diff --git a/99_utils/submitjob_sge_cluster/bash2sge.sh b/99_utils/submitjob_sge_cluster/bash2sge.sh
index 1fe9131bd42f407ce19a4ab28a2777d45b18fc03..be4ff6dde3aacca51acc9b403797f2deef11b172 100644
--- a/99_utils/submitjob_sge_cluster/bash2sge.sh
+++ b/99_utils/submitjob_sge_cluster/bash2sge.sh
@@ -38,6 +38,7 @@ sed -e "s/JOB_NAME/$nom_qsub_script/g" \
 -e "s|OUT_FILE|$run_output/$nom_qsub_script\.out|g" \
 -e "s|ERR_FILE|$run_output/$nom_qsub_script\.err|g" \
 $template_script  > $qsub_script/temp_script.sh
+echo -e "cd "$(pwd) >> $qsub_script/temp_script.sh
 echo -e "bash $location_bash_script/$nom_bash_script.sh\n" >> $qsub_script/temp_script.sh
 mv $qsub_script/temp_script.sh $qsub_script/$nom_qsub_script".sh"
 echo $qsub_script/$nom_qsub_script".sh is ready to be qsubmitted."
diff --git a/optimal_pipeline/optimal_pipeline.sh b/optimal_pipeline/optimal_pipeline.sh
index 1f06b7d1a62a9dd128e3cb710b28d47c14295218..029e7e7baf91188382068c59eabb75e62462ac1d 100644
--- a/optimal_pipeline/optimal_pipeline.sh
+++ b/optimal_pipeline/optimal_pipeline.sh
@@ -33,9 +33,9 @@ vsearch=${SINGULARITY_EXEC_CMD}" "${EDNATOOLS_SIMG}" vsearch"
 cutadapt=${SINGULARITY_EXEC_CMD}" "${EDNATOOLS_SIMG}" cutadapt"
 
 # Prefix for all generated files
-pref=grinder_teleo1
+pref="grinder_teleo1"
 # Prefix of the final table 
-step=optimal_pipeline
+step="optimal_pipeline"
 # Path to forward and reverse fastq files
 R1_fastq="${DATA_PATH}"/"$pref"/"$pref"_R1.fastq
 R2_fastq="${DATA_PATH}"/"$pref"/"$pref"_R2.fastq
@@ -51,9 +51,11 @@ base_pref=`ls $base_dir/*sdx | sed 's/_[0-9][0-9][0-9].sdx//g' | awk -F/ '{print
 main_dir=`pwd`"/optimal_pipeline/Outputs/main"
 fin_dir=`pwd`"/optimal_pipeline/Outputs/final"
 
-
 ###################################################################################################################
 
+## path to 'tags.fasta'
+Tags_F=`pwd`"/02_demultiplex/Tags_F.fasta"
+Tags_R=`pwd`"/02_demultiplex/Tags_R.fasta"
 ## assign each sequence to a sample
 $cutadapt --pair-adapters --pair-filter=both -g file:$Tags_F -G file:$Tags_R -y '; sample={name};' -e 0 -o $main_dir/R1.assigned.fastq -p $main_dir/R2.assigned.fastq --untrimmed-paired-output $main_dir/unassigned_R2.fastq --untrimmed-output $main_dir/unassigned_R1.fastq $R1_fastq $R2_fastq
 
@@ -116,5 +118,5 @@ $obisort -k count -r $all_sample_sequences_ann > $all_sample_sequences_sort
 # Create the final table
 $obitab -o $all_sample_sequences_sort > $fin_dir/"$step".csv
 
-gzip $main_dir/*
+#gzip $main_dir/*