(picrust2-dev) ursula:picrust2 yakshiortiz$ pytest
============================= test session starts ==============================
platform darwin -- Python 3.6.5, pytest-3.6.2, py-1.5.4, pluggy-0.6.0
rootdir: /Users/yakshiortiz/picrust2, inifile:
plugins: cov-2.5.1
collected 28 items                                                             

tests/test_hsp.py FFFFFFF                                                [ 25%]
tests/test_metagenome_pipeline.py .......                                [ 50%]
tests/test_place_seqs.py .FFFF.                                          [ 71%]
tests/test_run_minpath.py ..                                             [ 78%]
tests/test_util.py ....                                                  [ 92%]
tests/test_workflow.py FF                                                [100%]

=================================== FAILURES ===================================
________________ castor_hsp_workflow_tests.test_emp_prob_simple ________________

self = <tests.test_hsp.castor_hsp_workflow_tests testMethod=test_emp_prob_simple>

    def test_emp_prob_simple(self):
    
        predict_out, ci_out = castor_hsp_workflow(tree_path=in_tree1,
                                                 trait_table_path=in_traits1,
                                                 hsp_method="emp_prob",
>                                                ran_seed=10)

tests/test_hsp.py:73: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/wrap_hsp.py:65: in castor_hsp_workflow
    for trait_in in file_subsets)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:949: in __call__
    if self.dispatch_one_batch(iterator):
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:791: in dispatch_one_batch
    self._dispatch(tasks)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:748: in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:183: in apply_async
    result = ImmediateResult(func)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:543: in __init__
    self.results = batch()
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in __call__
    for func, args, kwargs in self.items]
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in <listcomp>
    for func, args, kwargs in self.items]
picrust2/wrap_hsp.py:126: in castor_hsp_wrapper
    system_call_check(hsp_cmd)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['Rscript', '/Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R', '/Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre', '/var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp34b217n5/subset_tab_0', 'emp_prob', 'FALSE', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           Rscript /Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R /Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp34b217n5/subset_tab_0 emp_prob FALSE FALSE /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp7jma9xbe/predicted_counts.txt /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp7jma9xbe/predicted_ci.txt 10

picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
 9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(castor, quietly = TRUE)
An irrecoverable exception occurred. R is aborting now ...
_____________________ castor_hsp_workflow_tests.test_mp_ci _____________________

self = <tests.test_hsp.castor_hsp_workflow_tests testMethod=test_mp_ci>

    def test_mp_ci(self):
        '''Test that MP confidence intervals calculated correctly.'''
        predict_out, ci_out = castor_hsp_workflow(tree_path=in_tree1,
                                                 trait_table_path=in_traits1,
                                                 hsp_method="mp",
                                                 ran_seed=10,
>                                                calc_ci=True)

tests/test_hsp.py:126: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/wrap_hsp.py:65: in castor_hsp_workflow
    for trait_in in file_subsets)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:949: in __call__
    if self.dispatch_one_batch(iterator):
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:791: in dispatch_one_batch
    self._dispatch(tasks)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:748: in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:183: in apply_async
    result = ImmediateResult(func)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:543: in __init__
    self.results = batch()
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in __call__
    for func, args, kwargs in self.items]
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in <listcomp>
    for func, args, kwargs in self.items]
picrust2/wrap_hsp.py:126: in castor_hsp_wrapper
    system_call_check(hsp_cmd)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['Rscript', '/Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R', '/Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre', '/var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp1fk2yvpl/subset_tab_0', 'mp', 'TRUE', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           Rscript /Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R /Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp1fk2yvpl/subset_tab_0 mp TRUE FALSE /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpurw96obt/predicted_counts.txt /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpurw96obt/predicted_ci.txt 10

picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
 9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(castor, quietly = TRUE)
An irrecoverable exception occurred. R is aborting now ...
___________________ castor_hsp_workflow_tests.test_mp_simple ___________________

self = <tests.test_hsp.castor_hsp_workflow_tests testMethod=test_mp_simple>

    def test_mp_simple(self):
    
        predict_out, ci_out = castor_hsp_workflow(tree_path=in_tree1,
                                                 trait_table_path=in_traits1,
                                                 hsp_method="mp",
>                                                ran_seed=10)

tests/test_hsp.py:60: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/wrap_hsp.py:65: in castor_hsp_workflow
    for trait_in in file_subsets)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:949: in __call__
    if self.dispatch_one_batch(iterator):
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:791: in dispatch_one_batch
    self._dispatch(tasks)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:748: in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:183: in apply_async
    result = ImmediateResult(func)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:543: in __init__
    self.results = batch()
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in __call__
    for func, args, kwargs in self.items]
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in <listcomp>
    for func, args, kwargs in self.items]
picrust2/wrap_hsp.py:126: in castor_hsp_wrapper
    system_call_check(hsp_cmd)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['Rscript', '/Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R', '/Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre', '/var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpt2imkmr_/subset_tab_0', 'mp', 'FALSE', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           Rscript /Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R /Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpt2imkmr_/subset_tab_0 mp FALSE FALSE /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpvtbmcd5n/predicted_counts.txt /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpvtbmcd5n/predicted_ci.txt 10

picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
 9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(castor, quietly = TRUE)
An irrecoverable exception occurred. R is aborting now ...
_____________________ castor_hsp_workflow_tests.test_nsti ______________________

self = <tests.test_hsp.castor_hsp_workflow_tests testMethod=test_nsti>

    def test_nsti(self):
        '''Test that calculated NSTI values match expected.'''
    
        in_traits1_df = pd.read_csv(in_traits1, sep="\t",
                                    index_col="assembly",
                                    dtype={'assembly' : str})
    
        nsti_out = castor_nsti(tree_path=in_tree1,
>                              known_tips=in_traits1_df.index.values)

tests/test_hsp.py:142: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/wrap_hsp.py:169: in castor_nsti
    nsti_tmp_out]))
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['Rscript', '/Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_nsti.R', '/Users/yakshiortiz/picrust2/tests/test_dat..._xk300000gr/T/tmpdsgk6pm2/known_tips.txt', '/var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpdsgk6pm2/nsti_out.txt']
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           Rscript /Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_nsti.R /Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpdsgk6pm2/known_tips.txt /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpdsgk6pm2/nsti_out.txt

picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
 9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(castor, quietly = TRUE)
An irrecoverable exception occurred. R is aborting now ...
__________________ castor_hsp_workflow_tests.test_pic_simple ___________________

self = <tests.test_hsp.castor_hsp_workflow_tests testMethod=test_pic_simple>

    def test_pic_simple(self):
    
        predict_out, ci_out = castor_hsp_workflow(tree_path=in_tree1,
                                                 trait_table_path=in_traits1,
                                                 hsp_method="pic",
>                                                ran_seed=10)

