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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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hal2maf : --start and --length require --refSequenceName #46

Closed shameem356 closed 5 years ago

shameem356 commented 5 years ago

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Running withs synteny block sizes '[5000, 500, 100]' [10:58:31] INFO: Extracting FASTA from HAL Warning: --inMemory is obsolete, use --hdf5InMemory [10:58:31] INFO: Converting HAL to MAF --start and --length require --refSequenceName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

shameem356 commented 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

mikolmogorov commented 5 years ago

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

shameem356 commented 5 years ago

thank you.