diff --git a/bcbio/bam/__init__.py b/bcbio/bam/__init__.py
index 4b8bcd6bd..2d205421c 100644
--- a/bcbio/bam/__init__.py
+++ b/bcbio/bam/__init__.py
@@ -1,6 +1,5 @@
 """Functionality to query and extract information from aligned BAM files.
 """
-from __future__ import print_function
 import collections
 import os
 import signal
@@ -10,7 +9,7 @@
 import pybedtools
 import pysam
 import toolz as tz
-from six.moves import zip_longest
+from itertools import zip_longest
 
 from bcbio import broad, utils
 from bcbio.bam import ref
diff --git a/bcbio/bam/counts.py b/bcbio/bam/counts.py
index de9ebcbaf..823b1a30d 100644
--- a/bcbio/bam/counts.py
+++ b/bcbio/bam/counts.py
@@ -3,7 +3,6 @@
 These are useful for plotting comparisons between BAM files to look at
 differences in defined or random regions.
 """
-from __future__ import print_function
 import random
 import collections
 
diff --git a/bcbio/bam/coverage.py b/bcbio/bam/coverage.py
index d33de1eb7..700a1b853 100644
--- a/bcbio/bam/coverage.py
+++ b/bcbio/bam/coverage.py
@@ -3,7 +3,6 @@
 """
 import os
 
-import six
 import pandas as pd
 import pybedtools
 
@@ -121,9 +120,9 @@ def plot_multiple_regions_coverage(samples, out_file, data, region_bed=None, ste
         return out_file
     in_bams = [dd.get_align_bam(x) for x in samples]
     samplenames = [dd.get_sample_name(x) for x in samples]
-    if isinstance(region_bed, six.string_types):
+    if isinstance(region_bed, str):
         region_bed = pybedtools.BedTool(region_bed)
-    if isinstance(stem_bed, six.string_types):
+    if isinstance(stem_bed, str):
         stem_bed = pybedtools.BedTool(stem_bed)
     if stem_bed is not None:  # tabix indexed bedtools eval to false
         stem_bed = stem_bed.tabix()
diff --git a/bcbio/bam/fastq.py b/bcbio/bam/fastq.py
index 7205d7a7f..7637cfe8a 100644
--- a/bcbio/bam/fastq.py
+++ b/bcbio/bam/fastq.py
@@ -1,8 +1,6 @@
 """Utilities for working with fastq files.
 """
 
-import six
-from six.moves import zip
 from itertools import product
 import os
 import random
@@ -250,7 +248,7 @@ def downsample(f1, f2, N, quick=False):
     out_files = (outf1, outf2) if outf2 else (outf1)
 
     with file_transaction(out_files) as tx_out_files:
-        if isinstance(tx_out_files, six.string_types):
+        if isinstance(tx_out_files, str):
             tx_out_f1 = tx_out_files
         else:
             tx_out_f1, tx_out_f2 = tx_out_files
diff --git a/bcbio/chipseq/macs2.py b/bcbio/chipseq/macs2.py
index 167c1a2ad..c7ed94b93 100644
--- a/bcbio/chipseq/macs2.py
+++ b/bcbio/chipseq/macs2.py
@@ -1,7 +1,6 @@
 import os
 import glob
 import subprocess
-import sys
 
 from bcbio import utils
 from bcbio.provenance import do
diff --git a/bcbio/cwl/create.py b/bcbio/cwl/create.py
index 45e8ad033..5ead4372b 100644
--- a/bcbio/cwl/create.py
+++ b/bcbio/cwl/create.py
@@ -1,6 +1,5 @@
 """Create Common Workflow Language (CWL) runnable files and tools from a world object.
 """
-from __future__ import print_function
 import collections
 import copy
 import dateutil
@@ -12,7 +11,6 @@
 import tarfile
 
 import requests
-import six
 import toolz as tz
 import yaml
 
@@ -402,7 +400,7 @@ def _get_cur_remotes(path):
     elif isinstance(path, dict):
         for v in path.values():
             cur_remotes |= _get_cur_remotes(v)
-    elif path and isinstance(path, six.string_types):
+    elif path and isinstance(path, str):
         if path.startswith(tuple(INTEGRATION_MAP.keys())):
             cur_remotes.add(INTEGRATION_MAP.get(path.split(":")[0] + ":"))
     return cur_remotes
@@ -624,7 +622,7 @@ def _get_avro_type(val):
     elif val is None:
         return ["null"]
     # encode booleans as string True/False and unencode on other side
-    elif isinstance(val, bool) or isinstance(val, six.string_types) and val.lower() in ["true", "false", "none"]:
+    elif isinstance(val, bool) or isinstance(val, str) and val.lower() in ["true", "false", "none"]:
         return ["string", "null", "boolean"]
     elif isinstance(val, int):
         return "long"
@@ -747,7 +745,7 @@ def _item_to_cwldata(x, get_retriever, indexes=None):
     """
     if isinstance(x, (list, tuple)):
         return [_item_to_cwldata(subx, get_retriever) for subx in x]
-    elif (x and isinstance(x, six.string_types) and
+    elif (x and isinstance(x, str) and
           (((os.path.isfile(x) or os.path.isdir(x)) and os.path.exists(x)) or
            objectstore.is_remote(x))):
         if _file_local_or_remote(x, get_retriever):
diff --git a/bcbio/cwl/cwlutils.py b/bcbio/cwl/cwlutils.py
index a1319d375..a210be512 100644
--- a/bcbio/cwl/cwlutils.py
+++ b/bcbio/cwl/cwlutils.py
@@ -10,7 +10,6 @@
 import pprint
 import tarfile
 
-import six
 import toolz as tz
 
 from bcbio import bam, utils
@@ -58,7 +57,7 @@ def normalize_missing(xs):
             xs[k] = normalize_missing(v)
     elif isinstance(xs, (list, tuple)):
         xs = [normalize_missing(x) for x in xs]
-    elif isinstance(xs, six.string_types):
+    elif isinstance(xs, str):
         if xs.lower() in ["none", "null"]:
             xs = None
         elif xs.lower() == "true":
@@ -81,7 +80,7 @@ def unpack_tarballs(xs, data, use_subdir=True):
             xs[k] = unpack_tarballs(v, data, use_subdir)
     elif isinstance(xs, (list, tuple)):
         xs = [unpack_tarballs(x, data, use_subdir) for x in xs]
-    elif isinstance(xs, six.string_types):
+    elif isinstance(xs, str):
         if os.path.isfile(xs.encode("utf-8", "ignore")) and xs.endswith("-wf.tar.gz"):
             if use_subdir:
                 tarball_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "wf-inputs"))
diff --git a/bcbio/cwl/tool.py b/bcbio/cwl/tool.py
index 7c06f4c46..6e06f8f5e 100644
--- a/bcbio/cwl/tool.py
+++ b/bcbio/cwl/tool.py
@@ -3,7 +3,6 @@
 Handles wrapping and integrating with multiple tools making it easier
 to run bcbio in a standard way in many environments.
 """
-from __future__ import print_function
 import glob
 import json
 import os
diff --git a/bcbio/cwl/workflow.py b/bcbio/cwl/workflow.py
index e0cc08db3..0641244f6 100644
--- a/bcbio/cwl/workflow.py
+++ b/bcbio/cwl/workflow.py
@@ -3,7 +3,6 @@
 import copy
 import pprint
 
-import six
 import toolz as tz
 
 from bcbio.pipeline import alignment
@@ -234,7 +233,7 @@ def _flatten_nested_input(v):
         for x in v["type"]:
             if isinstance(x, dict) and x["type"] == "array":
                 new_type = x["items"]
-            elif isinstance(x, six.string_types) and x == "null":
+            elif isinstance(x, str) and x == "null":
                 want_null = True
             else:
                 new_type = x
@@ -272,7 +271,7 @@ def _clean_output(v):
     return out
 
 def _get_string_vid(vid):
-    if isinstance(vid, six.string_types):
+    if isinstance(vid, str):
         return vid
     assert isinstance(vid, (list, tuple)), vid
     return "__".join(vid)
@@ -280,7 +279,7 @@ def _get_string_vid(vid):
 def _get_variable(vid, variables):
     """Retrieve an input variable from our existing pool of options.
     """
-    if isinstance(vid, six.string_types):
+    if isinstance(vid, str):
         vid = get_base_id(vid)
     else:
         vid = _get_string_vid(vid)
@@ -426,7 +425,7 @@ def _create_variable(orig_v, step, variables):
         v = _get_variable(orig_v["id"], variables)
     except ValueError:
         v = copy.deepcopy(orig_v)
-        if not isinstance(v["id"], six.string_types):
+        if not isinstance(v["id"], str):
             v["id"] = _get_string_vid(v["id"])
     for key, val in orig_v.items():
         if key not in ["id", "type"]:
diff --git a/bcbio/distributed/objectstore.py b/bcbio/distributed/objectstore.py
index c7ad7385f..681b0dac5 100644
--- a/bcbio/distributed/objectstore.py
+++ b/bcbio/distributed/objectstore.py
@@ -13,7 +13,6 @@
 import time
 import zlib
 
-import six
 
 from bcbio.distributed.transaction import file_transaction
 from bcbio.provenance import do
@@ -23,8 +22,7 @@
 BIODATA_INFO = {"s3": "s3://biodata/prepped/{build}/{build}-{target}.tar.gz"}
 REGIONS_NEWPERMS = {"s3": ["eu-central-1"]}
 
-@six.add_metaclass(abc.ABCMeta)
-class FileHandle(object):
+class FileHandle(metaclass=abc.ABCMeta):
 
     """Contract class for the file handle."""
 