tests/test_hsp.py:86: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/wrap_hsp.py:65: in castor_hsp_workflow
    for trait_in in file_subsets)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:949: in __call__
    if self.dispatch_one_batch(iterator):
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:791: in dispatch_one_batch
    self._dispatch(tasks)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:748: in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:183: in apply_async
    result = ImmediateResult(func)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:543: in __init__
    self.results = batch()
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in __call__
    for func, args, kwargs in self.items]
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in <listcomp>
    for func, args, kwargs in self.items]
picrust2/wrap_hsp.py:126: in castor_hsp_wrapper
    system_call_check(hsp_cmd)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['Rscript', '/Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R', '/Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre', '/var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpp5w68hjg/subset_tab_0', 'pic', 'FALSE', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           Rscript /Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R /Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpp5w68hjg/subset_tab_0 pic FALSE FALSE /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpgy9_zgq2/predicted_counts.txt /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpgy9_zgq2/predicted_ci.txt 10

picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
 9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(castor, quietly = TRUE)
An irrecoverable exception occurred. R is aborting now ...
__________________ castor_hsp_workflow_tests.test_scp_simple ___________________

self = <tests.test_hsp.castor_hsp_workflow_tests testMethod=test_scp_simple>

    def test_scp_simple(self):
    
        predict_out, ci_out = castor_hsp_workflow(tree_path=in_tree1,
                                                 trait_table_path=in_traits1,
                                                 hsp_method="scp",
>                                                ran_seed=10)

tests/test_hsp.py:99: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/wrap_hsp.py:65: in castor_hsp_workflow
    for trait_in in file_subsets)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:949: in __call__
    if self.dispatch_one_batch(iterator):
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:791: in dispatch_one_batch
    self._dispatch(tasks)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:748: in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:183: in apply_async
    result = ImmediateResult(func)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:543: in __init__
    self.results = batch()
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in __call__
    for func, args, kwargs in self.items]
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in <listcomp>
    for func, args, kwargs in self.items]
picrust2/wrap_hsp.py:126: in castor_hsp_wrapper
    system_call_check(hsp_cmd)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['Rscript', '/Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R', '/Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre', '/var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp1d6j9yi3/subset_tab_0', 'scp', 'FALSE', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           Rscript /Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R /Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp1d6j9yi3/subset_tab_0 scp FALSE FALSE /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpkup1ddgv/predicted_counts.txt /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpkup1ddgv/predicted_ci.txt 10

picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
 9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(castor, quietly = TRUE)
An irrecoverable exception occurred. R is aborting now ...
____________ castor_hsp_workflow_tests.test_subtree_average_simple _____________

self = <tests.test_hsp.castor_hsp_workflow_tests testMethod=test_subtree_average_simple>

    def test_subtree_average_simple(self):
    
        predict_out, ci_out = castor_hsp_workflow(tree_path=in_tree1,
                                                 trait_table_path=in_traits1,
                                                 hsp_method="subtree_average",
>                                                ran_seed=10)

tests/test_hsp.py:112: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/wrap_hsp.py:65: in castor_hsp_workflow
    for trait_in in file_subsets)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:949: in __call__
    if self.dispatch_one_batch(iterator):
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:791: in dispatch_one_batch
    self._dispatch(tasks)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:748: in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:183: in apply_async
    result = ImmediateResult(func)
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:543: in __init__
    self.results = batch()
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in __call__
    for func, args, kwargs in self.items]
../miniconda3/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:224: in <listcomp>
    for func, args, kwargs in self.items]
picrust2/wrap_hsp.py:126: in castor_hsp_wrapper
    system_call_check(hsp_cmd)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['Rscript', '/Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R', '/Users/yakshiortiz/picrust2/tests/test_data...ree.tre', '/var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpxirgx95y/subset_tab_0', 'subtree_average', 'FALSE', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           Rscript /Users/yakshiortiz/picrust2/picrust2/Rscripts/castor_hsp.R /Users/yakshiortiz/picrust2/tests/test_data/hsp/tree.tre /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpxirgx95y/subset_tab_0 subtree_average FALSE FALSE /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp_bxftajt/predicted_counts.txt /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmp_bxftajt/predicted_ci.txt 10

picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc,     quietly = quietly)
 9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(castor, quietly = TRUE)
An irrecoverable exception occurred. R is aborting now ...
_________________ place_seqs_tests.test_gappa_jplace_to_newick _________________

self = <tests.test_place_seqs.place_seqs_tests testMethod=test_gappa_jplace_to_newick>

    def test_gappa_jplace_to_newick(self):
        '''Basic test for gappa_jplace_to_newick function.'''
    
        # Read in expected newick output.
        exp_newick_in = open(exp_newick).read()
    
        with TemporaryDirectory() as temp_dir:
            newick_out = path.join(temp_dir, "out.tre")
    
>           gappa_jplace_to_newick(jplace_file=exp_jplace, outfile=newick_out)

tests/test_place_seqs.py:120: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/place_seqs.py:137: in gappa_jplace_to_newick
    print_out=print_cmds)
picrust2/util.py:157: in system_call_check
    return_value = call(cmd, stdout=stdout, stderr=stderr)
../miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:267: in call
    with Popen(*popenargs, **kwargs) as p:
../miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:709: in __init__
    restore_signals, start_new_session)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <subprocess.Popen object at 0x1197df278>
args = ['gappa', 'analyze', 'graft', '--jplace-path', '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/place_seqs_output/place_seqs_working/epa_out/epa_result.jplace', '--fully-resolve', ...]
executable = b'gappa', preexec_fn = None, close_fds = True, pass_fds = ()
cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False
p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1
errwrite = -1, restore_signals = True, start_new_session = False

    def _execute_child(self, args, executable, preexec_fn, close_fds,
                       pass_fds, cwd, env,
                       startupinfo, creationflags, shell,
                       p2cread, p2cwrite,
                       c2pread, c2pwrite,
                       errread, errwrite,
                       restore_signals, start_new_session):
        """Execute program (POSIX version)"""
    
        if isinstance(args, (str, bytes)):
            args = [args]
        else:
            args = list(args)
    
        if shell:
            args = ["/bin/sh", "-c"] + args
            if executable:
                args[0] = executable
    
        if executable is None:
            executable = args[0]
        orig_executable = executable
    
        # For transferring possible exec failure from child to parent.
        # Data format: "exception name:hex errno:description"
        # Pickle is not used; it is complex and involves memory allocation.
        errpipe_read, errpipe_write = os.pipe()
        # errpipe_write must not be in the standard io 0, 1, or 2 fd range.
        low_fds_to_close = []
        while errpipe_write < 3:
            low_fds_to_close.append(errpipe_write)
            errpipe_write = os.dup(errpipe_write)
        for low_fd in low_fds_to_close:
            os.close(low_fd)
        try:
            try:
                # We must avoid complex work that could involve
                # malloc or free in the child process to avoid
                # potential deadlocks, thus we do all this here.
                # and pass it to fork_exec()
    
                if env is not None:
                    env_list = []
                    for k, v in env.items():
                        k = os.fsencode(k)
                        if b'=' in k:
                            raise ValueError("illegal environment variable name")
                        env_list.append(k + b'=' + os.fsencode(v))
                else:
                    env_list = None  # Use execv instead of execve.
                executable = os.fsencode(executable)
                if os.path.dirname(executable):
                    executable_list = (executable,)
                else:
                    # This matches the behavior of os._execvpe().
                    executable_list = tuple(
                        os.path.join(os.fsencode(dir), executable)
                        for dir in os.get_exec_path(env))
                fds_to_keep = set(pass_fds)
                fds_to_keep.add(errpipe_write)
                self.pid = _posixsubprocess.fork_exec(
                        args, executable_list,
                        close_fds, tuple(sorted(map(int, fds_to_keep))),
                        cwd, env_list,
                        p2cread, p2cwrite, c2pread, c2pwrite,
                        errread, errwrite,
                        errpipe_read, errpipe_write,
                        restore_signals, start_new_session, preexec_fn)
                self._child_created = True
            finally:
                # be sure the FD is closed no matter what
                os.close(errpipe_write)
    
