diff --git a/.gitpod.yml b/.gitpod.yml
new file mode 100644
index 0000000..a565aba
--- /dev/null
+++ b/.gitpod.yml
@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6ddfafb..70413f1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,20 @@
 
 Started only in version 0.5
 
+## v1.2.3
+
+- Added ICEberg and PHAST results to bacannot json summary file
+
+## v1.2.2
+
+- Added a file size check, only enter bacannot summary creation if results files are not empty
+- Fixed mob_suite summary parsing (added .astype(str))
+- Moved MGE dict key generation for inside the integron_finder loop
+
+## v1.2.1
+
+- Added a quick fix for plasmid finder results parsing, as results from gram-negative have only one database, but for gram-positive it has >1.
+
 ## v0.5
 
 ### hotfix
diff --git a/build_conda.sh b/build_conda.sh
index ea63aba..d3d0571 100644
--- a/build_conda.sh
+++ b/build_conda.sh
@@ -9,7 +9,8 @@ conda convert -p osx-64 $(find build -name "falmeida-py*.tar.bz2")
 
 # upload osx
 anaconda upload $(find osx-64 -name "falmeida-py*.tar.bz2") --force
-( cd build && anaconda upload $(find linux-64 -name "falmeida-py*.tar.bz2") --force )
+sleep 140
+anaconda upload $(find build/linux-64 -name "falmeida-py*.tar.bz2") --force
 
 # rm dirs
 rm -rf build osx-64
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
index ff18464..b1e862a 100644
--- a/conda.recipe/meta.yaml
+++ b/conda.recipe/meta.yaml
@@ -1,20 +1,20 @@
 package:
   name: falmeida-py
-  version: '0.9'
+  version: '1.2.4'
 
 source:
   path: ..
 
 build:
   number: 0
-  script: python setup.py install --single-version-externally-managed --record=record.txt
+  script: pip install .
   entry_points:
     - processrcmfolder = uconnrcmpy.dataprocessing:process_folder
 
 
 requirements:
   build:
-    - python >=3.7,{{PY_VER}}*
+    - python>=3.8
     - setuptools
     - setuptools-git
     - pandas
@@ -26,7 +26,7 @@ requirements:
     - pyyaml
 
   run:
-    - python {{PY_VER}}*
+    - python>=3.8
     - setuptools
     - setuptools-git
     - pandas
diff --git a/falmeida_py/__main__.py b/falmeida_py/__main__.py
index be6003d..4b94bba 100644
--- a/falmeida_py/__main__.py
+++ b/falmeida_py/__main__.py
@@ -148,8 +148,8 @@ def main():
             print(f"Processing file: {args['--gbk']}!")
             gbk2fasta(gbk=args['--gbk'])
             blast(task='blastn', query=args['--fasta'], subject='tmp_gbk.fa',
-             culling=args['--culling_limit'], minid=args['--minid'], mincov=args['--mincov'],
-             out='out.blast', threads=1, twoway=None)
+            culling=args['--culling_limit'], minid=args['--minid'], mincov=args['--mincov'],
+            out='out.blast', threads=1, twoway=None)
             filtergbk(gbk=args['--gbk'], out=args['--out'], extension=int(args['--extension']))
 
             # Clean dir
@@ -241,8 +241,8 @@ def main():
     #######################################
     ### Without commands nor parameters ###
     #######################################
-    else:
-        print(usage.strip())
+    elif not arguments['<command>']:
+      print(usage.strip())
 
 ## Calling main
 if __name__ == '__main__':
diff --git a/falmeida_py/bacannot2json.py b/falmeida_py/bacannot2json.py
index 80a342a..b4a8b75 100644
--- a/falmeida_py/bacannot2json.py
+++ b/falmeida_py/bacannot2json.py
@@ -37,33 +37,25 @@
 from .plasmid_function import *
 from .virulence_function import *
 from .resistance_function import *
+from .mges_function import *
 