@@ -221,8 +219,7 @@ def close(self):
         pass
 
 
-@six.add_metaclass(abc.ABCMeta)
-class StorageManager(object):
+class StorageManager(metaclass=abc.ABCMeta):
 
     """The contract class for all the storage managers."""
 
diff --git a/bcbio/distributed/runfn.py b/bcbio/distributed/runfn.py
index 0345fad04..3becde412 100644
--- a/bcbio/distributed/runfn.py
+++ b/bcbio/distributed/runfn.py
@@ -10,7 +10,6 @@
 import pprint
 import shutil
 
-import six
 import toolz as tz
 import yaml
 
@@ -129,7 +128,7 @@ def _add_resources(data, runtime):
         data["config"] = {}
     # Convert input resources, which may be a JSON string
     resources = data.get("resources", {}) or {}
-    if isinstance(resources, six.string_types) and resources.startswith(("{", "[")):
+    if isinstance(resources, str) and resources.startswith(("{", "[")):
         resources = json.loads(resources)
         data["resources"] = resources
     assert isinstance(resources, dict), (resources, data)
@@ -561,7 +560,7 @@ def _file_and_exists(val, input_files):
 def _to_cwl(val, input_files):
     """Convert a value into CWL formatted JSON, handling files and complex things.
     """
-    if isinstance(val, six.string_types):
+    if isinstance(val, str):
         if _file_and_exists(val, input_files):
             val = {"class": "File", "path": val}
             secondary = []
diff --git a/bcbio/distributed/split.py b/bcbio/distributed/split.py
index 4ff878429..f985b5fd0 100644
--- a/bcbio/distributed/split.py
+++ b/bcbio/distributed/split.py
@@ -10,7 +10,6 @@
 """
 import collections
 
-import six
 
 from bcbio import utils
 
@@ -60,7 +59,7 @@ def parallel_split_combine(args, split_fn, parallel_fn,
     split_args, combine_map, finished_out, extras = _get_split_tasks(args, split_fn, file_key,
                                                                      split_outfile_i)
     split_output = parallel_fn(parallel_name, split_args)
-    if isinstance(combiner, six.string_types):
+    if isinstance(combiner, str):
         combine_args, final_args = _organize_output(split_output, combine_map,
                                                     file_key, combine_arg_keys)
         parallel_fn(combiner, combine_args)
diff --git a/bcbio/galaxy/api.py b/bcbio/galaxy/api.py
index 2a6b4dfcc..51a8e7daa 100644
--- a/bcbio/galaxy/api.py
+++ b/bcbio/galaxy/api.py
@@ -1,6 +1,7 @@
 """Access Galaxy NGLIMS functionality via the standard API.
 """
-from six.moves import urllib
+import urllib.parse
+import urllib.request
 import json
 import time
 
diff --git a/bcbio/galaxy/nglims.py b/bcbio/galaxy/nglims.py
index 50054d6aa..dd191f778 100644
--- a/bcbio/galaxy/nglims.py
+++ b/bcbio/galaxy/nglims.py
@@ -1,6 +1,5 @@
 """Integration with Galaxy nglims.
 """
-from __future__ import print_function
 import collections
 import copy
 import glob
@@ -9,7 +8,6 @@
 import subprocess
 
 import joblib
-import six
 import yaml
 
 from bcbio import utils
@@ -106,7 +104,7 @@ def _select_default_algorithm(analysis):
 def _relative_paths(xs, base_path):
     """Adjust paths to be relative to the provided base path.
     """
-    if isinstance(xs, six.string_types):
+    if isinstance(xs, str):
         if xs.startswith(base_path):
             return xs.replace(base_path + "/", "", 1)
         else:
diff --git a/bcbio/graph/graph.py b/bcbio/graph/graph.py
index 487b4e4b2..8ad0eaab5 100644
--- a/bcbio/graph/graph.py
+++ b/bcbio/graph/graph.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 
 from datetime import datetime
 import collections
diff --git a/bcbio/heterogeneity/__init__.py b/bcbio/heterogeneity/__init__.py
index 27763252d..6f6cec7e4 100644
--- a/bcbio/heterogeneity/__init__.py
+++ b/bcbio/heterogeneity/__init__.py
@@ -5,7 +5,6 @@
 to infer these sub-clones to help improve variant calls and interpretation
 especially in complex cancer samples.
 """
-from __future__ import print_function
 import collections
 import os
 
diff --git a/bcbio/heterogeneity/bubbletree.py b/bcbio/heterogeneity/bubbletree.py
index 516074957..426db3edf 100644
--- a/bcbio/heterogeneity/bubbletree.py
+++ b/bcbio/heterogeneity/bubbletree.py
@@ -3,7 +3,6 @@
 http://www.bioconductor.org/packages/release/bioc/html/BubbleTree.html
 http://www.bioconductor.org/packages/release/bioc/vignettes/BubbleTree/inst/doc/BubbleTree-vignette.html
 """
-from __future__ import print_function
 import collections
 import csv
 import os
diff --git a/bcbio/heterogeneity/loh.py b/bcbio/heterogeneity/loh.py
index 99c2f92cc..17ce7ee31 100644
--- a/bcbio/heterogeneity/loh.py
+++ b/bcbio/heterogeneity/loh.py
@@ -9,8 +9,7 @@
 import uuid
 
 import pandas as pd
-import six
-from six import StringIO
+from io import StringIO
 import toolz as tz
 import yaml
 
@@ -59,7 +58,7 @@ def _matches(tocheck, target):
 def _civic_regions(civic_file, variant_types=None, diseases=None, drugs=None):
     """Retrieve gene regions and names filtered by variant_types and diseases.
     """
-    if isinstance(diseases, six.string_types):
+    if isinstance(diseases, str):
         diseases = [diseases]
     with utils.open_gzipsafe(civic_file) as in_handle:
         reader = csv.reader(in_handle, delimiter="\t")
@@ -369,7 +368,7 @@ def __read_token(self):
                     cp = c
                     c = self.__read_fd(1)
                 e = c
-                v = unicode(''.join(buf).decode('unicode-escape'))
+                v = str(''.join(buf).decode('unicode-escape'))
 
             elif t == "datetime":
                 ## skip "inst"
@@ -377,7 +376,7 @@ def __read_token(self):
 
                 ## read next value as string
                 s = self.__read_token()
-                if not isinstance(s, six.string_types):
+                if not isinstance(s, str):
                     raise ValueError('Str expected, but got %s' % str(s))
 
                 ## remove read string from the value_stack
@@ -392,7 +391,7 @@ def __read_token(self):
 
                 ## read next value as string
                 s = self.__read_token()
-                if not isinstance(s, six.string_types):
+                if not isinstance(s, str):
                     raise ValueError('Str expected, but got %s' % str(s))
 
                 ## remove read string from the value_stack
diff --git a/bcbio/heterogeneity/phylowgs.py b/bcbio/heterogeneity/phylowgs.py
index f1d9b7621..c8b41893b 100644
--- a/bcbio/heterogeneity/phylowgs.py
+++ b/bcbio/heterogeneity/phylowgs.py
@@ -6,7 +6,6 @@
 https://github.com/morrislab/phylowgs
 http://genomebiology.com/2015/16/1/35
 """
-from __future__ import print_function
 import collections
 import os
 import sys
diff --git a/bcbio/hla/optitype.py b/bcbio/hla/optitype.py
index ae8a9168a..7aeb42c62 100644
--- a/bcbio/hla/optitype.py
+++ b/bcbio/hla/optitype.py
@@ -6,7 +6,6 @@
 import glob
 import os
 import re
-import sys
 import shutil
 
 import toolz as tz
diff --git a/bcbio/hmmer/search.py b/bcbio/hmmer/search.py
index 74934be0c..7ddd1cada 100644
--- a/bcbio/hmmer/search.py
+++ b/bcbio/hmmer/search.py
@@ -6,8 +6,8 @@
 
 https://github.com/nickloman/entrezajax
 """
-from __future__ import print_function
-from six.moves import urllib
+import urllib.parse
+import urllib.request
 import logging
 
 class SmartRedirectHandler(urllib.request.HTTPRedirectHandler):
diff --git a/bcbio/illumina/flowcell.py b/bcbio/illumina/flowcell.py
index 3ae07712d..a090cc93a 100644
--- a/bcbio/illumina/flowcell.py
+++ b/bcbio/illumina/flowcell.py
@@ -2,7 +2,9 @@
 """
 import os
 import glob
-from six.moves import urllib, http_cookiejar
+import urllib.parse
+import urllib.request
+import http.cookiejar
 import json
 
 def parse_dirname(fc_dir):
@@ -59,7 +61,7 @@ class GalaxySqnLimsApi:
     def __init__(self, base_url, user, passwd):
         self._base_url = base_url
         # build cookies so we keep track of being logged in
-        cj = http_cookiejar.LWPCookieJar()
+        cj = http.cookiejar.LWPCookieJar()
         opener = urllib.request.build_opener(urllib.request.HTTPCookieProcessor(cj))
         urllib.request.install_opener(opener)
         login = dict(email=user, password=passwd, login_button='Login')
diff --git a/bcbio/illumina/machine.py b/bcbio/illumina/machine.py
index e373ba815..7368cca82 100644
--- a/bcbio/illumina/machine.py
+++ b/bcbio/illumina/machine.py
@@ -1,6 +1,5 @@
 """Support integration with Illumina sequencer machines.
 """
-from __future__ import print_function
 import glob
 import json
 import os
diff --git a/bcbio/install.py b/bcbio/install.py
index d969c5a17..cf7b1fcbf 100644
--- a/bcbio/install.py
+++ b/bcbio/install.py
@@ -3,7 +3,6 @@
 Enables automated installation tool and in-place updates to install additional
 data and software.
 """
-from __future__ import print_function
 import argparse
 import collections
 import contextlib
@@ -17,9 +16,8 @@
 import subprocess
 import sys
 import glob
+import urllib.request
 