            # self._devnull is not always defined.
            devnull_fd = getattr(self, '_devnull', None)
            if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd:
                os.close(p2cread)
            if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd:
                os.close(c2pwrite)
            if errwrite != -1 and errread != -1 and errwrite != devnull_fd:
                os.close(errwrite)
            if devnull_fd is not None:
                os.close(devnull_fd)
            # Prevent a double close of these fds from __init__ on error.
            self._closed_child_pipe_fds = True
    
            # Wait for exec to fail or succeed; possibly raising an
            # exception (limited in size)
            errpipe_data = bytearray()
            while True:
                part = os.read(errpipe_read, 50000)
                errpipe_data += part
                if not part or len(errpipe_data) > 50000:
                    break
        finally:
            # be sure the FD is closed no matter what
            os.close(errpipe_read)
    
        if errpipe_data:
            try:
                pid, sts = os.waitpid(self.pid, 0)
                if pid == self.pid:
                    self._handle_exitstatus(sts)
                else:
                    self.returncode = sys.maxsize
            except ChildProcessError:
                pass
    
            try:
                exception_name, hex_errno, err_msg = (
                        errpipe_data.split(b':', 2))
                # The encoding here should match the encoding
                # written in by the subprocess implementations
                # like _posixsubprocess
                err_msg = err_msg.decode()
            except ValueError:
                exception_name = b'SubprocessError'
                hex_errno = b'0'
                err_msg = 'Bad exception data from child: {!r}'.format(
                              bytes(errpipe_data))
            child_exception_type = getattr(
                    builtins, exception_name.decode('ascii'),
                    SubprocessError)
            if issubclass(child_exception_type, OSError) and hex_errno:
                errno_num = int(hex_errno, 16)
                child_exec_never_called = (err_msg == "noexec")
                if child_exec_never_called:
                    err_msg = ""
                    # The error must be from chdir(cwd).
                    err_filename = cwd
                else:
                    err_filename = orig_executable
                if errno_num != 0:
                    err_msg = os.strerror(errno_num)
                    if errno_num == errno.ENOENT:
                        err_msg += ': ' + repr(err_filename)
>               raise child_exception_type(errno_num, err_msg, err_filename)
E               FileNotFoundError: [Errno 2] No such file or directory: 'gappa': 'gappa'

../miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:1344: FileNotFoundError
_______________________ place_seqs_tests.test_run_epa_ng _______________________

self = <tests.test_place_seqs.place_seqs_tests testMethod=test_run_epa_ng>

    def test_run_epa_ng(self):
        '''Basic test to check whether EPA-NG wrapper can be run. Exact
            matches to a treefile are not checked since slight differences
            are expected depending on different versions.'''
    
        with TemporaryDirectory() as temp_dir:
            run_epa_ng(tree=test_tree,
                       ref_msa_fastafile=exp_ref_fasta,
                       study_msa_fastafile=exp_study_fasta,
>                      out_dir=temp_dir)

tests/test_place_seqs.py:135: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
picrust2/place_seqs.py:125: in run_epa_ng
    str(threads) + " -w " + out_dir, print_out=print_cmds)
picrust2/util.py:157: in system_call_check
    return_value = call(cmd, stdout=stdout, stderr=stderr)
../miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:267: in call
    with Popen(*popenargs, **kwargs) as p:
../miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:709: in __init__
    restore_signals, start_new_session)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <subprocess.Popen object at 0x1196ed7b8>
args = ['epa-ng', '--tree', '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.tre', '--...iortiz/picrust2/tests/test_data/place_seqs/place_seqs_output/place_seqs_working/ref_seqs_papara.fasta', '--query', ...]
executable = b'epa-ng', preexec_fn = None, close_fds = True, pass_fds = ()
cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False
p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1
errwrite = -1, restore_signals = True, start_new_session = False

    def _execute_child(self, args, executable, preexec_fn, close_fds,
                       pass_fds, cwd, env,
                       startupinfo, creationflags, shell,
                       p2cread, p2cwrite,
                       c2pread, c2pwrite,
                       errread, errwrite,
                       restore_signals, start_new_session):
        """Execute program (POSIX version)"""
    
        if isinstance(args, (str, bytes)):
            args = [args]
        else:
            args = list(args)
    
        if shell:
            args = ["/bin/sh", "-c"] + args
            if executable:
                args[0] = executable
    
        if executable is None:
            executable = args[0]
        orig_executable = executable
    
        # For transferring possible exec failure from child to parent.
        # Data format: "exception name:hex errno:description"
        # Pickle is not used; it is complex and involves memory allocation.
        errpipe_read, errpipe_write = os.pipe()
        # errpipe_write must not be in the standard io 0, 1, or 2 fd range.
        low_fds_to_close = []
        while errpipe_write < 3:
            low_fds_to_close.append(errpipe_write)
            errpipe_write = os.dup(errpipe_write)
        for low_fd in low_fds_to_close:
            os.close(low_fd)
        try:
            try:
                # We must avoid complex work that could involve
                # malloc or free in the child process to avoid
                # potential deadlocks, thus we do all this here.
                # and pass it to fork_exec()
    
                if env is not None:
                    env_list = []
                    for k, v in env.items():
                        k = os.fsencode(k)
                        if b'=' in k:
                            raise ValueError("illegal environment variable name")
                        env_list.append(k + b'=' + os.fsencode(v))
                else:
                    env_list = None  # Use execv instead of execve.
                executable = os.fsencode(executable)
                if os.path.dirname(executable):
                    executable_list = (executable,)
                else:
                    # This matches the behavior of os._execvpe().
                    executable_list = tuple(
                        os.path.join(os.fsencode(dir), executable)
                        for dir in os.get_exec_path(env))
                fds_to_keep = set(pass_fds)
                fds_to_keep.add(errpipe_write)
                self.pid = _posixsubprocess.fork_exec(
                        args, executable_list,
                        close_fds, tuple(sorted(map(int, fds_to_keep))),
                        cwd, env_list,
                        p2cread, p2cwrite, c2pread, c2pwrite,
                        errread, errwrite,
                        errpipe_read, errpipe_write,
                        restore_signals, start_new_session, preexec_fn)
                self._child_created = True
            finally:
                # be sure the FD is closed no matter what
                os.close(errpipe_write)
    
