diff --git a/docs/SOP_alignment_variant_annotation_ultra2.md b/docs/SOP_alignment_variant_annotation_ultra2.md
index c9e3b691d045941bb17003cdbb5d8204455cb960..63157a060d77471b84802f4e090319c745c66e4e 100644
--- a/docs/SOP_alignment_variant_annotation_ultra2.md
+++ b/docs/SOP_alignment_variant_annotation_ultra2.md
@@ -122,12 +122,12 @@ project_id=<project_id>
 source /home/u035/u035/shared/scripts/trio_whole_exome_config.sh
 ```
 
-2. Copy the PED file for the batch to the params folder in the working area. It should be named <project_id>.ped, relating it to the input directory for the FASTQ files. If the PED file given was not named in this way, don’t rename it, create a symlink with the correct name.
+2. Copy the PED file for the batch to the params folder in the working area. It should be named <project_id>.ped, relating it to the input directory for the FASTQ files. If the PED file given was not named in this way, don’t rename it, copy it instead.
 
 ```
 cd $PARAMS_DIR
 ped_file=<input_ped_file>
-ln -s $ped_file $project_id.ped
+cp $ped_file $project_id.ped
 ```
 
 3. In the params folder, create the symlinks to the reads and the bcbio configuration files. If specifying a common sample suffix, ensure it includes any joining characters, e.g. “-“ or “_”, so that the family identifier can be cleanly separated from the suffix. Get the number of families from the batch. Version should be "v1" by default for the first analysis run of a batch, "v2" etc for subsequent runs.
@@ -141,7 +141,7 @@ version=<version>
 sample_suffix=<sample_suffix>
 /home/u035/u035/shared/scripts/prepare_bcbio_config.sh \
   /home/u035/u035/shared/scripts/trio_whole_exome_config.sh \
-  $project_id $version $sample_suffix &> ${version}_${project_id}.log
+  $project_id $version $sample_suffix &> ${project_id}_${version}_`date +%Y%m%d%H%M`.log
 X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 ```
 
@@ -153,7 +153,7 @@ version=<version>
 sample_suffix=<sample_suffix>
 /home/u035/u035/shared/scripts/prepare_bcbio_config_crf.sh \
   /home/u035/u035/shared/scripts/trio_whole_exome_crf_config.sh \
-  $project_id $version $sample_suffix &> ${version}_${project_id}.log
+  $project_id $version $sample_suffix &> ${project_id}_${version}_`date +%Y%m%d%H%M`.log
 X=`wc -l $PARAMS_DIR/$project_id.family_ids.txt | awk '{print $1}'`
 ```