Comments (5)
Hi, you may need to first compile the SE-MEI tool under the Scripts folder (tar vxzf SE-MEI-master.tar.gz & cd SE-MEI & make) and then use "export" command to add it to the $PATH.
Thanks,
Xun
from ervcaller.
Ok. Solved. Thank you. Another problem showed up after that and it is the following one:
[E::bwa_idx_load_from_disk] fail to locate the index files
I aligned the sequenes with BWA and the files of the indexation are: .fna, .amb, .ann, .bwt, .fai, .pac, .sa
What could be the problem in here?
from ervcaller.
it could due to the empty output. ERVcaller did a reciprocal alignment, if the output is empty the next alignment will fail and show this error.
You could show the file sizes of your input, ref (especially the chr IDs), and generated outputs. Maybe I could help to double check.
Thanks,
Xun
from ervcaller.
Hi,
About the error [E::bwa_idx_load_from_disk] fail to locate the index files
I downloaded the ref from here: GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
The file sizes of my input are 40Gb.
The generated outputs are an empty VCF file and a temp folder with the following information:
from ervcaller.
It looks like the error happened at an earlier time than the reciprocal alignment. The human reference file is okay.
Maybe you could show the full log information till the error for the debugging? It also depends on the ERV references that you are using, for example, no TE insertions of your ERV reference were detected.
Have you successfully run the test data yet which could confirm your successful installation of ERVcaller?
Xun
from ervcaller.
Related Issues (16)
- About input bam files HOT 2
- About required programs HOT 3
- About "xx_h1_sorted.bam" file HOT 4
- Step 2 - Improper reads onwards, bwa-mem fails to read index files
- 关于SE_MEI的问题 HOT 2
- Argument "-" isn't numeric in subtraction (-) at ERVcaller_v.1.3.pl line 1305, <OUT3> line 2. HOT 1
- failed at step 3 HOT 3
- Error unexpected end of file HOT 1
- The Requirement software HOT 1
- The help message of ERVcaller_v1.4.pl HOT 3
- Illegal division by zero HOT 8
- Error in User Manual HOT 1
- Error of Step 3 HOT 8
- Do you have any recommended standard filter? HOT 4
- same sample, different result. HOT 8
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from ervcaller.