            # self._devnull is not always defined.
            devnull_fd = getattr(self, '_devnull', None)
            if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd:
                os.close(p2cread)
            if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd:
                os.close(c2pwrite)
            if errwrite != -1 and errread != -1 and errwrite != devnull_fd:
                os.close(errwrite)
            if devnull_fd is not None:
                os.close(devnull_fd)
            # Prevent a double close of these fds from __init__ on error.
            self._closed_child_pipe_fds = True
    
            # Wait for exec to fail or succeed; possibly raising an
            # exception (limited in size)
            errpipe_data = bytearray()
            while True:
                part = os.read(errpipe_read, 50000)
                errpipe_data += part
                if not part or len(errpipe_data) > 50000:
                    break
        finally:
            # be sure the FD is closed no matter what
            os.close(errpipe_read)
    
        if errpipe_data:
            try:
                pid, sts = os.waitpid(self.pid, 0)
                if pid == self.pid:
                    self._handle_exitstatus(sts)
                else:
                    self.returncode = sys.maxsize
            except ChildProcessError:
                pass
    
            try:
                exception_name, hex_errno, err_msg = (
                        errpipe_data.split(b':', 2))
                # The encoding here should match the encoding
                # written in by the subprocess implementations
                # like _posixsubprocess
                err_msg = err_msg.decode()
            except ValueError:
                exception_name = b'SubprocessError'
                hex_errno = b'0'
                err_msg = 'Bad exception data from child: {!r}'.format(
                              bytes(errpipe_data))
            child_exception_type = getattr(
                    builtins, exception_name.decode('ascii'),
                    SubprocessError)
            if issubclass(child_exception_type, OSError) and hex_errno:
                errno_num = int(hex_errno, 16)
                child_exec_never_called = (err_msg == "noexec")
                if child_exec_never_called:
                    err_msg = ""
                    # The error must be from chdir(cwd).
                    err_filename = cwd
                else:
                    err_filename = orig_executable
                if errno_num != 0:
                    err_msg = os.strerror(errno_num)
                    if errno_num == errno.ENOENT:
                        err_msg += ': ' + repr(err_filename)
>               raise child_exception_type(errno_num, err_msg, err_filename)
E               FileNotFoundError: [Errno 2] No such file or directory: 'epa-ng': 'epa-ng'

../miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:1344: FileNotFoundError
_______________________ place_seqs_tests.test_run_papara _______________________

self = <tests.test_place_seqs.place_seqs_tests testMethod=test_run_papara>

    def test_run_papara(self):
        '''Basic test for run_papara function.'''
    
        exp_phylip = read_phylip(exp_papara_phylip)
        in_msa = read_fasta(test_msa)
    
        with TemporaryDirectory() as temp_dir:
            obs_phylip = run_papara(tree=test_tree,
                                    ref_msa=in_msa,
                                    out_dir=temp_dir,
>                                   study_fasta=test_study_seqs)

/Users/yakshiortiz/picrust2/tests/test_place_seqs.py:82: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/Users/yakshiortiz/picrust2/picrust2/place_seqs.py:85: in run_papara
    " -n out", print_out=print_cmds)
/Users/yakshiortiz/picrust2/picrust2/util.py:157: in system_call_check
    return_value = call(cmd, stdout=stdout, stderr=stderr)
/Users/yakshiortiz/miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:267: in call
    with Popen(*popenargs, **kwargs) as p:
/Users/yakshiortiz/miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:709: in __init__
    restore_signals, start_new_session)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <subprocess.Popen object at 0x1196fa898>
args = ['papara', '-t', '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.tre', '-s', 'ref_seqs.phylip', '-q', ...]
executable = b'papara', preexec_fn = None, close_fds = True, pass_fds = ()
cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False
p2cread = -1, p2cwrite = -1, c2pread = -1, c2pwrite = -1, errread = -1
errwrite = -1, restore_signals = True, start_new_session = False

    def _execute_child(self, args, executable, preexec_fn, close_fds,
                       pass_fds, cwd, env,
                       startupinfo, creationflags, shell,
                       p2cread, p2cwrite,
                       c2pread, c2pwrite,
                       errread, errwrite,
                       restore_signals, start_new_session):
        """Execute program (POSIX version)"""
    
        if isinstance(args, (str, bytes)):
            args = [args]
        else:
            args = list(args)
    
        if shell:
            args = ["/bin/sh", "-c"] + args
            if executable:
                args[0] = executable
    
        if executable is None:
            executable = args[0]
        orig_executable = executable
    
        # For transferring possible exec failure from child to parent.
        # Data format: "exception name:hex errno:description"
        # Pickle is not used; it is complex and involves memory allocation.
        errpipe_read, errpipe_write = os.pipe()
        # errpipe_write must not be in the standard io 0, 1, or 2 fd range.
        low_fds_to_close = []
        while errpipe_write < 3:
            low_fds_to_close.append(errpipe_write)
            errpipe_write = os.dup(errpipe_write)
        for low_fd in low_fds_to_close:
            os.close(low_fd)
        try:
            try:
                # We must avoid complex work that could involve
                # malloc or free in the child process to avoid
                # potential deadlocks, thus we do all this here.
                # and pass it to fork_exec()
    
                if env is not None:
                    env_list = []
                    for k, v in env.items():
                        k = os.fsencode(k)
                        if b'=' in k:
                            raise ValueError("illegal environment variable name")
                        env_list.append(k + b'=' + os.fsencode(v))
                else:
                    env_list = None  # Use execv instead of execve.
                executable = os.fsencode(executable)
                if os.path.dirname(executable):
                    executable_list = (executable,)
                else:
                    # This matches the behavior of os._execvpe().
                    executable_list = tuple(
                        os.path.join(os.fsencode(dir), executable)
                        for dir in os.get_exec_path(env))
                fds_to_keep = set(pass_fds)
                fds_to_keep.add(errpipe_write)
                self.pid = _posixsubprocess.fork_exec(
                        args, executable_list,
                        close_fds, tuple(sorted(map(int, fds_to_keep))),
                        cwd, env_list,
                        p2cread, p2cwrite, c2pread, c2pwrite,
                        errread, errwrite,
                        errpipe_read, errpipe_write,
                        restore_signals, start_new_session, preexec_fn)
                self._child_created = True
            finally:
                # be sure the FD is closed no matter what
                os.close(errpipe_write)
    
            # self._devnull is not always defined.
            devnull_fd = getattr(self, '_devnull', None)
            if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd:
                os.close(p2cread)
            if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd:
                os.close(c2pwrite)
            if errwrite != -1 and errread != -1 and errwrite != devnull_fd:
                os.close(errwrite)
            if devnull_fd is not None:
                os.close(devnull_fd)
            # Prevent a double close of these fds from __init__ on error.
            self._closed_child_pipe_fds = True
    
