make_lastz_chains

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Multiple Alignments

1

Dear Authors, thank you very much for providing the pipeline! I would like to run the pipeline on different genomes together to compute whole genome alignment of different species to...

lutfia95

Idea for the future: add a module that accumulates detailed statistics for each pipeline step. Like, as how many chains we get for each chromosome after axtChain, how many blocks...

kirilenkobm

self chains

2

Hi I want to do chainself. Can this pipeline do chainself?

BoBo2021jenny

Stalled at the doChainRun step

6

Hi, Bogdan and Michael @kirilenkobm @MichaelHiller, This was originally a comment on issue #9. Then, I realize it's a separate issue. When I tried human vs. Chimpanzee and human vs....

ohdongha

chainCleaner failure with chromosomes >1Gb (2^30)

7

Hello again, I was trying to align the corroboree frog and _X. tropicalis_ genomes. The corroboree frog genome ([GCF_028390025.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_028390025.1/)) is not prohibitingly large, but it includes a chromosome larger than...

ohdongha

lastz step terminated with an error exit status (132)

1

Hi @kirilenkobm and @MichaelHiller, Thank you for providing this pipeline! I am using make_lastz_chains version 2.0.8 in our Slurm cluster. When I run the test example `./make_chains.py target query test_data/test_reference.fa...

munegowda

The number of tasks submitted by SLURM exceeded the limit

16

Hello, professor I was running the pipeline to align my genome assemblies with mm10 genome via slurm: ` ./make_chains.py target query mm10.fasta Bsu.softmask.fasta --pd mm-Bsu -f --chaining_memory 30 --cluster_queue pNormal...

aaannaw

TypeError: 'bool' object is not iterable

2

I tested make _lastz _chains with the mouse genome mm10 and the human genome hg19, running the script as follows: `python3 /home/luria/make_lastz_chains-2.0.8/make_chains.py hg19 mm10 /home/luria/hg19_chrom.fa /home/luria/mm10_chrom.fa --project_dir /home/luria/mm10_vs_hg19` But I...

bioluria

A minor discrepancy between v1.0.0 and v2.0.8 at 'fill_chain' step

4

Hi again, Recently, we have been testing `make_lastz_chains` v2.0.8 (MLC v2) to run on our SGE grid. After adding some `clusterOptions` directives to the `Nextflow` template (`execute_joblist.nf`), the MLC v2...

ohdongha

Using an alternative scoring matrix in make_lastz_chains v.2.0.8

2

We have been adding `BLASTZ_Q` parameter when running `make_lastz_chains` v1.0.0 (MLC v1) to use an alternative scoring matrix (HoxD55 instead of the default HoxD70) for increased sensitivity when aligning more...

ohdongha