 ##############################
 ### fix keys in dictionary ###
 ##############################
+def convert_dictkey(d):
+    ###change all keys in a dict d
+    return { str(k): convert_dictvalue(v) for k,v in d.items() }
+
+def convert_dictvalue(v):
+    ###if v is a dict do convert_dictkey() for v, else raise v
+    if isinstance(v, dict):
+        return convert_dictkey(v)
+    else:
+        return v
+
 def stringify_keys(d):
     """Convert a dict's keys to strings if they are not."""
-    for key in d.keys():
-
-        # check inner dict
-        if isinstance(d[key], dict):
-            value = stringify_keys(d[key])
-        else:
-            value = d[key]
-
-        # convert nonstring to string if needed
-        if not isinstance(key, str):
-            try:
-                d[str(key)] = value
-            except Exception:
-                try:
-                    d[repr(key)] = value
-                except Exception:
-                    raise
-
-            # delete old key
-            del d[key]
-    return d
+    return convert_dictkey(d)
 
 ###############################################
 ### based on annotations figure sample name ###
@@ -112,6 +104,9 @@ def bacannot2json(indir, outfile, check):
     # check virulence annotation stats
     virulence_stats( bacannot_summary )
 
+    # check MGEs annotation stats
+    mges_stats( bacannot_summary )
+
     # check plasmids annotation stats
     plasmids_stats( bacannot_summary )
 
diff --git a/falmeida_py/general_stats_function.py b/falmeida_py/general_stats_function.py
index 74e0893..80e2590 100644
--- a/falmeida_py/general_stats_function.py
+++ b/falmeida_py/general_stats_function.py
@@ -37,10 +37,10 @@ def general_stats(bacannot_summary):
         # save annotation stats
         bacannot_summary[sample]['general_annotation'] = {}
         bacannot_summary[sample]['general_annotation']['mlst']  = str(mlst_results[2].item()).replace('-', 'null')
-        bacannot_summary[sample]['general_annotation']['cds']   = general_results['CDS']
-        bacannot_summary[sample]['general_annotation']['rrna']  = general_results['rRNA']
-        bacannot_summary[sample]['general_annotation']['trna']  = general_results['tRNA']
-        bacannot_summary[sample]['general_annotation']['tmrna'] = general_results['tmRNA']
+        bacannot_summary[sample]['general_annotation']['cds']   = general_results.get('CDS', 0)
+        bacannot_summary[sample]['general_annotation']['rrna']  = general_results.get('rRNA', 0)
+        bacannot_summary[sample]['general_annotation']['trna']  = general_results.get('tRNA', 0)
+        bacannot_summary[sample]['general_annotation']['tmrna'] = general_results.get('tmRNA', 0)
 