            # Wait for exec to fail or succeed; possibly raising an
            # exception (limited in size)
            errpipe_data = bytearray()
            while True:
                part = os.read(errpipe_read, 50000)
                errpipe_data += part
                if not part or len(errpipe_data) > 50000:
                    break
        finally:
            # be sure the FD is closed no matter what
            os.close(errpipe_read)
    
        if errpipe_data:
            try:
                pid, sts = os.waitpid(self.pid, 0)
                if pid == self.pid:
                    self._handle_exitstatus(sts)
                else:
                    self.returncode = sys.maxsize
            except ChildProcessError:
                pass
    
            try:
                exception_name, hex_errno, err_msg = (
                        errpipe_data.split(b':', 2))
                # The encoding here should match the encoding
                # written in by the subprocess implementations
                # like _posixsubprocess
                err_msg = err_msg.decode()
            except ValueError:
                exception_name = b'SubprocessError'
                hex_errno = b'0'
                err_msg = 'Bad exception data from child: {!r}'.format(
                              bytes(errpipe_data))
            child_exception_type = getattr(
                    builtins, exception_name.decode('ascii'),
                    SubprocessError)
            if issubclass(child_exception_type, OSError) and hex_errno:
                errno_num = int(hex_errno, 16)
                child_exec_never_called = (err_msg == "noexec")
                if child_exec_never_called:
                    err_msg = ""
                    # The error must be from chdir(cwd).
                    err_filename = cwd
                else:
                    err_filename = orig_executable
                if errno_num != 0:
                    err_msg = os.strerror(errno_num)
                    if errno_num == errno.ENOENT:
                        err_msg += ': ' + repr(err_filename)
>               raise child_exception_type(errno_num, err_msg, err_filename)
E               FileNotFoundError: [Errno 2] No such file or directory: 'papara': 'papara'

/Users/yakshiortiz/miniconda3/envs/picrust2-dev/lib/python3.6/subprocess.py:1344: FileNotFoundError
________________ place_seqs_tests.test_run_place_seqs_pipeline _________________

self = <tests.test_place_seqs.place_seqs_tests testMethod=test_run_place_seqs_pipeline>

    def test_run_place_seqs_pipeline(self):
        '''Basic test of full place seqs pipeline. As for EPA-NG, exact
            matches to a treefile are not checked since slight differences
            are expected depending on different versions.'''
    
        with TemporaryDirectory() as temp_dir:
            tmp_tree = path.join(temp_dir, "out.tre")
    
            place_seqs_pipeline(study_fasta=test_study_seqs,
                                ref_msa=test_msa,
                                tree=test_tree,
                                out_tree=tmp_tree,
                                threads=1,
                                papara_output=None,
                                out_dir=temp_dir,
                                chunk_size=5000,
>                               print_cmds=False)

/Users/yakshiortiz/picrust2/tests/test_place_seqs.py:153: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/Users/yakshiortiz/picrust2/picrust2/place_seqs.py:35: in place_seqs_pipeline
    threads=threads, print_cmds=print_cmds)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

tree = '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.tre'
ref_msa = {'2501846300_cluster': 'ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAGCGGAGCGGCGGACGGGTGAGTAATGCCTAGGA-ATCTGCCTGGTAGTGGGGGATA...CGTTCCCGGGCC-TGTACACACCGCCCGTCACACCATGGGAGTTTGTTGCACCAGAAGTA--TAC-CACGGTGTGGCCGATGACTGGGGTGAAGTCGTAACAAGGTAGCCGT', ...}
study_fasta = '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/study_seqs_test.fasta'
out_dir = '/var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpixi1dk16'
threads = 1, print_cmds = False

    def run_papara(tree: str, ref_msa: dict, study_fasta: str, out_dir: str,
                   threads=1, print_cmds=False):
        '''Run PaPaRa to place study sequences into reference multiple-sequence
        alignment (MSA). Will return dictionary of the the output MSA (sequence ids
        as keys). Expects path to tree and study FASTA as strings. Expects
        reference MSA as a dictionary output by read_fasta. This MSA will be
        converted to phylip format before running PaPaRa.'''
    
        # Get absolute paths to input files.
        tree = path.abspath(tree)
        study_fasta = path.abspath(study_fasta)
    
        # Change working directory to out directory (but keep track of original).
        # This is necessary because PaPaRa outputs into the current working
        # directory.
>       orig_wd = getcwd()
E       FileNotFoundError: [Errno 2] No such file or directory

/Users/yakshiortiz/picrust2/picrust2/place_seqs.py:76: FileNotFoundError
____________________ workflow_test.test_full_pipeline_biom _____________________

self = <tests.test_workflow.workflow_test testMethod=test_full_pipeline_biom>

    def test_full_pipeline_biom(self):
        '''Test that full pipeline can be run without error with
            BIOM sequence abundance table.'''
    
        with TemporaryDirectory() as temp_dir:
    
            out_tree = path.join(temp_dir, "out.tre")
    
            system_call_check("place_seqs.py -s " + test_study_seqs + " -r " +\
                              test_msa + " -t " + test_tree + " -o " +\
>                             out_tree)

/Users/yakshiortiz/picrust2/tests/test_workflow.py:97: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['place_seqs.py', '-s', '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/study_seqs_test.fasta', '-r', '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.fna', '-t', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           place_seqs.py -s /Users/yakshiortiz/picrust2/tests/test_data/place_seqs/study_seqs_test.fasta -r /Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.fna -t /Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.tre -o /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpuy2ivted/out.tre

/Users/yakshiortiz/picrust2/picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
Traceback (most recent call last):
  File "/Users/yakshiortiz/miniconda3/envs/picrust2-dev/bin/place_seqs.py", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/Users/yakshiortiz/picrust2/scripts/place_seqs.py", line 97, in <module>
    main()
  File "/Users/yakshiortiz/picrust2/scripts/place_seqs.py", line 93, in main
    print_cmds=args.print_cmds)
  File "/Users/yakshiortiz/picrust2/picrust2/place_seqs.py", line 35, in place_seqs_pipeline
    threads=threads, print_cmds=print_cmds)
  File "/Users/yakshiortiz/picrust2/picrust2/place_seqs.py", line 76, in run_papara
    orig_wd = getcwd()
FileNotFoundError: [Errno 2] No such file or directory
_____________________ workflow_test.test_full_pipeline_tsv _____________________

self = <tests.test_workflow.workflow_test testMethod=test_full_pipeline_tsv>

    def test_full_pipeline_tsv(self):
        '''Test that full pipeline can be run without error with
            TSV sequence abundance table.'''
    
        with TemporaryDirectory() as temp_dir:
    
            out_tree = path.join(temp_dir, "out.tre")
    
            system_call_check("place_seqs.py -s " + test_study_seqs + " -r " +\
                              test_msa + " -t " + test_tree + " -o " +\
>                             out_tree)

/Users/yakshiortiz/picrust2/tests/test_workflow.py:54: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

cmd = ['place_seqs.py', '-s', '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/study_seqs_test.fasta', '-r', '/Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.fna', '-t', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""
    
        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)
    
        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()
    
        return_value = call(cmd, stdout=stdout, stderr=stderr)
    
        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           place_seqs.py -s /Users/yakshiortiz/picrust2/tests/test_data/place_seqs/study_seqs_test.fasta -r /Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.fna -t /Users/yakshiortiz/picrust2/tests/test_data/place_seqs/img_centroid_16S_aligned_head30.tre -o /var/folders/_2/bs2w2q6n6n555b_bj3__xk300000gr/T/tmpzh3vt4vu/out.tre