-import six
-from six.moves import urllib
 import toolz as tz
 import yaml
 
diff --git a/bcbio/ngsalign/alignprep.py b/bcbio/ngsalign/alignprep.py
index 38a7a530e..2349055e9 100644
--- a/bcbio/ngsalign/alignprep.py
+++ b/bcbio/ngsalign/alignprep.py
@@ -7,7 +7,6 @@
 import shutil
 import subprocess
 
-import six
 import toolz as tz
 
 from bcbio import bam, utils
@@ -664,7 +663,7 @@ def _bgzip_file(finput, config, work_dir, needs_bgzip, needs_gunzip, needs_conve
 
     Handles cases where finput might be multiple files and need to be concatenated.
     """
-    if isinstance(finput, six.string_types):
+    if isinstance(finput, str):
         in_file = finput
     else:
         assert not needs_convert, "Do not yet handle quality conversion with multiple inputs"
diff --git a/bcbio/ngsalign/novoalign.py b/bcbio/ngsalign/novoalign.py
index de6062aca..00a62f8fc 100644
--- a/bcbio/ngsalign/novoalign.py
+++ b/bcbio/ngsalign/novoalign.py
@@ -15,7 +15,6 @@
 from bcbio.distributed.transaction import tx_tmpdir
 from bcbio.utils import (memoize_outfile, file_exists)
 
-import six
 
 
 # ## BAM realignment
@@ -100,7 +99,7 @@ def _novoalign_args_from_config(config, need_quality=True):
     multi_mappers = config["algorithm"].get("multiple_mappers")
     if multi_mappers is True:
         multi_flag = "Random"
-    elif isinstance(multi_mappers, six.string_types):
+    elif isinstance(multi_mappers, str):
         multi_flag = multi_mappers
     else:
         multi_flag = "None"
diff --git a/bcbio/ngsalign/postalign.py b/bcbio/ngsalign/postalign.py
index 92ff828db..60b8e74ff 100644
--- a/bcbio/ngsalign/postalign.py
+++ b/bcbio/ngsalign/postalign.py
@@ -21,7 +21,6 @@
 from bcbio.provenance import do
 from bcbio.variation import coverage
 
-import six
 
 
 pysam = utils.LazyImport("pysam")
@@ -310,7 +309,7 @@ def _check_dedup(data):
         dup_param = utils.get_in(data, ("config", "algorithm", "mark_duplicates"), False)
     else:
         dup_param = utils.get_in(data, ("config", "algorithm", "mark_duplicates"), True)
-    if dup_param and isinstance(dup_param, six.string_types):
+    if dup_param and isinstance(dup_param, str):
         logger.info("Warning: bcbio no longer support explicit setting of mark_duplicate algorithm. "
                     "Using best-practice choice based on input data.")
         dup_param = True
diff --git a/bcbio/pipeline/config_utils.py b/bcbio/pipeline/config_utils.py
index be648f7d9..ecc49f39d 100644
--- a/bcbio/pipeline/config_utils.py
+++ b/bcbio/pipeline/config_utils.py
@@ -11,7 +11,6 @@
 
 import toolz as tz
 
-import six
 
 
 class CmdNotFound(Exception):
@@ -218,7 +217,7 @@ def wrap(name, pconfig, config, default):
                 return apath
             if is_ok(os.path.join(adir, program)):
                 return os.path.join(adir, program)
-        raise CmdNotFound(" ".join(map(repr, (fn.__name__ if six.PY3 else fn.func_name, name, pconfig, default))))
+        raise CmdNotFound(" ".join(map(repr, (fn.__name__, name, pconfig, default))))
     return wrap
 
 @_get_check_program_cmd
@@ -227,7 +226,7 @@ def _get_program_cmd(name, pconfig, config, default):
     """
     if pconfig is None:
         return name
-    elif isinstance(pconfig, six.string_types):
+    elif isinstance(pconfig, str):
         return pconfig
     elif "cmd" in pconfig:
         return pconfig["cmd"]
@@ -241,7 +240,7 @@ def _get_program_dir(name, config):
     """
     if config is None:
         raise ValueError("Could not find directory in config for %s" % name)
-    elif isinstance(config, six.string_types):
+    elif isinstance(config, str):
         return config
     elif "dir" in config:
         return expand_path(config["dir"])
@@ -430,7 +429,7 @@ def use_vqsr(algs, call_file=None):
     coverage_intervals = set([])
     for alg in algs:
         callers = alg.get("variantcaller")
-        if isinstance(callers, six.string_types):
+        if isinstance(callers, str):
             callers = [callers]
         if not callers:  # no variant calling, no VQSR
             continue
diff --git a/bcbio/pipeline/disambiguate/__init__.py b/bcbio/pipeline/disambiguate/__init__.py
index 0b835e9e5..506205ba0 100644
--- a/bcbio/pipeline/disambiguate/__init__.py
+++ b/bcbio/pipeline/disambiguate/__init__.py
@@ -8,7 +8,6 @@
 bcbio-nextgen: https://github.com/mjafin/disambiguate
 """
 
-from __future__ import print_function
 import collections
 import copy
 import os
@@ -22,7 +21,6 @@
 from bcbio import bam
 
 
-import six
 
 
 def split(*items):
@@ -37,7 +35,7 @@ def split(*items):
                                         "base": True}
             out.append([data])
             # handle the instance where a single organism is disambiguated
-            if isinstance(dis_orgs, six.string_types):
+            if isinstance(dis_orgs, str):
                 dis_orgs = [dis_orgs]
             for dis_org in dis_orgs:
                 dis_data = copy.deepcopy(data)
diff --git a/bcbio/pipeline/disambiguate/run.py b/bcbio/pipeline/disambiguate/run.py
index f7a802e57..c5222cf46 100644
--- a/bcbio/pipeline/disambiguate/run.py
+++ b/bcbio/pipeline/disambiguate/run.py
@@ -25,7 +25,6 @@
 """
 
 
-from __future__ import print_function
 import sys, re, pysam
 from array import array
 from os import path, makedirs
diff --git a/bcbio/pipeline/genome.py b/bcbio/pipeline/genome.py
index c8d5584dc..19b0af25f 100644
--- a/bcbio/pipeline/genome.py
+++ b/bcbio/pipeline/genome.py
@@ -1,12 +1,10 @@
 """Read genome build configurations from Galaxy *.loc and bcbio-nextgen resource files.
 """
-from six.moves import configparser
+import configparser
 import glob
 import os
-import sys
 from xml.etree import ElementTree
 
-import six
 import toolz as tz
 import yaml
 
@@ -35,7 +33,7 @@ def get_resources(genome, ref_file, data):
         resources = yaml.safe_load(in_handle)
 
     def resource_file_path(x):
-        if isinstance(x, six.string_types) and os.path.exists(os.path.join(base_dir, x)):
+        if isinstance(x, str) and os.path.exists(os.path.join(base_dir, x)):
             return os.path.normpath(os.path.join(base_dir, x))
         return x
     cleaned = utils.dictapply(resources, resource_file_path)
@@ -88,7 +86,7 @@ def abs_file_paths(xs, base_dir=None, ignore_keys=None, fileonly_keys=None, cur_
     if isinstance(xs, dict):
         out = {}
         for k, v in xs.items():
-            if k not in ignore_keys and v and isinstance(v, six.string_types):
+            if k not in ignore_keys and v and isinstance(v, str):
                 if v.lower() == "none":
                     out[k] = None
                 else:
@@ -98,7 +96,7 @@ def abs_file_paths(xs, base_dir=None, ignore_keys=None, fileonly_keys=None, cur_
                           for x in v]
             else:
                 out[k] = v
-    elif isinstance(xs, six.string_types):
+    elif isinstance(xs, str):
         if os.path.exists(xs) or (do_download and objectstore.is_remote(xs)):
             dl = objectstore.download(xs, input_dir)
             if dl and cur_key not in ignore_keys and not (cur_key in fileonly_keys and not os.path.isfile(dl)):
diff --git a/bcbio/pipeline/main.py b/bcbio/pipeline/main.py
index d821333fb..047694294 100644
--- a/bcbio/pipeline/main.py
+++ b/bcbio/pipeline/main.py
@@ -2,7 +2,6 @@
 
 Handles running the full pipeline based on instructions
 """
-from __future__ import print_function
 from collections import defaultdict
 import copy
 import os
diff --git a/bcbio/pipeline/qcsummary.py b/bcbio/pipeline/qcsummary.py
index 19fb28eea..ed55c7a2d 100644
--- a/bcbio/pipeline/qcsummary.py
+++ b/bcbio/pipeline/qcsummary.py
@@ -3,6 +3,7 @@
 import collections
 import copy
 import csv
+import json
 import os
 
 import yaml
@@ -22,7 +23,6 @@
 from bcbio.rnaseq import gtf
 from bcbio.variation import damage, peddy, vcfutils, vcfanno
 
-import six
 
 
 # ## High level functions to generate summary
@@ -187,7 +187,7 @@ def _run_qc_tools(bam_file, data):
             # Check for files only output
             if "base" in out:
                 qc_files = out
-        elif out and isinstance(out, six.string_types) and os.path.exists(out):
+        elif out and isinstance(out, str) and os.path.exists(out):
             qc_files = {"base": out, "secondary": []}
         if not qc_files:
             qc_files = _organize_qc_files(program_name, cur_qc_dir)
@@ -315,7 +315,7 @@ def _merge_metadata(samples):
     sample_metrics = collections.defaultdict(dict)
     for s in samples:
         m = tz.get_in(['metadata'], s)
-        if isinstance(m, six.string_types):
+        if isinstance(m, str):
             m = json.loads(m)
         if m:
             for me in list(m.keys()):
diff --git a/bcbio/pipeline/region.py b/bcbio/pipeline/region.py
index 6bb27a568..a99035335 100644
--- a/bcbio/pipeline/region.py
+++ b/bcbio/pipeline/region.py
@@ -6,7 +6,6 @@
 import collections
 import os
 