         bacannot_summary[sample]['general_annotation']['closest_reference'] = {}
         bacannot_summary[sample]['general_annotation']['closest_reference']['strain'] = refseq_masher_results.head(1)['top_taxonomy_name'].item()
diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py
new file mode 100644
index 0000000..39014e0
--- /dev/null
+++ b/falmeida_py/mges_function.py
@@ -0,0 +1,169 @@
+##################################
+### Loading Necessary Packages ###
+##################################
+import pandas as pd
+import os
+from .utils import load_and_subset_gff
+
+####################################
+### check MGEs annotations stats ###
+####################################
+def mges_stats(bacannot_summary):
+    
+    # iterate over available samples
+    for sample in bacannot_summary:
+
+        # load dir of samples' results
+        results_dir = bacannot_summary[sample]['results_dir']
+
+        # load gff_file
+        gff_file = f"{results_dir}/gffs/{sample}.gff"
+            
+        # integron_finder
+        if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff") and os.stat(f"{results_dir}/integron_finder/{sample}_integrons.gff").st_size > 0:
+
+            # init MGE annotation dictionary
+            if 'MGE' not in bacannot_summary[sample]:
+                bacannot_summary[sample]['MGE'] = {}
+
+            # init integron_finder annotation dictionary
+            bacannot_summary[sample]['MGE']['integron_finder'] = {}
+
+            # load integron_finder results
+            results = pd.read_csv(
+                f"{results_dir}/integron_finder/{sample}_integrons.gff",
+                sep='\t',
+                header=None,
+                names=[
+                    'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'atts'
+                ]
+            )
+
+            # number of integron_finder annotations
+            total_number = len(results.index)
+            bacannot_summary[sample]['MGE']['integron_finder']['total'] = total_number
+
+            # per integron info
+            bacannot_summary[sample]['MGE']['integron_finder'] = {}
+            if int(results.shape[0]) > 0:
+                for seq in [ str(x) for x in results['chr'].unique() ]:
+                    
+                    bacannot_summary[sample]['MGE']['integron_finder'][seq] = {}
+                    for index, row in results[results['chr'] == seq].reset_index().iterrows():
+                        id = row['atts'].split(';')[0].split('=')[-1]
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id] = {}
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['id'] = id
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['contig'] = row['chr']
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['start'] = row['start']
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end']
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1]
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source']
+                        bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type']
+
+        # ICEberg database
+        ice_db_blastp = f"{results_dir}/ICEs/{sample}_iceberg_blastp_onGenes.summary.txt"
+        if os.path.exists(ice_db_blastp) and os.stat(ice_db_blastp).st_size > 0:
+
+            # init MGE annotation dictionary
+            if 'MGE' not in bacannot_summary[sample]:
+                bacannot_summary[sample]['MGE'] = {}
+            
+            # init iceberg annotation dictionary
+            if 'ICE' not in bacannot_summary[sample]['MGE']:
+                bacannot_summary[sample]['MGE']['ICEberg'] = {}
+
+            # init iceberg blastp annotation dictionary
+            bacannot_summary[sample]['MGE']['ICEberg']['blastp'] = {}
+
+            # load integron_finder results
+            results = pd.read_csv(
+                ice_db_blastp,
+                sep='\t'
+            )
+
+            # load gff
+            gff = load_and_subset_gff(gff_file, 'source', 'ICEberg')
+
+            # number of integron_finder annotations
+            total_number = len(results.index)
+            bacannot_summary[sample]['MGE']['ICEberg']['blastp']['total'] = total_number
+
+            # per gene info
+            if int(results.shape[0]) > 0:
+                for seq in [ str(x) for x in results['SEQUENCE'].unique() ]:
+
+                    # details missing in output but available in gff
+                    gff_row = gff[gff['attributes'].str.contains(seq)]
+                    contig = gff_row['seq'].item()
+                    start  = gff_row['start'].item()
+                    end    = gff_row['end'].item()
+                    
+                    bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq] = {}
+                    for index, row in results[results['SEQUENCE'] == seq].reset_index().iterrows():
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq] = {}
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['id']             = row['ICEBERG_ID']
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['contig']         = contig
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['start']          = start
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['end']            = end
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['accession']      = row['ACCESSION']
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['product']        = row['PRODUCT']
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['description']    = row['DESCRIPTION']
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_start']    = row['START']
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_end']      = row['END']
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_identity'] = row['%IDENTITY']
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_coverage'] = row['%COVERAGE']
+                        bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['strand']         = row['STRAND']
+
+        # PHAST database
+        phast_db_blastp = f"{results_dir}/prophages/phast_db/{sample}_phast_blastp_onGenes.summary.txt"
+        if os.path.exists(phast_db_blastp) and os.stat(phast_db_blastp).st_size > 0:
+
+            # init MGE annotation dictionary
+            if 'MGE' not in bacannot_summary[sample]:
+                bacannot_summary[sample]['MGE'] = {}
+            
+            # init phast annotation dictionary
+            if 'ICE' not in bacannot_summary[sample]['MGE']:
+                bacannot_summary[sample]['MGE']['PHAST'] = {}
+
+            # init phast blastp annotation dictionary
+            bacannot_summary[sample]['MGE']['PHAST']['blastp'] = {}
+
+            # load integron_finder results
+            results = pd.read_csv(
+                phast_db_blastp,
+                sep='\t'
+            )
+
+            # load gff
+            gff = load_and_subset_gff(gff_file, 'source', 'PHAST')
+
+            # number of integron_finder annotations
+            total_number = len(results.index)
+            bacannot_summary[sample]['MGE']['PHAST']['blastp']['total'] = total_number
+
+            # per gene info
+            if int(results.shape[0]) > 0:
+                for seq in [ str(x) for x in results['SEQUENCE'].unique() ]:
+
+                    # details missing in output but available in gff
+                    gff_row = gff[gff['attributes'].str.contains(seq)]
+                    contig = gff_row['seq'].item()
+                    start  = gff_row['start'].item()
+                    end    = gff_row['end'].item()
+                    
+                    bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq] = {}
+                    for index, row in results[results['SEQUENCE'] == seq].reset_index().iterrows():
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq] = {}
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['id']             = row['PHAST_ID']
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['contig']         = contig
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['start']          = start
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['end']            = end
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['accession']      = row['ACCESSION']
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['gene']           = row['GENE']
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['description']    = row['DESCRIPTION']
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_start']    = row['START']
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_end']      = row['END']
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_identity'] = row['%IDENTITY']
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_coverage'] = row['%COVERAGE']
+                        bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['strand']         = row['STRAND']
\ No newline at end of file
diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py
index aab1e37..789aa9a 100644
--- a/falmeida_py/plasmid_function.py
+++ b/falmeida_py/plasmid_function.py
@@ -2,11 +2,7 @@
 ### Loading Necessary Packages ###
 ##################################
 import pandas as pd
-from .utils import find_files
-import json
 import os
-import yaml
-from pathlib import Path
 