/Users/yakshiortiz/picrust2/picrust2/util.py:161: SystemExit
----------------------------- Captured stderr call -----------------------------
shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
Traceback (most recent call last):
  File "/Users/yakshiortiz/miniconda3/envs/picrust2-dev/bin/place_seqs.py", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/Users/yakshiortiz/picrust2/scripts/place_seqs.py", line 97, in <module>
    main()
  File "/Users/yakshiortiz/picrust2/scripts/place_seqs.py", line 93, in main
    print_cmds=args.print_cmds)
  File "/Users/yakshiortiz/picrust2/picrust2/place_seqs.py", line 35, in place_seqs_pipeline
    threads=threads, print_cmds=print_cmds)
  File "/Users/yakshiortiz/picrust2/picrust2/place_seqs.py", line 76, in run_papara
    orig_wd = getcwd()
FileNotFoundError: [Errno 2] No such file or directory
===================== 13 failed, 15 passed in 7.44 seconds =====================

(picrust2) []$ conda list | grep numpy
numpy                     1.15.4           py36h7e9f1db_0  
numpy-base                1.15.4           py36hde5b4d6_0  

joblib.externals.loky.process_executor._RemoteTraceback: 
""" 
Traceback (most recent call last):
File "/data/apps/miniconda/envs/qiime2-2018.8/plugins/picrust2/picrust2/util.py", line 249, in make_output_dir
makedirs(dirpath)
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/os.py", line 241, in makedirs
mkdir(name, mode)
FileExistsError: [Errno 17] File exists: '/data/c.older/FIV_ging/picrust2_pipe_output_12042018_2/intermediate/pathways/minpath_running'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/joblib/externals/loky/process_executor.py", line 420, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/joblib/_parallel_backends.py", line 563, in call
return self.func(*args, **kwargs)
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/joblib/parallel.py", line 261, in call
for func, args, kwargs in self.items]
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/joblib/parallel.py", line 261, in <listcomp>
for func, args, kwargs in self.items]
File "/data/apps/miniconda/envs/qiime2-2018.8/plugins/picrust2/picrust2/run_minpath.py", line 744, in unstrat_minpath
print_opt, extra_str)
File "/data/apps/miniconda/envs/qiime2-2018.8/plugins/picrust2/picrust2/run_minpath.py", line 536, in minpath_wrapper
make_output_dir(path.join(out_dir, "minpath_running"))
File "/data/apps/miniconda/envs/qiime2-2018.8/plugins/picrust2/picrust2/util.py", line 253, in make_output_dir
raise IOError(err_str)
OSError: Could not create directory '%s'. Are permissions set correctly? Got error: '[Errno 17] File exists: '/data/c.older/FIV_ging/picrust2_pipe_output_12042018_2/intermediate/pathways/minpath_running''
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/data/apps/miniconda/envs/qiime2-2018.8/bin/picrust2_pipeline.py", line 7, in <module>
exec(compile(f.read(), file, 'exec'))
File "/data/apps/miniconda/envs/qiime2-2018.8/plugins/picrust2/scripts/picrust2_pipeline.py", line 227, in <module>
main()
File "/data/apps/miniconda/envs/qiime2-2018.8/plugins/picrust2/scripts/picrust2_pipeline.py", line 220, in main
verbose=args.verbose)
File "/data/apps/miniconda/envs/qiime2-2018.8/plugins/picrust2/picrust2/pipeline.py", line 227, in full_pipeline
print_cmds=verbose)
File "/data/apps/miniconda/envs/qiime2-2018.8/plugins/picrust2/picrust2/run_minpath.py", line 397, in run_minpath_pipeline
for sample_id in samples)
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/joblib/parallel.py", line 996, in call
self.retrieve()
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/joblib/parallel.py", line 899, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/joblib/_parallel_backends.py", line 517, in wrap_future_result
return future.result(timeout=timeout)
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/concurrent/futures/_base.py", line 398, in result
return self.__get_result()
File "/data/apps/miniconda/envs/qiime2-2018.8/lib/python3.5/concurrent/futures/_base.py", line 357, in __get_result
raise self._exception
OSError: Could not create directory '%s'. Are permissions set correctly? Got error: '[Errno 17] File exists: '/data/c.older/FIV_ging/picrust2_pipe_output_12042018_2/intermediate/pathways/minpath_running''

____________________________________ ERROR collecting tests/test_metagenome_pipeline.py____________________________________
tests/test_metagenome_pipeline.py:10: in <module>
   import biom
../.conda/envs/picrust2/lib/python3.6/site-packages/biom/__init__.py:51: in <module>
   from .table import Table
../.conda/envs/picrust2/lib/python3.6/site-packages/biom/table.py:200: in <module>
   from ._filter import _filter
__init__.pxd:861: in init biom._filter (biom/_filter.c:6729)
   ???
E   ValueError: numpy.ufunc has the wrong size, try recompiling. Expected 192, got 216
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

$ run_minpath.py -i OUT_PREFIX.genefamilies.biom -m /path/to/MinPath/data/ec2path -o Pathway_abundances.tsv --keep_tmp
  File "/home/ubuntu/MinPath/MinPath12hmp.py", line 74
    print "now get SEED"
                       ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print("now get SEED")?
Error running this command:
MinPath12hmp.py -any minpath_tmp_jam0tj_8/W0-PIS10005_minpath_in.txt -map /path/to/MinPath/data/ec2path -report minpath_tmp_jam0tj_8/W0-PIS10005_minpath_report.txt -details minpath_tmp_jam0tj_8/W0-PIS10005_minpath_details.txt -mps minpath_tmp_jam0tj_8/W0-PIS10005_minpath.mps

def test_full_pipeline_tsv(self):
    '''Test that full pipeline can be run without error with
    TSV sequence abundance table.'''

    with TemporaryDirectory() as temp_dir:

        out_tree = path.join(temp_dir, "out.tre")

        system_call_check("place_seqs.py -s " + test_study_seqs + " -r " +
                          test_msa + " -t " + test_tree + " --hmm " +

def _execute_child(self, args, executable, preexec_fn, close_fds,
                   pass_fds, cwd, env,
                   startupinfo, creationflags, shell,
                   p2cread, p2cwrite,
                   c2pread, c2pwrite,
                   errread, errwrite,
                   restore_signals, start_new_session):
    """Execute program (POSIX version)"""

    if isinstance(args, (str, bytes)):
        args = [args]
    else:
        args = list(args)

    if shell:
        args = ["/bin/sh", "-c"] + args
        if executable:
            args[0] = executable

    if executable is None:
        executable = args[0]
    orig_executable = executable

