasue the sample BAM was on hg19/GRCh37, you have to stick to the version of the reference. You can just grep chr6 and 19 using the annotation file with 11 columns here to make the test case work. Thanks, Jin
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arnold.liao posted a comment on discussion General Discussion
The test data in sourceforce doesn't work for integrate 0.2.6. It must have been for previous version. Anyone has annotate for ensembl hg38 0.2.6 which needs 11 columns instead of 9? I see on sourceforge we have hg19 annotate file
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Hi, To make the test case work, the annot file need to be taylored. Pease see attached. Thanks, JIn
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cuiqinzhang posted a comment on discussion General Discussion
So happy to see your reply! I run the command "Integrate mkbwt reference.fasta" and the files in the bwts folder show as follows : 19.bwt 19.rbwt 6.bwt 6.rbwt
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Have you run "mkbwt"?
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Hi Jin! I have used the newest in the Files tab and your example data. And I met the same problem as chaoi mentioned which is pasted as follows: Integrate fusion reference.fasta annot.ensembl.GRCh37.txt ./bwts accepted_hits.bam unmapped.bam dna.tumor.bam dna.normal.bam INTEGRATE version 0.2.6 Loading reference... 6 1 47000000 19 47000001 87000000 0.06 seconds Loading genes... 16867 transcripts loaded. 0.4 seconds Loading BWTs for chromosomes... 0.95 seconds Handling RNA data... Insert sizes and stds...
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Problem with annotation file
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Hi Mauro, You can try using the file annot.ensembl.txt at https://sourceforge.net/projects/integrate-fusion/files. There is also a wiki page about creating gene annotation file for INTEGRATE, https://sourceforge.net/p/integrate-fusion/wiki/annotation/. Thanks, Jin
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mauro created ticket #6
Problem with annotation file
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The annotaion file in the test case is too old. Please use the one under the Files...
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Takeshi YAOI posted a comment on discussion General Discussion
Hi, jin and all users I tried to run INTEGRATE by using the test data and test annnotation...
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annotation
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Home
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Home
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INTEGRATE released /INTEGRATE.0.2.6.tar.gz
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The code is focusing on combining RNA-Seq and WGS data. It can also run using RNA-seq...
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heyao posted a comment on discussion General Discussion
Hi Jin, I was wondering that if I can compile a separated utility program from the...
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Please refer to the [home] and [annotation] pages in the wiki for the details. The...
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annotation
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annotation
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Naresh Prodduturi posted a comment on discussion General Discussion
Yes they were prepared the same way (aligner GSNAP). All new samples got failed.
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Are the BAMs for other successful finished samples prepared the same way as the mRNAseq...
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I'm getting segmentation fault error when i'm trying to run Integrate software on...
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Tom Smith posted a comment on discussion General Discussion
Is there any reason why INTEGRATE is not detecting inter-chromosomal events for my...
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Hi Jin, I've run INTEGRATE on a single sample and was suprised to see fusions annotated...
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RAM usage by Integrate and elapsed time
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Hi, Time and space may vary depending on the input BAM of different data. I tested...
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Hoon Kim posted a comment on discussion General Discussion
Dear Zhang, As a test run, I did BLAT (default parameter) with spanning WGS reads...
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Thank you very much for your quick response and suggestion.
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Thank you for your quick response. In this case, may I assume that all results except...
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It seems that something from the WGS alignments finally caused the issue. This is...
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It will need some work. I am panning to make it parallel in a future version.
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Installation:
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Hi, Thank you for sharing this installation solution. Compiling C++ code on different...
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Parallel version of Integrate
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I will need some work. I am panning to make it parallel in a future version.
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Dear Zhang, Running Integrate fusion to my data keeps causing "Segmentation fault...
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Integrate and GSNAP or START
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Integrate and GSNAP or START
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Hi, Please try this: gsnap -d hg19 -D ./hg19.gmap_index/ --format=sam --nthreads=8...
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Sergey Mitrofanov created ticket #4
Installation:
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Integrate and GSNAP or START
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RAM usage by Integrate and elapsed time
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Parallel version of Integrate
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