 ########################################
 ### check plasmids annotations stats ###
@@ -19,29 +15,27 @@ def plasmids_stats(bacannot_summary):
         # load dir of samples' results
         results_dir = bacannot_summary[sample]['results_dir']
 
-        # load annotation stats
-        if os.path.exists(f"{results_dir}/plasmids"):
-
-            # init plasmids annotation dictionary
-            bacannot_summary[sample]['plasmid'] = {}
+        # init plasmids annotation dictionary
+        bacannot_summary[sample]['plasmid'] = {}            
             
-            # platon
-            if os.path.exists(f"{results_dir}/plasmids/platon/{sample}.tsv"):
+        # platon
+        if os.path.exists(f"{results_dir}/plasmids/platon/{sample}.tsv") and os.stat(f"{results_dir}/plasmids/platon/{sample}.tsv").st_size > 0:
 
-                # init platon annotation dictionary
-                bacannot_summary[sample]['plasmid']['platon'] = {}
+            # init platon annotation dictionary
+            bacannot_summary[sample]['plasmid']['platon'] = {}
 
-                # load platon results
-                results = pd.read_csv(
-                    f"{results_dir}/plasmids/platon/{sample}.tsv",
-                    sep='\t'
-                )
+            # load platon results
+            results = pd.read_csv(
+                f"{results_dir}/plasmids/platon/{sample}.tsv",
+                sep='\t'
+            )
 
-                # number of plasmid annotations
-                total_number = len(results.index)
-                bacannot_summary[sample]['plasmid']['platon']['total'] = total_number
+            # number of plasmid annotations
+            total_number = len(results.index)
+            bacannot_summary[sample]['plasmid']['platon']['total'] = total_number
 
