diff --git a/artic/minion.py b/artic/minion.py
index 5666751..c00b414 100755
--- a/artic/minion.py
+++ b/artic/minion.py
@@ -2,6 +2,7 @@
 
 from clint.textui import colored
 import os
+import subprocess
 import sys
 import time
 from artic.utils import get_scheme, choose_model
@@ -131,18 +132,18 @@ def run(parser, args):
     ## create a holder to keep the pipeline commands in
     cmds = []
 
-    # 2) check the reference fasta has an index and create one if not
+    # check the reference fasta has an index and create one if not
     if not os.path.exists("%s.fai" % (ref)):
         cmds.append("samtools faidx %s" % (ref))
 
-    # 3) index the ref & align with minimap
+    # index the ref & align with minimap
     cmds.append(
         f"minimap2 -a -x map-ont -t {args.threads} {ref} {read_file} | samtools view -bS -F 4 - | samtools sort -o {args.sample}.sorted.bam -"
     )
 
     cmds.append(f"samtools index {args.sample}.sorted.bam")
 
-    # 4) trim the alignments to the primer start sites and normalise the coverage to save time
+    # trim the alignments to the primer start sites and normalise the coverage to save time
     normalise_string = f"--normalise {args.normalise}" if args.normalise else ""
 
     incorrect_pairs_string = (
@@ -160,7 +161,7 @@ def run(parser, args):
 
     cmds.append(f"samtools index {args.sample}.primertrimmed.rg.sorted.bam")
 
-    # 6) do variant calling on each read group
+    # do variant calling on each read group
     for p in pools:
         if os.path.exists("%s.%s.hdf" % (args.sample, p)):
             os.remove("%s.%s.hdf" % (args.sample, p))
@@ -182,7 +183,7 @@ def run(parser, args):
 
         cmds.append(f"rm {args.sample}.{p}.primertrimmed.rg.sorted.bam")
 
-    # 7) merge the called variants for each read group
+    # merge the called variants for each read group
     merge_vcf_cmd = "artic_vcf_merge %s %s 2> %s.primersitereport.txt" % (
         args.sample,
         bed,
@@ -203,7 +204,7 @@ def run(parser, args):
         f"artic_vcf_filter {fs_str} {indel_str} --min-depth {args.min_depth} {pre_filter_vcf}.gz {args.sample}.pass.vcf {args.sample}.fail.vcf"
     )
 
-    # 9) get the depth of coverage for each readgroup, create a coverage mask and plots, and add failed variants to the coverage mask (artic_mask must be run before bcftools consensus)
+    # get the depth of coverage for each readgroup, create a coverage mask and plots, and add failed variants to the coverage mask (artic_mask must be run before bcftools consensus)
     cmds.append(
         f"artic_make_depth_mask --depth {args.min_depth} {ref} {args.sample}.primertrimmed.rg.sorted.bam {args.sample}.coverage_mask.txt"
     )
@@ -214,7 +215,7 @@ def run(parser, args):
 
     post_filter_vcf_file = f"{args.sample}.pass.vcf"
 
-    # 10) generate the consensus sequence
+    # generate the consensus sequence
     cmds.append(f"bgzip -kf {post_filter_vcf_file}")
     cmds.append(f"tabix -f -p vcf {post_filter_vcf_file}.gz")
 
@@ -223,13 +224,12 @@ def run(parser, args):
     cmds.append(
         f"bcftools norm --check-ref x --fasta-ref {args.sample}.preconsensus.fasta -O z -o {post_normalisation_vcf_file} {post_filter_vcf_file}.gz"
     )
-    # cmds.append(f"bgzip -kf {post_normalisation_vcf_file}")
     cmds.append(f"tabix -f -p vcf {post_normalisation_vcf_file}")
     cmds.append(
         f"bcftools consensus -f {args.sample}.preconsensus.fasta {post_normalisation_vcf_file} -m {args.sample}.coverage_mask.txt -o {args.sample}.consensus.fasta"
     )
 
-    # 11) apply the header to the consensus sequence and run alignment against the reference sequence
+    # apply the header to the consensus sequence and run alignment against the reference sequence
     caller = "clair3"
     linearise_fasta = "--linearise-fasta" if args.linearise_fasta else ""
     cmds.append(
@@ -241,17 +241,97 @@ def run(parser, args):
             f"mafft --6merpair --addfragments {args.sample}.consensus.fasta {ref} > {args.sample}.aligned.fasta"
         )
 