-import six
 import toolz as tz
 
 from bcbio import utils
@@ -20,7 +19,7 @@ def get_max_counts(samples):
     for data in (x[0] for x in samples):
         count = tz.get_in(["config", "algorithm", "callable_count"], data, 1)
         vcs = tz.get_in(["config", "algorithm", "variantcaller"], data, [])
-        if isinstance(vcs, six.string_types):
+        if isinstance(vcs, str):
             vcs = [vcs]
         if vcs:
             count *= len(vcs)
diff --git a/bcbio/pipeline/run_info.py b/bcbio/pipeline/run_info.py
index d29b9185b..4fde2f68a 100644
--- a/bcbio/pipeline/run_info.py
+++ b/bcbio/pipeline/run_info.py
@@ -13,7 +13,6 @@
 import string
 import sys
 
-import six
 import toolz as tz
 import yaml
 from bcbio import install, utils, structural
@@ -70,7 +69,7 @@ def organize(dirs, config, run_info_yaml, sample_names=None, is_cwl=False,
         item["dirs"] = dirs
         if "name" not in item:
             item["name"] = ["", item["description"]]
-        elif isinstance(item["name"], six.string_types):
+        elif isinstance(item["name"], str):
             description = "%s-%s" % (item["name"], clean_name(item["description"]))
             item["name"] = [item["name"], description]
             item["description"] = description
@@ -346,11 +345,11 @@ def _clean_algorithm(data):
     for key in ["variantcaller", "jointcaller", "svcaller"]:
         val = tz.get_in(["algorithm", key], data)
         if val:
-            if not isinstance(val, (list, tuple)) and isinstance(val, six.string_types):
+            if not isinstance(val, (list, tuple)) and isinstance(val, str):
                 val = [val]
             # check for cases like [false] or [None]
             if isinstance(val, (list, tuple)):
-                if len(val) == 1 and not val[0] or (isinstance(val[0], six.string_types)
+                if len(val) == 1 and not val[0] or (isinstance(val[0], str)
                                                     and val[0].lower() in ["none", "false"]):
                     val = False
             data["algorithm"][key] = val
@@ -381,12 +380,12 @@ def _clean_background(data):
     if val:
         out = {}
         # old style specification, single string for variant
-        if isinstance(val, six.string_types):
+        if isinstance(val, str):
             out["variant"] = _file_to_abs(val, [os.getcwd()])
         elif isinstance(val, dict):
             for k, v in val.items():
                 if k in allowed_keys:
-                    if isinstance(v, six.string_types):
+                    if isinstance(v, str):
                         out[k] = _file_to_abs(v, [os.getcwd()])
                     else:
                         assert isinstance(v, dict)
@@ -408,7 +407,7 @@ def _clean_background(data):
 def _clean_characters(x):
     """Clean problem characters in sample lane or descriptions.
     """
-    if not isinstance(x, six.string_types):
+    if not isinstance(x, str):
         x = str(x)
     else:
         if not all(ord(char) < 128 for char in x):
@@ -822,9 +821,9 @@ def _file_to_abs(x, dnames, makedir=False):
     """
     if x is None or os.path.isabs(x):
         return x
-    elif isinstance(x, six.string_types) and objectstore.is_remote(x):
+    elif isinstance(x, str) and objectstore.is_remote(x):
         return x
-    elif isinstance(x, six.string_types) and x.lower() == "none":
+    elif isinstance(x, str) and x.lower() == "none":
         return None
     else:
         for dname in dnames:
@@ -843,7 +842,7 @@ def _normalize_files(item, fc_dir=None):
     """
     files = item.get("files")
     if files:
-        if isinstance(files, six.string_types):
+        if isinstance(files, str):
             files = [files]
         fastq_dir = flowcell.get_fastq_dir(fc_dir) if fc_dir else os.getcwd()
         files = [_file_to_abs(x, [os.getcwd(), fc_dir, fastq_dir]) for x in files]
@@ -961,7 +960,7 @@ def _run_info_from_yaml(dirs, run_info_yaml, config, sample_names=None,
         if "upload" not in item and not is_cwl:
             upload = global_config.get("upload", {})
             # Handle specifying a local directory directly in upload
-            if isinstance(upload, six.string_types):
+            if isinstance(upload, str):
                 upload = {"dir": upload}
             if not upload:
                 upload["dir"] = "../final"
@@ -987,7 +986,7 @@ def _run_info_from_yaml(dirs, run_info_yaml, config, sample_names=None,
                              for f in item["files"]]
         elif "files" in item:
             del item["files"]
-        if item.get("vrn_file") and isinstance(item["vrn_file"], six.string_types):
+        if item.get("vrn_file") and isinstance(item["vrn_file"], str):
             item["vrn_file"] = genome.abs_file_paths(item["vrn_file"],
                                                      do_download=all(not x for x in integrations.values()))
             if os.path.isfile(item["vrn_file"]):
@@ -1113,7 +1112,7 @@ def _add_algorithm_defaults(algorithm, analysis, is_cwl):
             elif v is None:
                 algorithm[k] = []
         elif k in convert_to_single:
-            if v and not isinstance(v, six.string_types):
+            if v and not isinstance(v, str):
                 if isinstance(v, (list, tuple)) and len(v) == 1:
                     algorithm[k] = v[0]
                 else:
@@ -1132,7 +1131,7 @@ def _replace_global_vars(xs, global_vars):
     elif isinstance(xs, dict):
         final = {}
         for k, v in xs.items():
-            if isinstance(v, six.string_types) and v in global_vars:
+            if isinstance(v, str) and v in global_vars:
                 v = global_vars[v]
             final[k] = v
         return final
diff --git a/bcbio/pipeline/shared.py b/bcbio/pipeline/shared.py
index b8497475f..05b321e07 100644
--- a/bcbio/pipeline/shared.py
+++ b/bcbio/pipeline/shared.py
@@ -8,7 +8,6 @@
 
 import pybedtools
 import pysam
-import six
 import toolz as tz
 
 from bcbio import bam, broad, utils
@@ -251,7 +250,7 @@ def remove_exclude_regions(f):
     @functools.wraps(f)
     def wrapper(variant_regions, region, out_file, items=None, do_merge=True, data=None):
         region_bed = f(variant_regions, region, out_file, items, do_merge, data)
-        if region_bed and isinstance(region_bed, six.string_types) and os.path.exists(region_bed) and items:
+        if region_bed and isinstance(region_bed, str) and os.path.exists(region_bed) and items:
             for e in get_exclude_regions(items):
                 if e in exclude_fns:
                     region_bed = exclude_fns[e](region_bed, items)
diff --git a/bcbio/provenance/do.py b/bcbio/provenance/do.py
index 8f90877e1..5fa15f72b 100644
--- a/bcbio/provenance/do.py
+++ b/bcbio/provenance/do.py
@@ -10,7 +10,6 @@
 from bcbio.provenance import diagnostics
 
 
-import six
 
 
 def run(cmd, descr=None, data=None, checks=None, region=None, log_error=True,
@@ -22,7 +21,7 @@ def run(cmd, descr=None, data=None, checks=None, region=None, log_error=True,
       logger.debug(descr)
     cmd_id = diagnostics.start_cmd(cmd, descr or "", data)
     try:
-        logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, six.string_types) else cmd)
+        logger_cl.debug(" ".join(str(x) for x in cmd) if not isinstance(cmd, str) else cmd)
         _do_run(cmd, checks, log_stdout, env=env)
     except:
         diagnostics.end_cmd(cmd_id, False)
@@ -62,7 +61,7 @@ def _normalize_cmd_args(cmd):
     Piped commands set pipefail and require use of bash to help with debugging
     intermediate errors.
     """
-    if isinstance(cmd, six.string_types):
+    if isinstance(cmd, str):
         # check for standard or anonymous named pipes
         if cmd.find(" | ") > 0 or cmd.find(">(") or cmd.find("<("):
             return "set -o pipefail; " + cmd, True, find_bash()
@@ -98,7 +97,7 @@ def _do_run(cmd, checks, log_stdout=False, env=None):
             for line in s.stdout:
                 debug_stdout.append(line.decode("utf-8", errors="replace"))
             if exitcode is not None and exitcode != 0:
-                error_msg = " ".join(cmd) if not isinstance(cmd, six.string_types) else cmd
+                error_msg = " ".join(cmd) if not isinstance(cmd, str) else cmd
                 error_msg += "\n"
                 error_msg += "".join(debug_stdout)
                 s.communicate()
diff --git a/bcbio/provenance/programs.py b/bcbio/provenance/programs.py
index e9166a890..87cb9e9c0 100644
--- a/bcbio/provenance/programs.py
+++ b/bcbio/provenance/programs.py
@@ -3,7 +3,6 @@
 Catalogs the full list of programs used in analysis, enabling reproduction of
 results and tracking of provenance in output files.
 """
-from __future__ import print_function
 import os
 import contextlib
 import subprocess
diff --git a/bcbio/qc/contamination.py b/bcbio/qc/contamination.py
index 6604cdbe8..025c0f65c 100644
--- a/bcbio/qc/contamination.py
+++ b/bcbio/qc/contamination.py
@@ -3,7 +3,6 @@
 import os
 import shutil
 import subprocess
-import sys
 
 from bcbio import utils
 from bcbio.log import logger
diff --git a/bcbio/qc/multiqc.py b/bcbio/qc/multiqc.py
index 3a8e847eb..d10db8400 100644
--- a/bcbio/qc/multiqc.py
+++ b/bcbio/qc/multiqc.py
@@ -14,7 +14,6 @@
 from collections import OrderedDict
 
