test_midas.py fail for test 7

[linzhouzz]

Hi, when I ran test_midas.py, I received an error message for the RunSNPs test. Do you potentially know what is causing this?

====================================================================== FAIL: test_class (main._07_RunSNPs)

Traceback (most recent call last): File "test_midas.py", line 102, in test_class self.assertTrue(code==0, msg=err) AssertionError: Traceback (most recent call last): File "/u/local/apps/midas/1.3.2/MIDAS/scripts/run_midas.py", line 757, in run_program(program, args) File "/u/local/apps/midas/1.3.2/MIDAS/scripts/run_midas.py", line 82, in run_program snps.run_pipeline(args) File "/u/local/apps/midas/1.3.2/MIDAS/midas/run/snps.py", line 301, in run_pipeline pysam_pileup(args, species, contigs) File "/u/local/apps/midas/1.3.2/MIDAS/midas/run/snps.py", line 228, in pysam_pileup aln_stats = utility.parallel(species_pileup, argument_list, args['threads']) File "/u/local/apps/midas/1.3.2/MIDAS/midas/utility.py", line 101, in parallel return [r.get() for r in results] File "/u/local/apps/anaconda2/2019.10/envs/midas/lib/python2.7/multiprocessing/pool.py", line 572, in get raise self._value AttributeError: 'pysam.calignmentfile.AlignmentFile' object has no attribute 'count_coverage'

[tbazilegith]

Hi also have issues with python test_midas.py -vf. Could anyone have an idea about this? test_class (main._01_CheckEnv) ... ok test_class (main._02_ImportDependencies) ... ok test_class (main._03_CheckVersions) ... ok test_class (main._04_HelpText) ... ok test_class (main._05_RunSpecies) ... FAIL

====================================================================== FAIL: test_class (main._05_RunSpecies)

Traceback (most recent call last): File "test_midas.py", line 90, in test_class self.assertTrue(code==0, msg=err) AssertionError: False is not true : b'\nError: could not execute samtools binary: /blue/bphl-username/directory/MIDAS/bin/Linux/samtools\n(exited with error code 1)\nTo solve this issue, follow these steps:\n 1) Download samtools v1.4: https://github.com/samtools/samtools/releases/download/1.4/samtools-1.4.tar.bz2\n 2) Unpack and compile the software on your system\n 3) Copy the new samtools binary to: sername/directory/MIDAS/bin/Linux\n\n'

When I download and unpack samtools-1.4.tar.bz2, the samtools binary is unseen.