-                # per plasmid info
+            # per plasmid info
+            if int(results.shape[0]) > 0:
                 for seq in [x for x in results['ID'].unique()]:
                     bacannot_summary[sample]['plasmid']['platon'][seq] = {}
                     bacannot_summary[sample]['plasmid']['platon'][seq]['Length'] = results.loc[results['ID'] == seq, 'Length'].item()
@@ -51,37 +45,89 @@ def plasmids_stats(bacannot_summary):
                     bacannot_summary[sample]['plasmid']['platon'][seq]['Replication'] = results.loc[results['ID'] == seq, '# Replication'].item()
                     bacannot_summary[sample]['plasmid']['platon'][seq]['Mobilization'] = results.loc[results['ID'] == seq, '# Mobilization'].item()
                     bacannot_summary[sample]['plasmid']['platon'][seq]['Conjugation'] = results.loc[results['ID'] == seq, '# Conjugation'].item()
-            
-            # plasmidfinder
-            if os.path.exists(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv"):
-
-                # init platon annotation dictionary
-                bacannot_summary[sample]['plasmid']['plasmidfinder'] = {}
-
-                # load platon results
-                results = pd.read_csv(
-                    f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv",
-                    sep='\t'
-                )
-
-                if not results.empty:
-
-                    # databases
-                    bacannot_summary[sample]['plasmid']['plasmidfinder']['meta'] = {}
-                    bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = results['Database'].unique().item()
-
-                    # number of plasmid annotations
-                    total_number = len(results['Contig'].unique())
-                    bacannot_summary[sample]['plasmid']['plasmidfinder']['total'] = total_number
-
-                    # plasmid annotations contigs
-                    for seq in [ str(x) for x in results['Contig'].unique() ]:
-                        bacannot_summary[sample]['plasmid']['plasmidfinder'][seq] = {}
-                        bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['inc_types'] = {}
-                        bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['identity'] = {}
-                        bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['accession'] = {}
-                    for index, row in results.iterrows():
-                        contig = row['Contig']
-                        bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['inc_types'] = row['Plasmid']
-                        bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['identity'] = row['Identity']
-                        bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number']
\ No newline at end of file
+        
+        # plasmidfinder
+        if os.path.exists(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv") and os.stat(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv").st_size > 0:
+
+            # init platon annotation dictionary
+            bacannot_summary[sample]['plasmid']['plasmidfinder'] = {}
+
+            # load platon results
+            results = pd.read_csv(
+                f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv",
+                sep='\t'
+            )
+
+            if not results.empty:
+
+                # databases
+                print( results['Database'].unique() )
+                bacannot_summary[sample]['plasmid']['plasmidfinder']['meta'] = {}
+                db_arr = results['Database'].unique()
+                bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = db_arr.tolist() if len(db_arr) > 1 else db_arr.item()
+
+                # number of plasmid annotations
+                total_number = len(results['Contig'].unique())
+                bacannot_summary[sample]['plasmid']['plasmidfinder']['total'] = total_number
+
+                # plasmid annotations contigs
+                for seq in [ str(x) for x in results['Contig'].unique() ]:
+                    bacannot_summary[sample]['plasmid']['plasmidfinder'][seq] = {}
+                    bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['inc_types'] = {}
+                    bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['identity'] = {}
+                    bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['accession'] = {}
+                
+                for index, row in results.iterrows():
+                    contig = str(row['Contig'])
+                    bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['inc_types'] = row['Plasmid']
+                    bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['identity'] = row['Identity']
+                    bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number']
+        
+        # mob suite
+        if os.path.exists(f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt") and os.stat(f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt").st_size > 0:
+
+            # init integron_finder annotation dictionary
+            bacannot_summary[sample]['plasmid']['mob_suite'] = {}
+
+            # load integron_finder results
+            results = pd.read_csv(
+                f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt",
+                sep='\t',
+                header='infer',
+                # sample_id	num_contigs	size	gc	md5	rep_type(s)	rep_type_accession(s)	relaxase_type(s)	relaxase_type_accession(s)	mpf_type	mpf_type_accession(s)	orit_type(s)	orit_accession(s)	predicted_mobility	mash_nearest_neighbor	mash_neighbor_distance	mash_neighbor_identification	primary_cluster_id	secondary_cluster_id	predicted_host_range_overall_rank	predicted_host_range_overall_name	observed_host_range_ncbi_rank	observed_host_range_ncbi_name	reported_host_range_lit_rank	reported_host_range_lit_name	associated_pmid(s)
+            )
+
+            # number of plasmid types annotated annotations
+            # total_number = len(results.index) - 1 # always counts chromosome
+            # bacannot_summary[sample]['plasmid']['mob_suite']['total'] = total_number
+
+            # per integron info
+            bacannot_summary[sample]['plasmid']['mob_suite'] = {}
+            if int(results.shape[0]) > 0:
+                for seq in [ str(x) for x in results['sample_id'].unique() ]:
+                    
+                    bacannot_summary[sample]['plasmid']['mob_suite'][seq] = {}
+                    for index, row in results[results['sample_id'].astype(str) == seq].reset_index().iterrows():
+                        id = row['sample_id'] # they are the same for this result
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id] = {}
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['size'] = row['size']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['rep_type'] = row['rep_type(s)'].replace(',', '; ')
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['rep_type_accession'] = row['rep_type_accession(s)'].replace(',', '; ')
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['relaxase_type'] = row['relaxase_type(s)']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['relaxase_type_accession(s)'] = row['relaxase_type_accession(s)']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mpf_type'] = row['mpf_type']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mpf_type_accession'] = row['mpf_type_accession(s)']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['orit_type'] = row['orit_type(s)']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['orit_accession'] = row['orit_accession(s)']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_nearest_neighbor'] = row['mash_nearest_neighbor']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_neighbor_distance'] = row['mash_neighbor_distance']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_neighbor_identification'] = row['mash_neighbor_identification']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['primary_cluster_id'] = row['primary_cluster_id']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['secondary_cluster_id'] = row['secondary_cluster_id']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['predicted_host_range_overall_rank'] = row['predicted_host_range_overall_rank']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['predicted_host_range_overall_name'] = row['predicted_host_range_overall_name']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['observed_host_range_ncbi_rank'] = row['observed_host_range_ncbi_rank']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['observed_host_range_ncbi_name'] = row['observed_host_range_ncbi_name']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['reported_host_range_lit_rank'] = row['reported_host_range_lit_rank']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['reported_host_range_lit_name'] = row['reported_host_range_lit_name']
+                        bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['associated_pmid'] = row['associated_pmid(s)']
\ No newline at end of file
diff --git a/falmeida_py/resistance_function.py b/falmeida_py/resistance_function.py
index 7a4460a..7f7ff01 100644
--- a/falmeida_py/resistance_function.py
+++ b/falmeida_py/resistance_function.py
@@ -33,7 +33,7 @@ def resistance_stats(bacannot_summary):
             ###########
             ### rgi ###
             ###########
-            if os.path.exists(f"{results_dir}/resistance/RGI/RGI_{sample}.txt"):
+            if os.path.exists(f"{results_dir}/resistance/RGI/RGI_{sample}.txt") and os.stat(f"{results_dir}/resistance/RGI/RGI_{sample}.txt").st_size > 0:
 
