Peregrine

Peregrine copied to clipboard

Exception: Some tasks are recently_done but not satisfied

6

Hello, I am using Peregrine with the following commands: ``` docker run -i -t cschin/peregrine:0.1.6.1 asm /hlilab/chhy/Peregrine/chm13-seqdata.lst 32 32 32 32 32 32 32 32 32 --with-consensus --shimmer-r 3 --best_n_ovlp...

chhylp123

Run peregrine with singularity

1

Good evening, I need to run singularity, and I'd like to use the containerised version since easier to implement. I can successfully pull the image with ``` singularity pull peregrine.sif...

RenzoTale88

Submit a job with peregrine

1

Good day, I would like to test peregrine on some data I got in hand. I need to run it on our cluster environment, which support singularity. Now, to run...

RenzoTale88

Peregrine wihout Docker?

9

Hello, I have one quick question. Is any other way to use peregrine without Docker ? Because my machine does not support Docker. Thank you

Tdanis

slow: containerized Peregrine on gpfs file system

1

Hi, no real bug report, just an info to potentially help others who run into similar problems: running the containerized version of Peregrine (tested with v0.1.6.1) with Singularity on infrastructure...

ptrebert

python2.7: command not found

2

hello Jason, Sorry for not being able to use docker. This error message of mine might be an issue with conda. So the error message from run-xxx.bash.stderr is as follows:...

zhenzhenyang-psu

core file produced but final output is created

1

I'm assembling a ~20MB fungi on a 120 Gb node. The assembly completes successfully and looks reasonable but I'm getting a core file in the 3-asm stage. When I run...

aclum

Upsteam kseq

1

Hello, why have you modified kseq.h? Is it just for the support of gzip file handles? Maybe it would be good to give this upstream? Why have you changed the...

Phhere

Peregrine not recognising options

7

Hello, I am using Peregrine on my computer, here is my commande ``` sudo docker run -it -v /mnt/sda1/Alessandro/07-12-2019_Peregrine/ cschin/peregrine:0.1.5.5 asm \ /mnt/sda1/Alessandro/07-12-2019_Peregrine/reads.lst 24 24 24 24 24 24 24...

ghost

error in 3-asm

2

Hi Jason, I had an error in the 3-asm assembly stage of Peregrine. The simple error message was below: """ 2019-11-19 13:22:08,022 - root - CRITICAL - Error in /share/home/yangzz/anaconda3/envs/peregrine/lib/python3.7/site-packages/pypeflow-2.1.1+git.d63b0e79f5a7b2d370b7de84a890f88271afa476-py3.7.egg/pypeflow/do_task.py...

zhenzhenyang-psu