I tried to run INTEGRATE by using the test data and test annnotation file and so on that were downloaded from the INTEGRATE sourceforge site.
My test run, however, failed.
My PC environment is Ubuntu 14.04LTS, i7-6700K, and 64GB RAM.
I use the required tools installed through Linuxbrew.
The file list in INTEGRATE-build/bin/bwts is
-rw-rw-r-- 1 tyaoi4 tyaoi4 97650885 Nov 29 17:23 19.bwt
-rw-rw-r-- 1 tyaoi4 tyaoi4 97651845 Nov 29 17:23 19.rbwt
-rw-rw-r-- 1 tyaoi4 tyaoi4 114603484 Nov 29 17:23 6.bwt
-rw-rw-r-- 1 tyaoi4 tyaoi4 114609261 Nov 29 17:23 6.rbwt
My test run failed in all cases as the follows:
(1) RNA-Seq Tumor + WGS Tumor + WGS Normal
(2) RNA-Seq Tumor + WGS Tumor
(3) RNA-Seq Tumor
Moreover, the same error was replied in the above all.
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
Insert sizes and stds tested by different RGs:
2891354555 247 1500
Getting graph by encompassing RNA reads...
This graph has 42 vertexes and 34 edges.
2.58 seconds
Reducing Graph by removing encompassing pair with a hit in one gene mapped in BAM ...
This graph has 34 vertexes and 27 edges.
0.69 seconds
Getting BWTs for genes in the graph...
Segmentation fault
I also tried the commands you gave from the annotation tab. I downloaded the UCSC orginial annotation file from UCSC website. And it happened the same error. So I don't think it's because of the version of annotation file.
Could you help me?
best,
cuisine
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
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
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi, jin and all users
I tried to run INTEGRATE by using the test data and test annnotation file and so on that were downloaded from the INTEGRATE sourceforge site.
My test run, however, failed.
My PC environment is Ubuntu 14.04LTS, i7-6700K, and 64GB RAM.
I use the required tools installed through Linuxbrew.
The file list in INTEGRATE-build/bin/bwts is
-rw-rw-r-- 1 tyaoi4 tyaoi4 97650885 Nov 29 17:23 19.bwt
-rw-rw-r-- 1 tyaoi4 tyaoi4 97651845 Nov 29 17:23 19.rbwt
-rw-rw-r-- 1 tyaoi4 tyaoi4 114603484 Nov 29 17:23 6.bwt
-rw-rw-r-- 1 tyaoi4 tyaoi4 114609261 Nov 29 17:23 6.rbwt
My test run failed in all cases as the follows:
(1) RNA-Seq Tumor + WGS Tumor + WGS Normal
(2) RNA-Seq Tumor + WGS Tumor
(3) RNA-Seq Tumor
Moreover, the same error was replied in the above all.
For exmple,
tyaoi4@tyaoi4-Diginnos-PC:~/tools/INTEGRATE_0_2_6/INTEGRATE-build/bin$ ./Integrate fusion /home/tyaoi4/tools/INTEGRATE_0_2_6/test-data/reference.fasta /home/tyaoi4/tools/INTEGRATE_0_2_6/annot.ensembl.txt /home/tyaoi4/tools/INTEGRATE_0_2_6/INTEGRATE-build/bin/bwts /home/tyaoi4/tools/INTEGRATE_0_2_6/test-data/accepted_hits.bam /home/tyaoi4/tools/INTEGRATE_0_2_6/test-data/unmapped.bam
INTEGRATE version 0.2.6
Loading reference...
6 1 47000000
19 47000001 87000000
0.033683 seconds
Loading genes...
16867 transcripts loaded.
0.272081 seconds
Loading BWTs for chromosomes...
0.594668 seconds
Handling RNA data...
Insert sizes and stds tested by different RGs:
2891354555 247 1500
Getting graph by encompassing RNA reads...
This graph has 42 vertexes and 34 edges.
1.75173 seconds
Reducing Graph by removing encompassing pair with a hit in one gene mapped in BAM ...
This graph has 34 vertexes and 27 edges.
0.542568 seconds
Getting BWTs for genes in the graph...
Segmentation fault(core dumped)
Then, exit status is the follows:
tyaoi4@tyaoi4-Diginnos-PC:~/tools/INTEGRATE_0_2_6/INTEGRATE-build/bin$ $?
139: command not found
I will appreciate any comment and advice.
Thanks,
chaoi
The annotaion file in the test case is too old. Please use the one under the Files tab.
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 tested by different RGs:
2891354555 247 1500
Getting graph by encompassing RNA reads...
This graph has 42 vertexes and 34 edges.
2.58 seconds
Reducing Graph by removing encompassing pair with a hit in one gene mapped in BAM ...
This graph has 34 vertexes and 27 edges.
0.69 seconds
Getting BWTs for genes in the graph...
Segmentation fault
I also tried the commands you gave from the annotation tab. I downloaded the UCSC orginial annotation file from UCSC website. And it happened the same error. So I don't think it's because of the version of annotation file.
Could you help me?
best,
cuisine
Have you run "mkbwt"?
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
Hi,
To make the test case work, the annot file need to be taylored. Pease see attached.
Thanks,
JIn