                 # init rgi annotation dictionary
                 bacannot_summary[sample]['resistance']['rgi'] = {}
@@ -84,7 +84,7 @@ def resistance_stats(bacannot_summary):
             #####################
             ### amrfinderplus ###
             #####################
-            if os.path.exists(f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv"):
+            if os.path.exists(f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv") and os.stat(f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv").st_size > 0:
 
                 # init amrfinderplus annotation dictionary
                 bacannot_summary[sample]['resistance']['amrfinderplus'] = {}
@@ -130,10 +130,13 @@ def resistance_stats(bacannot_summary):
                     #
                     # check for rgi orthologies
                     #
-                    if gene in bacannot_summary[sample]['resistance']['rgi']:
-                        bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro']
-                    else:
-                        bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = None
+                    try:
+                      if gene in bacannot_summary[sample]['resistance']['rgi']:
+                          bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro']
+                      else:
+                          bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = None
+                    except:
+                      bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = None
             
             #################
             ### resfinder ###
@@ -141,7 +144,7 @@ def resistance_stats(bacannot_summary):
             #
             # TODO: Include genomic coordinates info
             #
-            if os.path.exists(f"{results_dir}/resistance/resfinder/ResFinder_results_tab.txt"):
+            if os.path.exists(f"{results_dir}/resistance/resfinder/ResFinder_results_tab.txt") and os.stat(f"{results_dir}/resistance/resfinder/ResFinder_results_tab.txt").st_size > 0:
 