 import pybedtools
-import six
 import toolz as tz
 import yaml
 
@@ -242,7 +241,7 @@ def _get_input_files(samples, base_dir, tx_out_dir):
         sum_qc = tz.get_in(["summary", "qc"], data, {})
         if sum_qc in [None, "None"]:
             sum_qc = {}
-        elif isinstance(sum_qc, six.string_types):
+        elif isinstance(sum_qc, str):
             sum_qc = {dd.get_algorithm_qc(data)[0]: sum_qc}
         elif not isinstance(sum_qc, dict):
             raise ValueError("Unexpected summary qc: %s" % sum_qc)
@@ -250,7 +249,7 @@ def _get_input_files(samples, base_dir, tx_out_dir):
             if isinstance(pfiles, dict):
                 pfiles = [pfiles["base"]] + pfiles.get("secondary", [])
             # CWL: presents output files as single file plus associated secondary files
-            elif isinstance(pfiles, six.string_types):
+            elif isinstance(pfiles, str):
                 if os.path.exists(pfiles):
                     pfiles = [os.path.join(basedir, f) for basedir, subdir, filenames in os.walk(os.path.dirname(pfiles)) for f in filenames]
                 else:
@@ -477,7 +476,7 @@ def _merge_metrics(samples, out_dir):
         s = _add_disambiguate(s)
         s = _add_atac(s)
         m = tz.get_in(['summary', 'metrics'], s)
-        if isinstance(m, six.string_types):
+        if isinstance(m, str):
             m = json.loads(m)
         if m:
             for me in list(m.keys()):
diff --git a/bcbio/qc/srna.py b/bcbio/qc/srna.py
index 2798aa935..a15b9973b 100644
--- a/bcbio/qc/srna.py
+++ b/bcbio/qc/srna.py
@@ -1,7 +1,6 @@
 """
 Create log files to be parsed by multiqc
 """
-from __future__ import print_function
 
 import os
 import pandas as pd
diff --git a/bcbio/qc/variant.py b/bcbio/qc/variant.py
index 76f699173..aab7883ac 100644
--- a/bcbio/qc/variant.py
+++ b/bcbio/qc/variant.py
@@ -6,7 +6,6 @@
 import os
 import shutil
 
-import six
 import toolz as tz
 
 from bcbio import utils
@@ -101,10 +100,10 @@ def _get_variants(data):
             variants = variants["samples"]
         for v in variants:
             # CWL -- a single variant file
-            if isinstance(v, six.string_types) and os.path.exists(v):
+            if isinstance(v, str) and os.path.exists(v):
                 active_vs.append(_add_filename_details(v))
             elif (isinstance(v, (list, tuple)) and len(v) > 0 and
-                  isinstance(v[0], six.string_types) and os.path.exists(v[0])):
+                  isinstance(v[0], str) and os.path.exists(v[0])):
                 for subv in v:
                     active_vs.append(_add_filename_details(subv))
             elif isinstance(v, dict):
diff --git a/bcbio/rnaseq/bcbiornaseq.py b/bcbio/rnaseq/bcbiornaseq.py
index 1c1711c85..fc37f7343 100644
--- a/bcbio/rnaseq/bcbiornaseq.py
+++ b/bcbio/rnaseq/bcbiornaseq.py
@@ -10,7 +10,6 @@
 from pathlib import Path
 from bcbio.log import logger
 
-import six
 
 
 def make_bcbiornaseq_object(data):
@@ -185,7 +184,7 @@ def _quotestring(string, double=True):
 
 def _list2Rlist(xs):
     """ convert a python list to an R list """
-    if isinstance(xs, six.string_types):
+    if isinstance(xs, str):
         xs = [xs]
     rlist = ",".join([_quotestring(x) for x in xs])
     return "c(" + rlist + ")"
diff --git a/bcbio/rnaseq/dexseq.py b/bcbio/rnaseq/dexseq.py
index c3a2a4ef6..f65ac80d9 100644
--- a/bcbio/rnaseq/dexseq.py
+++ b/bcbio/rnaseq/dexseq.py
@@ -1,7 +1,6 @@
 """
 perform exon-level counting using DEXSeq
 """
-import sys
 import os
 from bcbio.utils import R_sitelib, file_exists, safe_makedir, which
 from bcbio.distributed.transaction import file_transaction
diff --git a/bcbio/rnaseq/oncofuse.py b/bcbio/rnaseq/oncofuse.py
index 888524c02..a9193ab03 100644
--- a/bcbio/rnaseq/oncofuse.py
+++ b/bcbio/rnaseq/oncofuse.py
@@ -4,7 +4,6 @@
   oncofuse: http://www.unav.es/genetica/oncofuse.html
   github: https://github.com/mikessh/oncofuse
 """
-from __future__ import print_function
 import os
 import pysam
 import toolz as tz
diff --git a/bcbio/rnaseq/pizzly.py b/bcbio/rnaseq/pizzly.py
index a4ce32a0e..ee5e83b79 100644
--- a/bcbio/rnaseq/pizzly.py
+++ b/bcbio/rnaseq/pizzly.py
@@ -3,7 +3,6 @@
 https://github.com/pmelsted/pizzly
 http://www.biorxiv.org/content/early/2017/07/20/166322
 """
-from __future__ import print_function
 
 import os
 
diff --git a/bcbio/rnaseq/singlecellexperiment.py b/bcbio/rnaseq/singlecellexperiment.py
index 10ee19760..743b4d654 100644
--- a/bcbio/rnaseq/singlecellexperiment.py
+++ b/bcbio/rnaseq/singlecellexperiment.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 
 import os
 import subprocess
diff --git a/bcbio/rnaseq/umi.py b/bcbio/rnaseq/umi.py
index d7a53ea93..d1b1322b8 100644
--- a/bcbio/rnaseq/umi.py
+++ b/bcbio/rnaseq/umi.py
@@ -24,7 +24,6 @@
 from bcbio.log import logger
 from bcbio.rnaseq import gtf
 
-import six
 
 
 class SparseMatrix(object):
@@ -207,7 +206,7 @@ def filter_barcodes(data):
     bc2 = None
     bc3 = None
     umi_dir = os.path.join(dd.get_work_dir(data), "umis")
-    if isinstance(bc, six.string_types):
+    if isinstance(bc, str):
         bc1 = bc
     if len(bc) == 1:
         bc1 = bc[0]
diff --git a/bcbio/server/background.py b/bcbio/server/background.py
index ce96e7650..a0069f305 100644
--- a/bcbio/server/background.py
+++ b/bcbio/server/background.py
@@ -6,7 +6,6 @@
 
 Copyright (c) 2012, Vukasin Toroman <vukasin@toroman.name>
 """
-from __future__ import print_function
 import subprocess
 import tornado.ioloop
 import time
diff --git a/bcbio/server/run.py b/bcbio/server/run.py
index 3424f2d63..69f65121c 100644
--- a/bcbio/server/run.py
+++ b/bcbio/server/run.py
@@ -4,8 +4,7 @@
 import os
 import sys
 import uuid
-
-from six import StringIO
+from io import StringIO
 
 import tornado.gen
 import tornado.web
diff --git a/bcbio/setpath.py b/bcbio/setpath.py
index fa72d2ae8..c1a1dd7b0 100644
--- a/bcbio/setpath.py
+++ b/bcbio/setpath.py
@@ -1,7 +1,6 @@
 """Update the PATH environment variable to reflect the value of BCBIOPATH.
 
 """
-from __future__ import print_function
 import contextlib
 import os
 
diff --git a/bcbio/srna/mirge.py b/bcbio/srna/mirge.py
index db96a7690..d36f81c9d 100644
--- a/bcbio/srna/mirge.py
+++ b/bcbio/srna/mirge.py
@@ -1,6 +1,5 @@
 """Run mirge tool"""
 import os
-import sys
 import shutil
 import glob
 from bcbio.distributed.transaction import tx_tmpdir
diff --git a/bcbio/structural/__init__.py b/bcbio/structural/__init__.py
index 579d80def..92a8eb57e 100644
--- a/bcbio/structural/__init__.py
+++ b/bcbio/structural/__init__.py
@@ -16,7 +16,6 @@
 from bcbio.variation import validate as vcvalidate
 from bcbio.variation import vcfutils
 
-import six
 from functools import reduce
 
 
@@ -58,7 +57,7 @@ def get_svcallers(data):
     svs = data["config"]["algorithm"].get("svcaller")
     if svs is None:
         svs = []
-    elif isinstance(svs, six.string_types):
+    elif isinstance(svs, str):
         svs = [svs]
     return svs
 
@@ -193,7 +192,7 @@ def _batch_split_by_sv(samples, stage):
                 svcaller = tz.get_in(["config", "algorithm", "svcaller"], x)
                 batch = dd.get_batch(x) or dd.get_sample_name(x)
                 if stage in ["ensemble"]:  # no batching for ensemble methods
-                    if isinstance(batch, six.string_types) and batch != dd.get_sample_name(x):
+                    if isinstance(batch, str) and batch != dd.get_sample_name(x):
                         batch += "_%s" % dd.get_sample_name(x)
                     else:
                         batch = dd.get_sample_name(x)
@@ -375,7 +374,7 @@ def standardize_cnv_reference(data):
     """
     out = tz.get_in(["config", "algorithm", "background", "cnv_reference"], data, {})
     cur_callers = set(data["config"]["algorithm"].get("svcaller")) & _CNV_REFERENCE
-    if isinstance(out, six.string_types):
+    if isinstance(out, str):
         if not len(cur_callers) == 1:
             raise ValueError("Multiple CNV callers and single background reference for %s: %s" %
                                 data["description"], list(cur_callers))
diff --git a/bcbio/structural/lumpy.py b/bcbio/structural/lumpy.py
index d2f7c9d16..4146c3ae1 100644
--- a/bcbio/structural/lumpy.py
+++ b/bcbio/structural/lumpy.py
@@ -9,7 +9,6 @@
 import re
 import subprocess
 
