Hannah1746
Hannah1746
I am in huge support for getting "Proportion of Variance" for the x and y axes labels for the PCA plot as well as being able to choose colors and...
I believe I am running into the same issue on my end. Did this ever get resolved?
I ran one of the jobs from lastz_joblist.txt: /home/hwaterma/Documents/make_lastz_chains/standalone_scripts/run_lastz_intermediate_layer.py BULK_1:/home/hwaterma/Documents/MX_TOGA/test_out/target.2bit:MYX_Chr1 /home/hwaterma/Documents/MX_TOGA/test_out/query.2bit:NC_007112_7:0-50000000 /home/hwaterma/Documents/MX_TOGA/test_out/pipeline_parameters.json /home/hwaterma/Documents/MX_TOGA/test_out/temp_lastz_psl_output/bucket_ref_bulk_1/BULK_1_NC_007112_7__1.psl /home/hwaterma/Documents/make_lastz_chains/standalone_scripts/run_lastz.py --output_format psl --axt_to_psl /home/hwaterma/Documents/make_lastz_chains/HL_kent_binaries/axtToPsl That has been running for a few hours now with no errors.
Our first chromosome is 69,199,620 bp. The command did run to completion too. I just do not understand why the larger script is not working.
hwaterma@cast-bio540ws02:~/Documents/MX_TOGA$ /usr/bin/time -v lastz You must specify a target file lastz-- Local Alignment Search Tool, blastZ-like (version 1.04.15 released 20210827) usage: lastz target [query] [options] (common options; use --help for...
I don't think I am doing this right. I'm sorry for being a little slow to this computer coding but this is what I ran and got: (TOGA) hwaterma@cast-bio540ws02:~/Documents/MX_TOGA$ /usr/bin/time...
when I run that I get: /usr/bin/time -v find . | wc Command being timed: "find ." User time (seconds): 0.00 System time (seconds): 0.00 Percent of CPU this job...
when I run /usr/bin/time -v find . | wc Command being timed: "find ." User time (seconds): 0.00 System time (seconds): 0.00 Percent of CPU this job got: 1% Elapsed...
Oh I am sorry I was running the full command here is just /usr/bin/time -v find . | wc (TOGA) hwaterma@cast-bio540ws02:~/Documents/MX_TOGA$ /usr/bin/time -v find . | wc Command being timed:...
(TOGA) hwaterma@cast-bio540ws02:~/Documents/MX_TOGA/test_out$ ls -lh total 1.1G -rw-rw-r-- 1 hwaterma biograd 1.5K Nov 8 11:28 pipeline_parameters.json -rw-rw-r-- 1 hwaterma biograd 483M Nov 8 11:28 query.2bit -rw-rw-r-- 1 hwaterma biograd 41K Nov...