                 # init resfinder annotation dictionary
                 bacannot_summary[sample]['resistance']['resfinder'] = {}
@@ -177,7 +180,10 @@ def resistance_stats(bacannot_summary):
                     #
                     # check for rgi orthologies
                     #
-                    if gene in bacannot_summary[sample]['resistance']['rgi']:
-                        bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro']
-                    else:
-                        bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = None
+                    try:
+                      if gene in bacannot_summary[sample]['resistance']['rgi']:
+                          bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro']
+                      else:
+                          bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = None
+                    except:
+                      bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = None
diff --git a/falmeida_py/version.py b/falmeida_py/version.py
index 5a92447..e524e2d 100644
--- a/falmeida_py/version.py
+++ b/falmeida_py/version.py
@@ -14,7 +14,7 @@
 If not, see <http://www.gnu.org/licenses/>.
 """
 
-__version__ = '0.9'
+__version__ = '1.2.4'
 
 def get_version():
     return __version__
diff --git a/falmeida_py/virulence_function.py b/falmeida_py/virulence_function.py
index 8656e30..91e912d 100644
--- a/falmeida_py/virulence_function.py
+++ b/falmeida_py/virulence_function.py
@@ -30,7 +30,7 @@ def virulence_stats(bacannot_summary):
             bacannot_summary[sample]['virulence'] = {}
             
             # vfdb
-            if os.path.exists(f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt"):
+            if os.path.exists(f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt") and os.stat(f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt").st_size > 0:
 
                 # init VFDB annotation dictionary
                 bacannot_summary[sample]['virulence']['VFDB'] = {}
@@ -73,7 +73,7 @@ def virulence_stats(bacannot_summary):
                     bacannot_summary[sample]['virulence']['VFDB'][gene]['end'] = end
             
             # victors
-            if os.path.exists(f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt"):
+            if os.path.exists(f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt") and os.stat(f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt").st_size > 0:
 
                 # init victors annotation dictionary
                 gff = bacannot_summary[sample]['virulence']['Victors'] = {}
diff --git a/requirements.txt b/requirements.txt
index baf0574..eff09bb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,4 +4,4 @@ tabulate
 biopython
 simplejson
 importlib_metadata
-yaml
+pyyaml
diff --git a/setup.py b/setup.py
index 0535747..7b2d7ed 100644
--- a/setup.py
+++ b/setup.py
@@ -30,18 +30,20 @@ def readme():
 with open('requirements.txt') as f:
     required = f.read().splitlines()
 
-setup(name='falmeida-py',
-      version=__version__,
-      description='falmeida-py: a package to the simple distribution of my custom scripts.',
-      long_description=readme(),
-      long_description_content_type='text/markdown',
-      url='https://github.com/fmalmeida/pythonScripts',
-      author='Felipe Almeida',
-      author_email='almeidafmarques@gmail.com',
-      license='GPLv3',
-      packages=['falmeida_py'],
-      install_requires=required,
-      entry_points={"console_scripts": ['falmeida-py = falmeida_py.__main__:main']},
-      include_package_data=True,
-      zip_safe=False,
-      python_requires='>=3.6')
+setup(
+    name='falmeida-py',
+    version=__version__,
+    description='falmeida-py: a package to the simple distribution of my custom scripts.',
+    long_description=readme(),
+    long_description_content_type='text/markdown',
+    url='https://github.com/fmalmeida/pythonScripts',
+    author='Felipe Almeida',
+    author_email='almeidafmarques@gmail.com',
+    license='GPLv3',
+    packages=['falmeida_py'],
+    install_requires=required,
+    entry_points={"console_scripts": ['falmeida-py = falmeida_py.__main__:main']},
+    include_package_data=True,
+    zip_safe=False,
+    python_requires='>=3.6'
+)