Closed shameem356 closed 5 years ago
hello @fenderglass , Temporarily I removed opt == 'start' and opt == 'length' lines (line # 49 and 50) from hal/bin/hal2mafMP.py and ragout worked fine. Please have a look into this for a permanent solution
Thank you. It looks like an error in the latest HAL revision (https://github.com/ComparativeGenomicsToolkit/hal/issues/88)
In the mean time, you can try to use the HAL github revision 276eb8c - this is the one I used for my assemblies previously.
Hope this helps, Mikhail
thank you.
Hello @fenderglass I tried to run Ragout with hal option along with the example data which you provided . But I am getting the following hal error. Is it possible to run hal2maf with deafult value of --start and --length
Command : bin/ragout examples/hal_example/cholerae.rcp -o example_out --refine --overwrite -s hal ? Error :
10:58:31] INFO: Starting Ragout v2.2 [10:58:31] INFO: Running withs synteny block sizes '[5000, 500, 100]' [10:58:31] INFO: Extracting FASTA from HAL Warning: --inMemory is obsolete, use --hdf5InMemory [10:58:31] INFO: Converting HAL to MAF --start and --length require --refSequenceName
hal2maf v2.1: Convert hal database to maf.
USAGE: hal2maf [Options] <
mafFile>
Traceback (most recent call last): File "/data/labs/genomics_lab/shared/apps/HAL/hal/bin/hal2mafMP.py", line 338, in
sys.exit(main())
File "/data/labs/genomics_lab/shared/apps/HAL/hal/bin/hal2mafMP.py", line 335, in main
runParallelSlices(args)
File "/data/labs/genomics_lab/shared/apps/HAL/hal/bin/hal2mafMP.py", line 190, in runParallelSlices
runParallelShellCommands(sliceCmds, options.numProc)
File "/data/labs/genomics_lab/shared/apps/HAL/hal/stats/halStats.py", line 35, in runParallelShellCommands
map(runShellCommand, cmdList)
File "/data/labs/genomics_lab/shared/apps/HAL/hal/stats/halStats.py", line 28, in runShellCommand
(command, sts))
RuntimeError: Command: hal2maf examples/hal_example/alignment.hal example_out/hal-workdir/alignment.maf --unique --noAncestors --refGenome h1 --start 0 --length 4041199 --targetGenomes o395,h1,inaba,biovar exited with non-zero status 1
Traceback (most recent call last):
File "/data/labs/genomics_lab/shared/apps/Ragout/bin/ragout", line 32, in
sys.exit(main())
File "/data/labs/genomics_lab/shared/apps/Ragout/ragout/main.py", line 290, in main
_run_ragout(args)
File "/data/labs/genomics_lab/shared/apps/Ragout/ragout/main.py", line 175, in _run_ragout
args.threads)
File "/data/labs/genomics_lab/shared/apps/Ragout/ragout/synteny_backend/synteny_backend.py", line 36, in make_permutations
files = self.run_backend(recipe, output_dir, overwrite)
File "/data/labs/genomics_lab/shared/apps/Ragout/ragout/synteny_backend/hal.py", line 103, in run_backend
subprocess.check_call(cmdline, stdout=open(os.devnull, "w"))
File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['hal2mafMP.py', 'examples/hal_example/alignment.hal', 'example_out/hal-workdir/alignment.maf', '--noAncestors', '--numProc', '1', '--refGenome', 'h1', '--targetGenomes', 'o395,h1,inaba,biovar']' returned non-zero exit status 1