How to creat *over.chain.gz file
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2.4 years ago
afli ▴ 190

Hello, I want to creat a chain file using the pipeline "http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl", I get the following error when excute doSameSpeciesLiftOver.pl.

>doSameSpeciesLiftOver.pl -verbose=2 -buildDir=/home/afli/work/data/tmp/liftover/GCA_000004515.3_Glycine_max_v2.0 -ooc=GCA_000004515.3_Glycine_max_v1.1.ooc -fileServer=localhost -localTmp="/dev/shm"  -dbHost=localhost -bigClusterHub=localhost -target2Bit=GCA_000004515.3_Glycine_max_v2.0.2bit -targetSizes=GCA_000004515.3_Glycine_max_v2.0.chrom.sizes -query2Bit=GCF_000004515.3_V1.1.2bit -querySizes=GCF_000004515.3_V1.1.chrom.sizes GCA_000004515.3_Glycine_max_v1.1 GCF_000004515.3_V1.1

ssh: connect to host localhost port 22: Connection refused
HgStepManager: executing from step 'align' through step 'cleanup'.
HgStepManager: executing step 'align' Tue Jun  4 10:30:17 2019.
Using localhost, GCA_000004515.3_Glycine_max_v2.0.2bit and GCF_000004515.3_V1.1.2bit
align: localhost does not have GCA_000004515.3_Glycine_max_v1.1.ooc -- if that is not the correct location, please run again with -ooc.

My system is Ubuntu 14.04.5 LTS, it seems that the ssh part get some errors, how can I solve this problem? Thank you!

liftover chain file • 931 views
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perhaps you might try flo (https://github.com/wurmlab/flo) a re-implementation of the SameSpeciesLiftOver pipeline (although it generates the chain file as in intermediate step).

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Thank you very much! It is helpful!

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flo eventually generates a file called liftover.chn in the directory run, which is what I think you are looking for

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