I am working on macOS High Sierra.
I am following the steps described here to lift an annotation over from one version of a genome to another. I am now just using the example genomes provided in the tutorial.
At this step:
time (doSameSpeciesLiftOver.pl -verbose=2 -buildDir=`pwd` \
-ooc=`pwd`/${target}.ooc -fileServer=localhost -localTmp="/dev/shm" \
-bigClusterHub=localhost -dbHost=localhost -workhorse=localhost \
-target2Bit=`pwd`/${target}.2bit -targetSizes=`pwd`/${target}.chrom.sizes \
-query2Bit=../${query}/${query}.2bit \
-querySizes=../${query}/${query}.chrom.sizes ${target} ${query}) > do.log 2>&1
I get the following error in the do.log
file:
Warning: Permanently added 'localhost' (ECDSA) to the list of known hosts.
username@localhost: Permission denied (publickey,password,keyboard-interactive).
HgStepManager: executing from step 'align' through step 'cleanup'.
HgStepManager: executing step 'align' Thu Nov 8 14:27:32 2018.
Using localhost, /Users/username/Documents/projects/main/output/software/liftover/data/genomes/GCA_000004515.3_Glycine_max_v2.0/GCA_000004515.3_Glycine_max_v2.0.2bit and ../GCF_000004515.3_V1.1/GCF_000004515.3_V1.1.2bit
align: localhost does not have /Users/username/Documents/projects/main/output/software/liftover/data/genomes/GCA_000004515.3_Glycine_max_v2.0/GCA_000004515.3_Glycine_max_v2.0.ooc -- if that is not the correct location, please run again with -ooc.
I think the main problem is here:
username@localhost: Permission denied (publickey,password,keyboard-interactive).
This post describes this issue. However:
- I do not have this file: ~/.ssh/authorized_keys. My files in ~/.ssh are:
github_rsa github_rsa.pub known_hosts
. One of the lines ofknown_hosts
is localhost. Does this presumably allow me to ssh to my own laptop? I still don't understand why I need to ssh in this script if it's run locally. PasswordAuthentication yes
is already in/etc/ssh/sshd_config
- If I run the command without the
time
command, I still get the same error. I am not prompted to give a password.
Could anyone help me overcome this problem, please?