-import six
 import vcf
 
 from bcbio import utils
@@ -95,10 +94,7 @@ def _prepare_smoove_bams(full_bams, sr_bams, disc_bams, items, tx_work_dir):
     return out
 
 def _allowed_errors(msg):
-    if six.PY3:
-        msg = str(msg)
-    else:
-        msg = unicode(msg).encode("ascii", "replace")
+    msg = str(msg)
     allowed = ["covmed: not enough reads to sample for bam stats",
                "missing pair end parameters:",
                "mean stdev read_length min_non_overlap"]
diff --git a/bcbio/structural/metasv.py b/bcbio/structural/metasv.py
index 94bd080fc..0f5f7d300 100644
--- a/bcbio/structural/metasv.py
+++ b/bcbio/structural/metasv.py
@@ -4,7 +4,6 @@
 http://dx.doi.org/10.1093/bioinformatics/btv204
 """
 import os
-import sys
 
 from bcbio import utils
 from bcbio.provenance import do
diff --git a/bcbio/structural/pindel.py b/bcbio/structural/pindel.py
index c587762a5..be18b8256 100644
--- a/bcbio/structural/pindel.py
+++ b/bcbio/structural/pindel.py
@@ -3,9 +3,7 @@
 http://gmt.genome.wustl.edu/packages/pindel/
 """
 
-from __future__ import print_function
 import os
-import six
 import time
 import shutil
 from bcbio import bam, utils, broad
@@ -15,7 +13,6 @@
 from bcbio.variation.vcfutils import bgzip_and_index, get_paired_bams
 from bcbio.variation import annotation
 from bcbio.provenance import do
-from six.moves import zip
 
 def _pindel_options(items, config, out_file, region, tmp_path):
     """parse pindel options. Add region to cmd.
@@ -29,7 +26,7 @@ def _pindel_options(items, config, out_file, region, tmp_path):
     target = subset_variant_regions(variant_regions, region, out_file, items)
     opts = ""
     if target:
-        if isinstance(target, six.string_types) and os.path.isfile(target):
+        if isinstance(target, str) and os.path.isfile(target):
             target_bed = target
         else:
             target_bed = os.path.join(tmp_path, "tmp.bed")
diff --git a/bcbio/structural/validate.py b/bcbio/structural/validate.py
index 585640601..72bb96027 100644
--- a/bcbio/structural/validate.py
+++ b/bcbio/structural/validate.py
@@ -3,7 +3,6 @@
 import csv
 import os
 
-import six
 import toolz as tz
 import numpy as np
 import pandas as pd
@@ -384,7 +383,7 @@ def evaluate(data):
             summary_plots = _plot_evaluation(df_csv)
             data["sv-validate"] = {"csv": val_summary, "plot": summary_plots, "df": df_csv}
         else:
-            assert isinstance(truth_sets, six.string_types) and utils.file_exists(truth_sets), truth_sets
+            assert isinstance(truth_sets, str) and utils.file_exists(truth_sets), truth_sets
             val_summary = _evaluate_vcf(data["sv"], truth_sets, work_dir, data)
             title = "%s structural variants" % dd.get_sample_name(data)
             summary_plots = validateplot.classifyplot_from_valfile(val_summary, outtype="png", title=title)
diff --git a/bcbio/upload/__init__.py b/bcbio/upload/__init__.py
index 05d4002c5..3151813fc 100644
--- a/bcbio/upload/__init__.py
+++ b/bcbio/upload/__init__.py
@@ -3,7 +3,6 @@
 import datetime
 import os
 
-import six
 import toolz as tz
 
 from bcbio import log, utils
@@ -157,7 +156,7 @@ def _add_meta(xs, sample=None, config=None):
     """
     out = []
     for x in xs:
-        if not isinstance(x["path"], six.string_types) or not os.path.exists(x["path"]):
+        if not isinstance(x["path"], str) or not os.path.exists(x["path"]):
             raise ValueError("Unexpected path for upload: %s" % x)
         x["mtime"] = shared.get_file_timestamp(x["path"])
         if sample:
diff --git a/bcbio/upload/galaxy.py b/bcbio/upload/galaxy.py
index 88947125a..e3e1e57eb 100644
--- a/bcbio/upload/galaxy.py
+++ b/bcbio/upload/galaxy.py
@@ -3,7 +3,6 @@
 Required configurable variables in upload:
   dir
 """
-from __future__ import print_function
 import collections
 import os
 import shutil
diff --git a/bcbio/utils.py b/bcbio/utils.py
index 3927019ec..2b7a61970 100644
--- a/bcbio/utils.py
+++ b/bcbio/utils.py
@@ -1,5 +1,7 @@
 """Helpful utilities for building analysis pipelines.
 """
+
+import configparser
 import glob
 import gzip
 import os
@@ -15,7 +17,6 @@
 import sys
 import types
 
-import six
 import toolz as tz
 import yaml
 
@@ -284,7 +285,7 @@ def read_galaxy_amqp_config(galaxy_config, base_dir):
     """Read connection information on the RabbitMQ server from Galaxy config.
     """
     galaxy_config = add_full_path(galaxy_config, base_dir)
-    config = six.moves.configparser.ConfigParser()
+    config = configparser.ConfigParser()
     config.read(galaxy_config)
     amqp_config = {}
     for option in config.options("galaxy_amqp"):
@@ -379,15 +380,9 @@ def symlink_plus(orig, new):
 
 def open_gzipsafe(f, is_gz=False):
     if f.endswith(".gz") or is_gz:
-        if six.PY3:
-            return gzip.open(f, "rt", encoding="utf-8", errors="ignore")
-        else:
-            return gzip.open(f)
+        return gzip.open(f, "rt", encoding="utf-8", errors="ignore")
     else:
-        if six.PY3:
-            return open(f, encoding="utf-8", errors="ignore")
-        else:
-            return open(f)
+        return open(f, encoding="utf-8", errors="ignore")
 
 def is_empty_gzipsafe(f):
     h = open_gzipsafe(f)
@@ -467,8 +462,8 @@ def partition(pred, iterable, tolist=False):
     'Use a predicate to partition entries into false entries and true entries'
     # partition(is_odd, range(10)) --> 0 2 4 6 8   and  1 3 5 7 9
     t1, t2 = itertools.tee(iterable)
-    ifalse = six.moves.filterfalse(pred, t1)
-    itrue = six.moves.filter(pred, t2)
+    ifalse = itertools.filterfalse(pred, t1)
+    itrue = filter(pred, t2)
     if tolist:
         return list(ifalse), list(itrue)
     else:
@@ -572,7 +567,7 @@ def is_pair(arg):
     return is_sequence(arg) and len(arg) == 2
 
 def is_string(arg):
-    return isinstance(arg, six.string_types)
+    return isinstance(arg, str)
 
 
 def locate(pattern, root=os.curdir):
diff --git a/bcbio/variation/cortex.py b/bcbio/variation/cortex.py
index 4ec546b7e..1dfb68227 100644
--- a/bcbio/variation/cortex.py
+++ b/bcbio/variation/cortex.py
@@ -7,7 +7,6 @@
 
 http://cortexassembler.sourceforge.net/index_cortex_var.html
 """
-from __future__ import print_function
 import os
 import glob
 import subprocess
diff --git a/bcbio/variation/effects.py b/bcbio/variation/effects.py
index f20ed2831..446bde14e 100644
--- a/bcbio/variation/effects.py
+++ b/bcbio/variation/effects.py
@@ -10,7 +10,6 @@
 import subprocess
 import string
 
-import six
 import toolz as tz
 import yaml
 
@@ -330,7 +329,7 @@ def get_db(data):
     snpeff_base_dir = None
     if snpeff_db:
         snpeff_base_dir = utils.get_in(data, ("reference", "snpeff"))
-        if not (isinstance(snpeff_base_dir, six.string_types) and os.path.isdir(snpeff_base_dir)):
+        if not (isinstance(snpeff_base_dir, str) and os.path.isdir(snpeff_base_dir)):
             snpeff_base_dir = utils.get_in(data, ("reference", "snpeff", snpeff_db))
         if not snpeff_base_dir:
             # We need to mask '.' characters for CWL/WDL processing, check for them here
@@ -339,9 +338,9 @@ def get_db(data):
                 snpeff_db = snpeff_db.replace("_", ".")
         if isinstance(snpeff_base_dir, dict) and snpeff_base_dir.get("base"):
             snpeff_base_dir = snpeff_base_dir["base"]
-        if (snpeff_base_dir and isinstance(snpeff_base_dir, six.string_types) and os.path.isfile(snpeff_base_dir)):
+        if (snpeff_base_dir and isinstance(snpeff_base_dir, str) and os.path.isfile(snpeff_base_dir)):
             snpeff_base_dir = os.path.dirname(snpeff_base_dir)
-        if (snpeff_base_dir and isinstance(snpeff_base_dir, six.string_types)
+        if (snpeff_base_dir and isinstance(snpeff_base_dir, str)
               and snpeff_base_dir.endswith("%s%s" % (os.path.sep, snpeff_db))):
             snpeff_base_dir = os.path.dirname(snpeff_base_dir)
         if not snpeff_base_dir:
diff --git a/bcbio/variation/freebayes.py b/bcbio/variation/freebayes.py
index 0b8d3c525..5b44497f8 100644
--- a/bcbio/variation/freebayes.py
+++ b/bcbio/variation/freebayes.py
@@ -6,7 +6,6 @@
 import os
 import sys
 
