fixed multiprocess Pool freeze on subprocess error and added better m…

…essages when file list is provided listing missing files

ectyper/ectyper.py

@@ -120,10 +120,10 @@ def run_program():
     os.makedirs(temp_dir, exist_ok=True)
 
     LOG.info("Gathering genome files list ...")
-    raw_genome_files = decompress_gunzip_files(genomeFunctions.get_files_as_list(args.input), temp_dir)
+    input_files_list = genomeFunctions.get_files_as_list(args.input)
+    raw_genome_files = decompress_gunzip_files(input_files_list, temp_dir)
 
-    LOG.info("Identifying genome file types")
-
+    LOG.info(f"Identifying genome file types on {len(raw_genome_files)} inputs ...")
     raw_files_dict = genomeFunctions.identify_raw_files(raw_genome_files,
                                                             args)
 

ectyper/genomeFunctions.py

@@ -38,12 +38,18 @@ def get_files_as_list(file_or_directory):
             for root, dirs, files in os.walk(file_or_directory):
                 for filename in files:
                     files_list.append(os.path.join(root, filename))
+            LOG.info(f"Identified {len(files_list)} genomes in {file_or_directory}")        
         # check if input is concatenated file locations separated by , (comma)
         elif ',' in file_or_directory:
-            LOG.info("Using genomes in the input list")
+            LOG.info("Using genomes in the input list separated by ','")
+            missing_inputs_count = 0
             for filename in file_or_directory.split(','):
                 if os.path.exists(os.path.abspath(filename)):
                     files_list.append(os.path.abspath(filename))
+                else:
+                    LOG.warning(f"File {filename} not found in the ',' separated list")
+                    missing_inputs_count += 1
+            LOG.info(f"Total of {len(files_list)} genomes identified with a valid path and {missing_inputs_count} missing")           
         else:
             LOG.info("Checking existence of file " + file_or_directory)
             input_abs_file_path = os.path.abspath(file_or_directory)
@@ -213,8 +219,10 @@ def assemble_reads(reads, bowtie_base, combined_fasta, temp_dir, cores=1):
         '-U', reads,
         '-S', sam_reads
     ]
+
     subprocess_util.run_subprocess(bowtie_run)
 
+
     # Convert reads from sam to bam
     bam_reads = os.path.join(temp_dir, output_name + '.bam')
     sam_convert = [

ectyper/subprocess_util.py

@@ -38,4 +38,5 @@ def run_subprocess(cmd, input_data=None, un=False, ignorereturncode=False):
         LOG.error("Error in subprocess. The following command failed: {}".format(cmd))
         LOG.error("Subprocess failed with error: \"{}\"".format(comp_proc.stderr.decode("utf-8")))
         LOG.critical("ectyper has stopped")
-        exit("subprocess failure")
+        raise Exception(f"subprocess failure while running {cmd} command")
+