Comments (5)
leepc12
commented on July 21, 2024
Hello,
Did you follow the installation instruction for dependencies (
https://github.com/kundajelab/chipseq_pipeline#dependencies)? twoBitToFa is
included in that.
It is not recommended to manually install dependencies. It's very tricky.
The pipeline needs two conda environments for each python version 2/3 and
some required softwares are not available on official conda repos.
Please use the dependency installer in the repo.
Thanks,
Jin
…On Thu, Apr 27, 2017 at 2:55 AM, AHCChan ***@***.***> wrote:
Hi!
I installed the pipeline then tried to install a genome but came across
this
install_genome_data.sh: line 171: twoBitToFa: command not found
I tried to install twobittofa using conda but ran into some issues. Is
there any workaround?
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#13>, or mute the
thread
<https://github.com/notifications/unsubscribe-auth/AIOd_IMQw8yK5qQOxMdHEPeyoDrNJ96jks5r0GYmgaJpZM4NJ_pt>
.
from chipseq_pipeline.
AHCChan
commented on July 21, 2024
Hello,
Yes, I followed the installation instructions and used the dependency installer (install_dependencies.sh). I received a message saying that the dependency installation was successful
Finished processing dependencies for idr==2.0.3 == Installing dependencies has been successfully done. ==
For good measure, I uninstalled the dependencies and ran the dependency installation script again. I still get the same error when trying to install a genome.
install_genome_data.sh: line 171: twoBitToFa: command not found
Many thanks,
Angelo
from chipseq_pipeline.
leepc12
commented on July 21, 2024
It's fixed. Please try with the latest code.
from chipseq_pipeline.
AHCChan
commented on July 21, 2024
Hi, sorry to bother you again. I tried with the new code and received this message:
Extracting/processing data files... Building bwa index... [bwa_index] Pack FASTA... 47.76 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=5451530962, availableWord=395589816 [BWTIncConstructFromPacked] 10 iterations done. 99999986 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999986 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999986 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999986 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999986 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999986 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999986 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999986 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999986 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999986 characters processed. install_genome_data.sh: line 221: 20197 Killed bwa index ${REF_FA_PREFIX}
from chipseq_pipeline.
leepc12
commented on July 21, 2024
Did you run the installer script on a login node (if you are working on a cluster)? Does your computer have enough memory to run bwa index?
from chipseq_pipeline.
Related Issues (20)
- aquas_chipseq pipline SPP error HOT 6
- Trimmed data-sets HOT 1
- Read length HOT 2
- shuf: end of file HOT 8
- "-q [SLURM_ACCOUNT_NAME]" interpreted as file HOT 1
- ERROR:root:--extsize must >= 1! HOT 2
- Fatal error: chipseq.bds, line 1354, pos 2. Task/s failed. HOT 4
- [fread] Unexpected end of file (bwa_sai2sam_pe_core) HOT 6
- dead loop HOT 18
- job submission command HOT 2
- [Error] two same tag align file in (z)cat and shuf in pipe HOT 1
- Missing `-c` for `macs2 peakcall` ? HOT 1
- pipeline deprecated? HOT 2
- Can't download hg19 genome data HOT 2
- Some reps get ERROR:root:--extsize must >= 1! HOT 2
- Documentation for macs2? HOT 2
- Citing the AQUAS Pipeline HOT 1
- ERROR:root:--extsize must >= 1! and chipseq.bds can not get all replicates go through HOT 25
- mm10 HOT 1
- JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa" HOT 1
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 chipseq_pipeline.