    # For transferring possible exec failure from child to parent.
    # Data format: "exception name:hex errno:description"
    # Pickle is not used; it is complex and involves memory allocation.
    errpipe_read, errpipe_write = os.pipe()
    # errpipe_write must not be in the standard io 0, 1, or 2 fd range.
    low_fds_to_close = []
    while errpipe_write < 3:
        low_fds_to_close.append(errpipe_write)
        errpipe_write = os.dup(errpipe_write)
    for low_fd in low_fds_to_close:
        os.close(low_fd)
    try:
        try:
            # We must avoid complex work that could involve
            # malloc or free in the child process to avoid
            # potential deadlocks, thus we do all this here.
            # and pass it to fork_exec()

            if env is not None:
                env_list = []
                for k, v in env.items():
                    k = os.fsencode(k)
                    if b'=' in k:
                        raise ValueError("illegal environment variable name")
                    env_list.append(k + b'=' + os.fsencode(v))
            else:
                env_list = None  # Use execv instead of execve.
            executable = os.fsencode(executable)
            if os.path.dirname(executable):
                executable_list = (executable,)
            else:
                # This matches the behavior of os._execvpe().
                executable_list = tuple(
                    os.path.join(os.fsencode(dir), executable)
                    for dir in os.get_exec_path(env))
            fds_to_keep = set(pass_fds)
            fds_to_keep.add(errpipe_write)
            self.pid = _posixsubprocess.fork_exec(
                    args, executable_list,
                    close_fds, tuple(sorted(map(int, fds_to_keep))),
                    cwd, env_list,
                    p2cread, p2cwrite, c2pread, c2pwrite,
                    errread, errwrite,
                    errpipe_read, errpipe_write,
                    restore_signals, start_new_session, preexec_fn)
            self._child_created = True
        finally:
            # be sure the FD is closed no matter what
            os.close(errpipe_write)

        # self._devnull is not always defined.
        devnull_fd = getattr(self, '_devnull', None)
        if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd:
            os.close(p2cread)
        if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd:
            os.close(c2pwrite)
        if errwrite != -1 and errread != -1 and errwrite != devnull_fd:
            os.close(errwrite)
        if devnull_fd is not None:
            os.close(devnull_fd)
        # Prevent a double close of these fds from __init__ on error.
        self._closed_child_pipe_fds = True

        # Wait for exec to fail or succeed; possibly raising an
        # exception (limited in size)
        errpipe_data = bytearray()
        while True:
            part = os.read(errpipe_read, 50000)
            errpipe_data += part
            if not part or len(errpipe_data) > 50000:
                break
    finally:
        # be sure the FD is closed no matter what
        os.close(errpipe_read)

    if errpipe_data:
        try:
            pid, sts = os.waitpid(self.pid, 0)
            if pid == self.pid:
                self._handle_exitstatus(sts)
            else:
                self.returncode = sys.maxsize
        except ChildProcessError:
            pass

        try:
            exception_name, hex_errno, err_msg = (
                    errpipe_data.split(b':', 2))
            # The encoding here should match the encoding
            # written in by the subprocess implementations
            # like _posixsubprocess
            err_msg = err_msg.decode()
        except ValueError:
            exception_name = b'SubprocessError'
            hex_errno = b'0'
            err_msg = 'Bad exception data from child: {!r}'.format(
                          bytes(errpipe_data))
        child_exception_type = getattr(
                builtins, exception_name.decode('ascii'),
                SubprocessError)
        if issubclass(child_exception_type, OSError) and hex_errno:
            errno_num = int(hex_errno, 16)
            child_exec_never_called = (err_msg == "noexec")
            if child_exec_never_called:
                err_msg = ""
                # The error must be from chdir(cwd).
                err_filename = cwd
            else:
                err_filename = orig_executable
            if errno_num != 0:
                err_msg = os.strerror(errno_num)
                if errno_num == errno.ENOENT:
                    err_msg += ': ' + repr(err_filename)

def test_picrust2_pipeline_script(self):
    '''Test that full pipeline can be run successfully with
    picrust2_pipeline.py'''

    with TemporaryDirectory() as temp_dir:

        out_dir = path.join(temp_dir, "pipeline_out")

        system_call_check("picrust2_pipeline.py -s " + test_study_seqs +
                          " -i " + test_seq_abun_tsv + " -o " + out_dir +
                          " -r " + test_msa + " -t " + test_tree +
                          " --hmm " + test_hmm +
                          " --custom_trait_tables " + test_known_traits +
                          " --marker_gene_table " + test_known_marker +

def _execute_child(self, args, executable, preexec_fn, close_fds,
                   pass_fds, cwd, env,
                   startupinfo, creationflags, shell,
                   p2cread, p2cwrite,
                   c2pread, c2pwrite,
                   errread, errwrite,
                   restore_signals, start_new_session):
    """Execute program (POSIX version)"""

    if isinstance(args, (str, bytes)):
        args = [args]
    else:
        args = list(args)

    if shell:
        args = ["/bin/sh", "-c"] + args
        if executable:
            args[0] = executable

    if executable is None:
        executable = args[0]
    orig_executable = executable

    # For transferring possible exec failure from child to parent.
    # Data format: "exception name:hex errno:description"
    # Pickle is not used; it is complex and involves memory allocation.
    errpipe_read, errpipe_write = os.pipe()
    # errpipe_write must not be in the standard io 0, 1, or 2 fd range.
    low_fds_to_close = []
    while errpipe_write < 3:
        low_fds_to_close.append(errpipe_write)
        errpipe_write = os.dup(errpipe_write)
    for low_fd in low_fds_to_close:
        os.close(low_fd)
    try:
        try:
            # We must avoid complex work that could involve
            # malloc or free in the child process to avoid
            # potential deadlocks, thus we do all this here.
            # and pass it to fork_exec()

            if env is not None:
                env_list = []
                for k, v in env.items():
                    k = os.fsencode(k)
                    if b'=' in k:
                        raise ValueError("illegal environment variable name")
                    env_list.append(k + b'=' + os.fsencode(v))
            else:
                env_list = None  # Use execv instead of execve.
            executable = os.fsencode(executable)
            if os.path.dirname(executable):
                executable_list = (executable,)
            else:
                # This matches the behavior of os._execvpe().
                executable_list = tuple(
                    os.path.join(os.fsencode(dir), executable)
                    for dir in os.get_exec_path(env))
            fds_to_keep = set(pass_fds)
            fds_to_keep.add(errpipe_write)
            self.pid = _posixsubprocess.fork_exec(
                    args, executable_list,
                    close_fds, tuple(sorted(map(int, fds_to_keep))),
                    cwd, env_list,
                    p2cread, p2cwrite, c2pread, c2pwrite,
                    errread, errwrite,
                    errpipe_read, errpipe_write,
                    restore_signals, start_new_session, preexec_fn)
            self._child_created = True
        finally:
            # be sure the FD is closed no matter what
            os.close(errpipe_write)

        # self._devnull is not always defined.
        devnull_fd = getattr(self, '_devnull', None)
        if p2cread != -1 and p2cwrite != -1 and p2cread != devnull_fd:
            os.close(p2cread)
        if c2pwrite != -1 and c2pread != -1 and c2pwrite != devnull_fd:
            os.close(c2pwrite)
        if errwrite != -1 and errread != -1 and errwrite != devnull_fd:
            os.close(errwrite)
        if devnull_fd is not None:
            os.close(devnull_fd)
        # Prevent a double close of these fds from __init__ on error.
        self._closed_child_pipe_fds = True