-import six
 import toolz as tz
 
 from bcbio import utils
@@ -51,7 +50,7 @@ def _freebayes_options_from_config(items, config, out_file, region=None):
     no_target_regions = False
     target = shared.subset_variant_regions(variant_regions, region, out_file, items)
     if target:
-        if isinstance(target, six.string_types) and os.path.isfile(target):
+        if isinstance(target, str) and os.path.isfile(target):
             if os.path.getsize(target) == 0:
                 no_target_regions = True
             else:
diff --git a/bcbio/variation/gatkfilter.py b/bcbio/variation/gatkfilter.py
index d9e1dcf6d..456c8a61e 100644
--- a/bcbio/variation/gatkfilter.py
+++ b/bcbio/variation/gatkfilter.py
@@ -2,6 +2,7 @@
 """
 import os
 import gzip
+import sys
 from distutils.version import LooseVersion
 
 from bcbio import broad, utils
diff --git a/bcbio/variation/genotype.py b/bcbio/variation/genotype.py
index 877372be5..f84e5e7cf 100644
--- a/bcbio/variation/genotype.py
+++ b/bcbio/variation/genotype.py
@@ -5,7 +5,6 @@
 import copy
 import pprint
 
-import six
 import toolz as tz
 
 from bcbio import bam, utils
@@ -294,7 +293,7 @@ def handle_multiple_callers(data, key, default=None, require_bam=True):
     """Split samples that potentially require multiple variant calling approaches.
     """
     callers = get_variantcaller(data, key, default, require_bam=require_bam)
-    if isinstance(callers, six.string_types):
+    if isinstance(callers, str):
         return [data]
     elif not callers:
         return []
@@ -309,7 +308,7 @@ def handle_multiple_callers(data, key, default=None, require_bam=True):
             # if splitting by variant caller, also split by jointcaller
             if key == "variantcaller":
                 jcallers = get_variantcaller(data, "jointcaller", [])
-                if isinstance(jcallers, six.string_types):
+                if isinstance(jcallers, str):
                     jcallers = [jcallers]
                 if jcallers:
                     base["config"]["algorithm"]["orig_jointcaller"] = jcallers
diff --git a/bcbio/variation/octopus.py b/bcbio/variation/octopus.py
index 1c602297a..a82aaa40e 100644
--- a/bcbio/variation/octopus.py
+++ b/bcbio/variation/octopus.py
@@ -6,7 +6,6 @@
 import subprocess
 
 import pysam
-import six
 
 from bcbio import utils
 from bcbio.distributed.transaction import file_transaction
@@ -33,7 +32,7 @@ def _get_regions(region, out_file, items):
     vrs = bedutils.population_variant_regions(items)
     target = shared.subset_variant_regions(vrs, region, out_file, items=items, do_merge=True)
     if target:
-        if isinstance(target, six.string_types) and os.path.isfile(target):
+        if isinstance(target, str) and os.path.isfile(target):
             return "--regions-file %s" % target
         else:
             return "--regions %s" % bamprep.region_to_gatk(target)
diff --git a/bcbio/variation/platypus.py b/bcbio/variation/platypus.py
index ec157c53d..0d474a1a1 100644
--- a/bcbio/variation/platypus.py
+++ b/bcbio/variation/platypus.py
@@ -13,7 +13,6 @@
 from bcbio.provenance import do
 from bcbio.variation import bamprep, bedutils, vcfutils
 
-import six
 
 
 def run(align_bams, items, ref_file, assoc_files, region, out_file):
@@ -66,7 +65,7 @@ def _subset_regions(region, base_file, items):
     """
     variant_regions = bedutils.population_variant_regions(items, merged=True)
     target = pshared.subset_variant_regions(variant_regions, region, base_file, items)
-    if isinstance(target, six.string_types) and os.path.isfile(target):
+    if isinstance(target, str) and os.path.isfile(target):
         return target
     else:
         return bamprep.region_to_gatk(target)
diff --git a/bcbio/variation/qsnp.py b/bcbio/variation/qsnp.py
index 84cb45cf5..b58b576cb 100644
--- a/bcbio/variation/qsnp.py
+++ b/bcbio/variation/qsnp.py
@@ -3,7 +3,6 @@
 https://qcmg.org/bioinformatics/tiki-index.php?page=qSNP#EXAMPLES
 """
 
-from __future__ import print_function
 import os
 import shutil
 from re import sub
@@ -16,7 +15,6 @@
 from bcbio.variation import annotation, bedutils
 from bcbio.variation.vcfutils import get_paired_bams, bgzip_and_index, combine_variant_files, PairedData
 
-import six
 
 
 def is_installed(config):
@@ -87,7 +85,7 @@ def _clean_regions(items, region):
     with utils.tmpfile() as tx_out_file:
         target = subset_variant_regions(variant_regions, region, tx_out_file, items)
         if target:
-            if isinstance(target, six.string_types) and os.path.isfile(target):
+            if isinstance(target, str) and os.path.isfile(target):
                 target = _load_regions(target)
             else:
                 target = [target]
diff --git a/bcbio/variation/realign.py b/bcbio/variation/realign.py
index 391d0baf3..300d0d01b 100644
--- a/bcbio/variation/realign.py
+++ b/bcbio/variation/realign.py
@@ -7,7 +7,6 @@
 from bcbio.distributed.transaction import file_transaction
 from bcbio.pipeline.shared import subset_variant_regions
 
-import six
 
 
 # ## GATK realignment
@@ -79,14 +78,14 @@ def has_aligned_reads(align_bam, region=None):
     """
     import pybedtools
     if region is not None:
-        if isinstance(region, six.string_types) and os.path.isfile(region):
+        if isinstance(region, str) and os.path.isfile(region):
             regions = [tuple(r) for r in pybedtools.BedTool(region)]
         else:
             regions = [region]
     with pysam.Samfile(align_bam, "rb") as cur_bam:
         if region is not None:
             for region in regions:
-                if isinstance(region, six.string_types):
+                if isinstance(region, str):
                     for item in cur_bam.fetch(str(region)):
                         return True
                 else:
diff --git a/bcbio/variation/samtools.py b/bcbio/variation/samtools.py
index 2a72d5b0f..2677593fa 100644
--- a/bcbio/variation/samtools.py
+++ b/bcbio/variation/samtools.py
@@ -13,7 +13,6 @@
 from bcbio.provenance import do, programs
 from bcbio.variation import annotation, bamprep, bedutils, vcfutils
 
-import six
 
 
 def shared_variantcall(call_fn, name, align_bams, ref_file, items,
@@ -31,7 +30,7 @@ def shared_variantcall(call_fn, name, align_bams, ref_file, items,
               name=name, region=region, fname=os.path.basename(align_bams[0])))
         variant_regions = bedutils.population_variant_regions(items, merged=True)
         target_regions = subset_variant_regions(variant_regions, region, out_file, items=items)
-        if (variant_regions is not None and isinstance(target_regions, six.string_types)
+        if (variant_regions is not None and isinstance(target_regions, str)
               and not os.path.isfile(target_regions)):
             vcfutils.write_empty_vcf(out_file, config)
         else:
diff --git a/bcbio/variation/scalpel.py b/bcbio/variation/scalpel.py
index 6a9221678..3dd9dc6ab 100644
--- a/bcbio/variation/scalpel.py
+++ b/bcbio/variation/scalpel.py
@@ -3,7 +3,6 @@
 https://sourceforge.net/p/scalpel/code/ci/master/tree/
 """
 
-from __future__ import print_function
 import os
 import shutil
 
@@ -20,14 +19,13 @@
 from bcbio.variation import annotation, bedutils, vcfutils
 from bcbio.variation.vcfutils import get_paired_bams, is_paired_analysis, bgzip_and_index
 
-import six
 
 
 def _scalpel_bed_file_opts(items, config, out_file, region, tmp_path):
     variant_regions = bedutils.population_variant_regions(items)
     target = shared.subset_variant_regions(variant_regions, region, out_file, items)
     if target:
-        if isinstance(target, six.string_types) and os.path.isfile(target):
+        if isinstance(target, str) and os.path.isfile(target):
             target_bed = target
         else:
             target_bed = os.path.join(tmp_path, "tmp.bed")
diff --git a/bcbio/variation/sentieon.py b/bcbio/variation/sentieon.py
index 373cf2615..e0985688c 100644
--- a/bcbio/variation/sentieon.py
+++ b/bcbio/variation/sentieon.py
@@ -19,7 +19,6 @@
 from bcbio.provenance import do
 from bcbio.variation import bamprep, bedutils, joint, vcfutils
 
-import six
 
 
 def license_export(data):
@@ -34,7 +33,7 @@ def license_export(data):
                          "environmental variables to export \n"
                          "http://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html#resources\n"
                          "Configuration: %s" % pprint.pformat(data))
-    if isinstance(server, six.string_types):
+    if isinstance(server, str):
         return "export SENTIEON_LICENSE=%s && " % server
     else:
         assert isinstance(server, dict), server
@@ -50,7 +49,7 @@ def _get_interval(variant_regions, region, out_file, items):
     """
     target = shared.subset_variant_regions(variant_regions, region, out_file, items)
     if target:
-        if isinstance(target, six.string_types) and os.path.isfile(target):
+        if isinstance(target, str) and os.path.isfile(target):
             return "--interval %s" % target
         else:
             return "--interval %s" % bamprep.region_to_gatk(target)
diff --git a/bcbio/variation/strelka2.py b/bcbio/variation/strelka2.py
index 801809077..1af40f139 100644
--- a/bcbio/variation/strelka2.py
+++ b/bcbio/variation/strelka2.py
@@ -2,7 +2,6 @@
 """
 import collections
 import os
-import six
 import sys
 import numpy as np
 
