make_lastz_chains

make_lastz_chains copied to clipboard

PBSpro support

7

Hi, Our HPC uses PBSpro. Does `make_lastz_chains` support PBSpro? Best wishes, MIchal

mictadlo

Some problems during execution

1

Hi To obtain the prequel input file for TOGA, I attempted the process based on the information provided, but encountered some difficulties. I'm unsure how to proceed and would appreciate...

duan12345678

Speed up task processing

3

Hi,I'm hoping you could provide some guidance or suggestions. my command: ./make_chains.py hg38 Ea /data/groups/home/make_lastz_chains/genome/hg38.2bit /data/groups/home/make_lastz_chains/genome/Ea.2bit --pd /data/groups/public/home/Chains/Ea -f --chaining_memory 16 I use --executor local instead of --executor slurm, is...

molinfzl

speeding up/parallelizing make_chains.py with Slurm: NOTE: Error submitting process 'execute_jobs (##)' for execution -- Execution is retried

3

I'm trying to help a researcher speed up `make_chains.py` results for a mammal. Using [this closed issue regarding parallelization](https://github.com/hillerlab/make_lastz_chains/issues/2), as inspiration, we'd like to speed up the process via our...

SomePersonSomeWhereInTheWorld

make_chains.py in pipeline: modules.error_classes.PipelineFileNotFoundError: Error! No non-empty files found at make_lastz_chains/test_out/temp_concat_lastz_output. The failed operation label is: cat_step

2

On RHEL8, nextflow 23.10.0, anaconda/3-2023.09 on a shared HPC cluster, running the below example from [Running the pipeline](https://github.com/hillerlab/make_lastz_chains?tab=readme-ov-file#running-the-pipeline), results in the below. Did I miss a step? ``` ./make_chains.py target...

SomePersonSomeWhereInTheWorld

pipeline fails clean chain step - ERROR: cannot create a tempfile for netting the chain file: Permission denied

1

Hello! I am messaging because I am encountering a problem with the clean_chains part of this pipeline when run from a compute node on a HPC cluster. Everything works great...

d6948739

NOTE: Process `execute_jobs (605)` terminated with an error exit status (1) -- Execution is retried (1)

2

Hi ! I get this error if I use 'slurm' to submit the job, but I don't get it if I run the command directly on another server. The programme...

kuangzhuoran

chain_run error

2

Hi, I am trying it to run it and it fails at what looks like the last step after a long time running. I dont understand what this error means...

LliliansCalvo

Pipeline failed at last clean_chains step

7

Hello, got an error at last Clean chains step: ### Clean Chains Step ### Chains were filled: using /users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/deschrambler_test_files/temp_chain_run/human.cow.filled.chain.gz as input Chain to be cleaned saved to: /users/hpctestuser/mprylutskyi/makechains/make_lastz_chains/deschrambler_test_files/temp_chain_run/human.cow.before_cleaning.chain.gz An error...

Alchimic007

Alignment of a large genome in 2bit

1

Hello again, Bogdan and Michael, So far, `make_lastz_chains` has been working great, and the largest successfully aligned was the wheat genome (14.6 Gb). This time, I was asked to see...

ohdongha