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Hey I have beed tryin to run make_chains.py locally and keep getting shutdown by terminated with an error exit status (1).
(TOGA) hwaterma@cast-bio540ws02:~/Documents/MX_TOGA$ ../make_lastz_chain…
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Hi,
I have a question regarding running LASTZ similar to what they did for the TOGA paper. In my case, I have Cactus 447 mammalian genome dataset. I converted it from Hal to fasta, removed ancestral …
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Hi,
I am trying to run AliTV for three plant genomes (same species but different sub-species). the genomes have been assembled using HifiAsm. As they are from the same species the sequences have long…
onbio updated
1 month ago
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Hi
This looks like a super nice tool and I am excited to try and use it. However, I was wondering if there was any way around the need for the GLIBC v2.29? I had our admin install the software and …
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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`…
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Hello professor:
When I use the lastz to get *_lastz.txt file using
`lastz *.genomic.fa[multiple] *.genomic.fa[multiple] --chain --format=general:name1,strand1,start1,end1,name2,strand2,start2,end…
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Hi All - having many jobs fail with this type of error, which seems to indicated perhaps something about a poorly formatted fasta file? One issue is that I can't seem to find the offending file `GCF_0…
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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/hg1…
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High I am running, when I run in my data I got the error "Could not split CESAR jobs".
I run the following line:
./toga.py make_lastz_chains/make_lastz_chains/chicken_turkey/target.query.final.cha…
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Hello mahulchak !
In the latest version , you use the alignment result of both mummer and lastz. But when the alignment result is different between these two softwares . which one is used to detect …