-    # 13) setup the log file and run the pipeline commands
+    # define anticipated error codes and messages
+    general_error_codes = {
+        137: {
+            "message": "Process ran out of memory, please try running on a machine with more memory available.",
+        },
+        143: {
+            "message": "Process was terminated, this is likely due to a user or system interrupt.",
+        },
+        127: {
+            "message": "A required tool was not found, please ensure all dependencies are installed and available in your PATH.",
+        },
+    }
+
+    anticipated_tool_specific_error_codes = {
+        "align_trim": [
+            {
+                "input_exit_code": 1,
+                "message": "No reads aligned to the reference sequence, this could be due to an incorrect reference / primer scheme, or very low depth input data. Please check your input files.",
+                "output_exit_code": 2,
+            }
+        ]
+    }
+
+    # setup the log file and run the pipeline commands
     log = "%s.minion.log.txt" % (args.sample)
     logfh = open(log, "w")
     for cmd in cmds:
         print(colored.green("Running: ") + cmd, file=sys.stderr)
         if not args.dry_run:
             timerStart = time.perf_counter()
-            retval = os.system(cmd)
-            if retval != 0:
-                print(colored.red("Command failed:") + cmd, file=sys.stderr)
-                raise SystemExit(20)
+            subprocess_return = subprocess.run(cmd, shell=True, capture_output=True)
+            if subprocess_return.returncode != 0:
+                ## Check for general anticipated errors
+                if subprocess_return.returncode in general_error_codes:
+                    print(
+                        colored.yellow(
+                            general_error_codes[subprocess_return.returncode]["message"]
+                        ),
+                        file=sys.stderr,
+                    )
+                    print(colored.red("Command failed: ") + cmd, file=sys.stderr)
+                    print(
+                        colored.red("Command stderr: ")
+                        + subprocess_return.stderr.decode(errors="replace"),
+                    )
+                    raise SystemExit(subprocess_return.returncode)
+
+                ## check for anticipated tool-specific errors
+                cmd_parts = []
+                for cmd_part in cmd.split(" ")[0:1]:
+                    if "-" not in cmd_part:
+                        cmd_parts.append(cmd_part)
+                        continue
+
+                    break
+
+                if cmd_parts:
+                    base_cmd = " ".join(cmd_parts)
+
+                    if base_cmd in anticipated_tool_specific_error_codes:
+                        for error_case in anticipated_tool_specific_error_codes[
+                            base_cmd
+                        ]:
+                            if (
+                                subprocess_return.returncode
+                                == error_case["input_exit_code"]
+                            ):
+                                print(
+                                    colored.yellow(error_case["message"]),
+                                    file=sys.stderr,
+                                )
+                                print(
+                                    colored.red("Command failed: ") + cmd,
+                                    file=sys.stderr,
+                                )
+                                print(
+                                    colored.red("Command stderr: ")
+                                    + subprocess_return.stderr.decode(errors="replace"),
+                                )
+                                raise SystemExit(error_case["output_exit_code"])
+
+                print(
+                    colored.red("Unexpected command failure: ") + cmd, file=sys.stderr
+                )
+                print(
+                    colored.red("Command stderr: ")
+                    + subprocess_return.stderr.decode(errors="replace"),
+                    file=sys.stderr,
+                )
+
+                raise SystemExit(subprocess_return.returncode)
             timerStop = time.perf_counter()
 
             ## print the executed command and the runtime to the log file
diff --git a/artic/utils.py b/artic/utils.py
index 7adba47..415bce8 100644
--- a/artic/utils.py
+++ b/artic/utils.py
@@ -322,7 +322,7 @@ def get_scheme(
     scheme_version: str,
     scheme_directory: str,
     scheme_length: int = False,
-    read_file: str = False,
+    read_file: str = "",
 ):
     """Get the primer scheme and reference fasta file from the manifest
 
diff --git a/environment.yml b/environment.yml
index 8384ba5..5cd6abf 100644
--- a/environment.yml
+++ b/environment.yml
@@ -23,4 +23,4 @@ dependencies:
   - tqdm
   - seqtk
   - align_trim>=1.0.2
-  - primalbedtools>=0.10.1
+  - primalbedtools>=1.0.0
diff --git a/pyproject.toml b/pyproject.toml
index 1c10bed..d7d5b0f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "artic"
-version = "1.8.5"
+version = "1.9.0"
 authors = [
     { name = "Nick Loman", email = "n.j.loman@bham.ac.uk" },
 ]
diff --git a/tests/get_scheme_unit_test.py b/tests/get_scheme_unit_test.py
index a100b97..ed03be2 100644
--- a/tests/get_scheme_unit_test.py
+++ b/tests/get_scheme_unit_test.py
@@ -8,18 +8,18 @@ class get_scheme_unit_test(unittest.TestCase):
     def test_get_scheme_no_length(self):
 
         bed, ref, scheme_version = get_scheme(
-            scheme_name="nCoV-2019",
+            scheme_name="artic-pan-dengue",
             scheme_version="v1.0.0",
             scheme_directory=f"{os.getcwd()}/primer-schemes",
         )
 
         self.assertEqual(
-            bed, f"{os.getcwd()}/primer-schemes/artic-sars-cov-2/400/v1.0.0/primer.bed"
+            bed, f"{os.getcwd()}/primer-schemes/artic-pan-dengue/400/v1.0.0/primer.bed"
         )
 
         self.assertEqual(
             ref,
-            f"{os.getcwd()}/primer-schemes/artic-sars-cov-2/400/v1.0.0/reference.fasta",
+            f"{os.getcwd()}/primer-schemes/artic-pan-dengue/400/v1.0.0/reference.fasta",
         )
 
     def test_get_scheme_unclear_length(self):
diff --git a/tests/minion_validator.py b/tests/minion_validator.py
index fe2f908..b97de38 100644
--- a/tests/minion_validator.py
+++ b/tests/minion_validator.py
@@ -164,6 +164,8 @@ def genCommand(sampleID, workflow):
     cmd.append("SARS-CoV-2")
     cmd.append("--scheme-version")
     cmd.append("v1.0.0")
+    cmd.append("--scheme-length")
+    cmd.append("400")
     cmd.append(sampleID)
     return cmd