@@ -40,7 +39,7 @@ def get_region_bed(region, items, out_file, want_gzip=True):
     target = shared.subset_variant_regions(variant_regions, region, out_file, items)
     if not target:
         raise ValueError("Need BED input for strelka2 regions: %s %s" % (region, target))
-    if not isinstance(target, six.string_types) or not os.path.isfile(target):
+    if not isinstance(target, str) or not os.path.isfile(target):
         chrom, start, end = target
         target = "%s-regions.bed" % utils.splitext_plus(out_file)[0]
         with file_transaction(items[0], target) as tx_out_file:
diff --git a/bcbio/variation/validate.py b/bcbio/variation/validate.py
index 682f95af4..1f4db2d9f 100644
--- a/bcbio/variation/validate.py
+++ b/bcbio/variation/validate.py
@@ -14,7 +14,6 @@
 import time
 
 from pysam import VariantFile
-import six
 import toolz as tz
 import yaml
 
@@ -548,7 +547,7 @@ def _group_validate_samples(samples, vkey, batch_keys):
         if is_v:
             for batch_key in batch_keys:
                 vname = tz.get_in(batch_key, data)
-                if vname and not (isinstance(vname, six.string_types) and vname.lower() in ["none", "false"]):
+                if vname and not (isinstance(vname, str) and vname.lower() in ["none", "false"]):
                     break
             if isinstance(vname, (list, tuple)):
                 vname = vname[0]
diff --git a/bcbio/variation/vardict.py b/bcbio/variation/vardict.py
index a5509be9d..41bdcb3b6 100644
--- a/bcbio/variation/vardict.py
+++ b/bcbio/variation/vardict.py
@@ -11,14 +11,12 @@
 
 specify 'vardict-perl'.
 """
-from decimal import *
+from decimal import Decimal
 
 from distutils.version import LooseVersion
 import os
 import sys
-from six.moves import zip
 
-import six
 import toolz as tz
 import pybedtools
 
@@ -31,7 +29,7 @@
 from bcbio.variation import bamprep, bedutils, vcfutils
 
 def _is_bed_file(target):
-    return target and isinstance(target, six.string_types) and os.path.isfile(target)
+    return target and isinstance(target, str) and os.path.isfile(target)
 
 def _vardict_options_from_config(items, config, out_file, target=None, is_rnaseq=False):
     var2vcf_opts = []
diff --git a/bcbio/variation/vcfanno.py b/bcbio/variation/vcfanno.py
index 4d792bc2e..e2280c953 100644
--- a/bcbio/variation/vcfanno.py
+++ b/bcbio/variation/vcfanno.py
@@ -2,7 +2,6 @@
 """
 import os
 
-import six
 import toolz as tz
 
 from bcbio import utils
@@ -79,7 +78,7 @@ def _find_file(xs, target):
                 f = _find_file(x, target)
                 if f:
                     return f
-        elif isinstance(xs, six.string_types) and os.path.exists(xs) and xs.endswith("/%s" % target):
+        elif isinstance(xs, str) and os.path.exists(xs) and xs.endswith("/%s" % target):
             return xs
     orig_file = line.split("=")[-1].replace('"', '').strip()
     full_file = _find_file(data, os.path.basename(orig_file))
diff --git a/bcbio/variation/vcfutils.py b/bcbio/variation/vcfutils.py
index ac9a36c63..85fa8e415 100644
--- a/bcbio/variation/vcfutils.py
+++ b/bcbio/variation/vcfutils.py
@@ -10,9 +10,6 @@
 
 import toolz as tz
 
-import six
-from six.moves import zip
-
 from bcbio import broad, utils
 from bcbio.bam import ref
 from bcbio.distributed.multi import run_multicore, zeromq_aware_logging
@@ -376,7 +373,7 @@ def _sort_by_region(fnames, regions, ref_file, config):
         if fname not in added_fnames:
             if isinstance(region, (list, tuple)):
                 c, s, e = region
-            elif isinstance(region, six.string_types) and region.find(":") >= 0:
+            elif isinstance(region, str) and region.find(":") >= 0:
                 c, coords = region.split(":")
                 s, e = [int(x) for x in coords.split("-")]
             else:
diff --git a/bcbio/workflow/template.py b/bcbio/workflow/template.py
index ca4812b53..122c2c4b4 100644
--- a/bcbio/workflow/template.py
+++ b/bcbio/workflow/template.py
@@ -4,7 +4,6 @@
 YAML template. Default templates are provided for common approaches which can be tweaked
 as needed.
 """
-from __future__ import print_function
 import collections
 import contextlib
 import copy
@@ -15,9 +14,9 @@
 import itertools
 import os
 import shutil
-from six.moves import urllib
+import urllib.error
+import urllib.request
 
-import six
 import toolz as tz
 import yaml
 import sys
@@ -241,7 +240,7 @@ def _set_global_vars(metadata):
     fnames = collections.defaultdict(list)
     for sample in metadata.keys():
         for k, v in metadata[sample].items():
-            if isinstance(v, six.string_types) and os.path.isfile(v):
+            if isinstance(v, str) and os.path.isfile(v):
                 v = _expand_file(v)
                 metadata[sample][k] = v
                 fnames[v].append(k)
@@ -257,7 +256,7 @@ def _set_global_vars(metadata):
     #         global_vars[name] = fname
     # for sample in metadata.keys():
     #     for k, v in metadata[sample].items():
-    #         if isinstance(v, six.string_types) and v in global_var_sub:
+    #         if isinstance(v, str) and v in global_var_sub:
     #             metadata[sample][k] = global_var_sub[v]
     return metadata, global_vars
 
@@ -267,7 +266,7 @@ def _clean_string(v, sinfo):
     if isinstance(v, (list, tuple)):
         return [_clean_string(x, sinfo) for x in v]
     else:
-        assert isinstance(v, six.string_types), v
+        assert isinstance(v, str), v
         try:
             if hasattr(v, "decode"):
                 return str(v.decode("ascii"))
@@ -499,7 +498,7 @@ def _convert_to_relpaths(data, work_dir):
     data["files"] = [os.path.relpath(f, work_dir) for f in data["files"]]
     for topk in ["metadata", "algorithm"]:
         for k, v in data[topk].items():
-            if isinstance(v, six.string_types) and os.path.isfile(v) and os.path.isabs(v):
+            if isinstance(v, str) and os.path.isfile(v) and os.path.isabs(v):
                 data[topk][k] = os.path.relpath(v, work_dir)
     return data
 
diff --git a/scripts/bcbio_fastq_umi_prep.py b/scripts/bcbio_fastq_umi_prep.py
index 4e59799d2..ffcad1276 100755
--- a/scripts/bcbio_fastq_umi_prep.py
+++ b/scripts/bcbio_fastq_umi_prep.py
@@ -31,7 +31,6 @@
 If you're using a different approach to generate the UMIs, please
 maintain the same R1/R2/R3 naming scheme.
 """
-from __future__ import print_function
 import argparse
 import math
 import os
diff --git a/scripts/bcbio_nextgen.py b/scripts/bcbio_nextgen.py
index 75bd49118..abe303c3a 100755
--- a/scripts/bcbio_nextgen.py
+++ b/scripts/bcbio_nextgen.py
@@ -26,7 +26,6 @@
      -s scheduler for ipython parallelization (lsf, sge, slurm, torque, pbspro)
      -q queue to submit jobs for ipython parallelization
 """
-from __future__ import print_function
 import os
 import argparse
 import sys
diff --git a/scripts/bcbio_nextgen_install.py b/scripts/bcbio_nextgen_install.py
index 845f7bbfd..8647e8717 100755
--- a/scripts/bcbio_nextgen_install.py
+++ b/scripts/bcbio_nextgen_install.py
@@ -6,7 +6,6 @@
 
 Requires: git, wget, bgzip2, Python 3 or 2.7
 """
-from __future__ import print_function
 import argparse
 import collections
 import contextlib
diff --git a/scripts/bcbio_setup_genome.py b/scripts/bcbio_setup_genome.py
index 17a4b6365..f2f65ae34 100755
--- a/scripts/bcbio_setup_genome.py
+++ b/scripts/bcbio_setup_genome.py
@@ -2,7 +2,6 @@
 """
 Script to set up a custom genome for bcbio-nextgen
 """
-from __future__ import print_function
 
 from argparse import ArgumentParser
 import collections
diff --git a/scripts/cwl/arvados_bcbio_runtimes.py b/scripts/cwl/arvados_bcbio_runtimes.py
index d118eef67..1cf040596 100644
--- a/scripts/cwl/arvados_bcbio_runtimes.py
+++ b/scripts/cwl/arvados_bcbio_runtimes.py
@@ -11,6 +11,7 @@
 import os
 import pprint
 import sys
+from functools import reduce
 
 import arrow
 
diff --git a/scripts/cwltool2wdl.py b/scripts/cwltool2wdl.py
index b811951e6..771e7c73c 100755
--- a/scripts/cwltool2wdl.py
+++ b/scripts/cwltool2wdl.py
@@ -22,7 +22,6 @@
 - Associate secondary files (like `bai`, `tbi`) with primary file ('bam`, 'vcf.gz`)
   https://github.com/broadinstitute/cromwell/issues/2269
 """
-from __future__ import print_function
 import collections
 import os
 import subprocess
@@ -233,7 +232,7 @@ def _variable_type_to_read_fn(vartype, records):
     return fn_map[vartype]
 
 def _arg_to_dict(x, requirements):
-    if isinstance(x, basestring):
+    if isinstance(x, str):
         return {"prefix": "", "position": None, "value": x}
     elif isinstance(x, dict) and "valueFrom" in x and x["valueFrom"].startswith("sentinel_runtime"):
         for r in requirements: