--assembly_report does not work in Singularity

[maressyl]

Hi,

It seems that the bash code relative to --assembly_report does not work when executing in a Singularity environment, but works in a native terminal. I can't figure out why, but here is how I tested :

grep -v "#" ${pathToConvert} | awk 'BEGIN{OFS="|"}{print $7,$11}' > tmp_convert.txt

OLDIFS=$IFS
IFS=$'\n'
for line in $(cat tmp_convert.txt)
   do 
   IFS="|"
   read -a convert <<< $line
   IFS=$'\n'
   if [ `echo -e ${#convert[1]}` -gt 3 ]; then
      ucsc_name=${convert[1]}
      ucsc_name=${ucsc_name//\\n/""}
      echo -e "replace ${convert[0]} by ${ucsc_name}"
   fi
done
IFS=$OLDIFS

In a terminal I get the expected messages ("replace ..."), but not in Singularity (3.8.0, in a freshly built container).

Best regards,
Sylvain