diff --git a/.gitignore b/.gitignore
index 90c55553b9e42e7b49d9ebd7b5f4cc779edc0fb1..b4aab9586fdd862f8238e00cc6d14ecaeb0ed252 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
 /.snakemake
 /logs/*
-/resources/*
+/benchmarks/*
 /results/*
 /tools/
diff --git a/config/config.yaml b/config/config.yaml
index 90b249f79c2f78865e375007ff42ba9e68623493..4cbf648ec1126458f55f75e84a2c273a675b21d7 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -1,11 +1,11 @@
 output_name_prefix:
-  "Homo_sapiens_4"
+#  "Homo_sapiens_4"
 
 input_HiFi_reads:
-  "test_datasets/dataset3_sim_hChr19.fastq"
+#  "dataset3_sim_hChr19.fastq"
 
 input_reference:
-  "test_datasets/Homo_sapiens_ch19.fasta"
+#  "Homo_sapiens_ch19.fasta"
 
   
 
diff --git a/resources/.gitignore b/resources/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..86d0cb2726c6c7c179b99520c452dd1b68e7a813
--- /dev/null
+++ b/resources/.gitignore
@@ -0,0 +1,4 @@
+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore
\ No newline at end of file
diff --git a/run_snakemake.sh b/run_snakemake.sh
index ce727c8645620acc13be670c91c6a64022e5488f..e3530b31fc3133401d352e0971533f4fff61544f 100644
--- a/run_snakemake.sh
+++ b/run_snakemake.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-#cd "$(dirname "$0")"
+cd "$(dirname "$0")"
 
 snakemake --cores 10 --use-conda
 
diff --git a/workflow/rules/gffcompare.smk b/workflow/rules/gffcompare.smk
index bae396b5232396717ef606c8ef6e7ca8ab56ccc2..2ae008eaff83cdaad8d6a54deb7b76c8ee7ba964 100644
--- a/workflow/rules/gffcompare.smk
+++ b/workflow/rules/gffcompare.smk
@@ -8,7 +8,7 @@ rule convert_bed_gtf:
     conda:
         "../envs/py27tama.yaml"
     shell:
-        "python tools/tama/tama_go/format_converter/tama_convert_bed_gtf_ensembl_no_cds.py {input} {output} 2>{log}"
+        "python tools/tama/tama_go/format_converter/tama_convert_bed_gtf_ensembl_no_cds.py {input} {output} 1>&2>{log}"
 
 
 def get_output_files(wildcards):
@@ -16,13 +16,13 @@ def get_output_files(wildcards):
     
     if config["RUN_TAMA_COLLAPSE"] and config["TAMA_split_input"]:
         input_list.append("results/structural_annotation/TAMA_collapse_merged_{output_name}/{output_name}.gtf") 
-    if config["RUN_TAMA_COLLAPSE"] and not config["TAMA_split_input"]:
-        input_list.append("results/structural_annotation/TAMA_collapse_unmerged_{output_name}/{output_name}.gtf")
+    # if config["RUN_TAMA_COLLAPSE"] and not config["TAMA_split_input"]:    # bugs with wildcards
+    #     input_list.append("results/structural_annotation/TAMA_collapse_unmerged_{output_name}/{output_name}.gtf")
     if config["RUN_ISO_SEQ_COLLAPSE"]:
         input_list.extend(rules.iso_seq_collapse.output)
     if config["RUN_STRINGTIE"]:
         input_list.extend(rules.stringtie.output) 
-    #print(input_list)
+
     return input_list
 
 rule compare_gtf:
@@ -37,4 +37,4 @@ rule compare_gtf:
     conda:
         "../envs/gffcompare.yaml"
     shell: 
-        "gffcompare {input} -o {output}"
\ No newline at end of file
+        "gffcompare {input} -o {output} 1>&2>{log}"
\ No newline at end of file