        # Wait for exec to fail or succeed; possibly raising an
        # exception (limited in size)
        errpipe_data = bytearray()
        while True:
            part = os.read(errpipe_read, 50000)
            errpipe_data += part
            if not part or len(errpipe_data) > 50000:
                break
    finally:
        # be sure the FD is closed no matter what
        os.close(errpipe_read)

    if errpipe_data:
        try:
            pid, sts = os.waitpid(self.pid, 0)
            if pid == self.pid:
                self._handle_exitstatus(sts)
            else:
                self.returncode = sys.maxsize
        except ChildProcessError:
            pass

        try:
            exception_name, hex_errno, err_msg = (
                    errpipe_data.split(b':', 2))
            # The encoding here should match the encoding
            # written in by the subprocess implementations
            # like _posixsubprocess
            err_msg = err_msg.decode()
        except ValueError:
            exception_name = b'SubprocessError'
            hex_errno = b'0'
            err_msg = 'Bad exception data from child: {!r}'.format(
                          bytes(errpipe_data))
        child_exception_type = getattr(
                builtins, exception_name.decode('ascii'),
                SubprocessError)
        if issubclass(child_exception_type, OSError) and hex_errno:
            errno_num = int(hex_errno, 16)
            child_exec_never_called = (err_msg == "noexec")
            if child_exec_never_called:
                err_msg = ""
                # The error must be from chdir(cwd).
                err_filename = cwd
            else:
                err_filename = orig_executable
            if errno_num != 0:
                err_msg = os.strerror(errno_num)
                if errno_num == errno.ENOENT:
                    err_msg += ': ' + repr(err_filename)

platform linux -- Python 3.6.5, pytest-3.6.0, py-1.5.3, pluggy-0.6.0
rootdir: /home/ubuntu/downloads/picrust2, inifile:
plugins: cov-2.5.1
collected 28 items

tests/test_hsp.py FFFFFFF                                                                                                       [ 25%]
tests/test_metagenome_pipeline.py .......                                                                                       [ 50%]
tests/test_place_seqs.py ......                                                                                                 [ 71%]
tests/test_run_minpath.py ..                                                                                                    [ 78%]
tests/test_util.py ....                                                                                                         [ 92%]
tests/test_workflow.py FF                                                                                                       [100%]

============================================================== FAILURES ===============================================================
___________________________________________ castor_hsp_workflow_tests.test_emp_prob_simple ____________________________________________

self = <tests.test_hsp.castor_hsp_workflow_tests testMethod=test_emp_prob_simple>

    def test_emp_prob_simple(self):

        predict_out, ci_out = castor_hsp_workflow(tree_path=in_tree1,
                                                 trait_table_path=in_traits1,
                                                 hsp_method="emp_prob",
>                                                ran_seed=10)

tests/test_hsp.py:73:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
picrust2/wrap_hsp.py:65: in castor_hsp_workflow
    for trait_in in file_subsets)
../../miniconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:779: in __call__
    while self.dispatch_one_batch(iterator):
../../miniconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:625: in dispatch_one_batch
    self._dispatch(tasks)
../../miniconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:588: in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
../../miniconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:111: in apply_async
    result = ImmediateResult(func)
../../miniconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py:332: in __init__
    self.results = batch()
../../miniconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:131: in __call__
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
../../miniconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py:131: in <listcomp>
    return [func(*args, **kwargs) for func, args, kwargs in self.items]
picrust2/wrap_hsp.py:126: in castor_hsp_wrapper
    system_call_check(hsp_cmd)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

cmd = ['Rscript', '/home/ubuntu/downloads/picrust2/picrust2/Rscripts/castor_hsp.R', '/home/ubuntu/downloads/picrust2/tests/test_data/hsp/tree.tre', '/tmp/tmpb3627unh/subset_tab_0', 'emp_prob', 'FALSE', ...]
print_out = False, stdout = None, stderr = None

    def system_call_check(cmd, print_out=False, stdout=None, stderr=None):
        """Run system command and throw and error if return is not 0. Input command
        can be a list containing the command or a string."""

        # Print command out if option set.
        if print_out:
            if type(cmd) is list:
                print(" ".join(cmd))
            else:
                print(cmd)

        # Convert command to list if input as string.
        if type(cmd) is str:
            cmd = cmd.split()

        return_value = call(cmd, stdout=stdout, stderr=stderr)

        # Exit with error if command did not finish successfully.
        if return_value != 0:
>           raise SystemExit("Error running this command:\n" + " ".join(cmd))
E           SystemExit: Error running this command:
E           Rscript /home/ubuntu/downloads/picrust2/picrust2/Rscripts/castor_hsp.R /home/ubuntu/downloads/picrust2/tests/test_data/hsp/tree.tre /tmp/tmpb3627unh/subset_tab_0 emp_prob FALSE FALSE /tmp/tmpaf7krjxy/predicted_counts.txt /tmp/tmpaf7krjxy/predicted_ci.txt 10

picrust2/util.py:161: SystemExit

in_tab_df = pd.concat(in_tab, axis=1)

humann2_combined = pd.concat(humann2_samples, axis=1)

new_tab = pd.concat([new_tab, in_table], axis=1)

Error running this command:
epa-ng --tree /strg1/users/apcamargo/PICRUSt2/picrust2-2.0.3-b/default_files/prokaryotic/reference.tre --ref-msa picrust2_out_pipeline/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query picrust2_out_pipeline/intermediate/place_seqs/epa_out/study_seqs_hmmalign.fasta.bfast --chunk-size 5000 -T 100 -m GTR+G -w picrust2_out_pipeline/intermediate/place_seqs/epa_out

$ metagenome_pipeline.py -i CHI4831_mothur_biom.reformated.full.json.biom -m CHI4831.picrust2.16S.tsv -f CHI4831.picrust2.KO.tsv -p 4 --strat_out -o CHI4831.picrust2.meta
Traceback (most recent call last):
  File "/home/z3382651/anaconda2/envs/picrust2-dev/bin/metagenome_pipeline.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/home/z3382651/bin/picrust2/scripts/metagenome_pipeline.py", line 102, in <module>
    main()
  File "/home/z3382651/bin/picrust2/scripts/metagenome_pipeline.py", line 88, in main
    output_normfile=True)
  File "/home/z3382651/bin/picrust2/picrust2/metagenome_pipeline.py", line 103, in run_metagenome_pipeline
    strat_out=strat_out))
  File "/home/z3382651/bin/picrust2/picrust2/metagenome_pipeline.py", line 174, in funcs_by_sample
    for sample in sample_ids)
  File "/home/z3382651/anaconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py", line 962, in __call__
    self.retrieve()
  File "/home/z3382651/anaconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/parallel.py", line 865, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/home/z3382651/anaconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 515, in wrap_future_result
    return future.result(timeout=timeout)
  File "/home/z3382651/anaconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/externals/loky/_base.py", line 431, in result
    return self.__get_result()
  File "/home/z3382651/anaconda2/envs/picrust2-dev/lib/python3.6/site-packages/joblib/externals/loky/_base.py", line 382, in __get_result
    raise self._exception
joblib.externals.loky.process_executor.BrokenProcessPool: A process in the executor was terminated abruptly while the future was running or pending.