"juicer_tools: Permission denied" error

[wen10-git]

Hello everyone. I've encountered a permission-related issue, even though I've already enabled all access rights to the relevant files.

Command: ./scripts/juicer.sh -g jls -D . -z ./reference/jls.p_ctg.fa -p ./reference/jls.chrom.sizes -y ./reference/jls_DpnII.txt -t 80 -S final
Feedback:

./scripts/juicer.sh: line 711: ./scripts/common/juicer_tools: Permission denied
./scripts/juicer.sh: line 712: ./scripts/common/juicer_tools: Permission denied
./scripts/juicer.sh: line 745: ./scripts/common/juicer_tools: Permission denied

real 0m0.001s
user 0m0.001s
sys 0m0.001s
./scripts/juicer.sh: line 746: ./scripts/common/juicer_tools: Permission denied

real 0m0.002s
user 0m0.000s
sys 0m0.002s
Sun Nov 2 22:04:32 CST 2025
./scripts/juicer.sh: line 751: ./scripts/common/juicer_tools: Permission denied

real 0m0.001s
user 0m0.000s
sys 0m0.001s
./scripts/juicer.sh: line 752: ./scripts/common/juicer_tools: Permission denied

real 0m0.001s
user 0m0.001s
sys 0m0.001s
./scripts/juicer.sh: line 758: ./scripts/common/juicer_postprocessing.sh: Permission denied
./scripts/juicer.sh: line 765: ./scripts/common/check.sh: Permission denied

Document status:

drwxr-xr-x  3 nizai6a nizai6a     4096 10月 30 19:49 ./
drwxr-xr-x 18 nizai6a nizai6a     4096 11月  2 22:02 ../
drwxrwxrwx  2 nizai6a nizai6a     4096 10月 30 19:49 common/
-rwxrwxrwx  1 nizai6a nizai6a    30443 10月 30 19:47 juicer.sh*
-rwxrwxr-x  1 nizai6a nizai6a 36188666 10月 30 19:47 juicer_tools_1.22.01.jar*
-rwxrwxr-x  1 nizai6a nizai6a    32982 10月 30 19:47 mega_from_bams_diploid.sh*
-rwxrwxr-x  1 nizai6a nizai6a    10455 10月 30 19:47 mega_from_bams.sh*


-rwxrwxrwx 1 nizai6a nizai6a     2886 10月 30 19:47 juicer_arrowhead.sh*
-rwxrwxrwx 1 nizai6a nizai6a     3919 10月 30 19:47 juicer_hiccups.sh*
-rwxrwxrwx 1 nizai6a nizai6a     4332 10月 30 19:47 juicer_postprocessing.sh*
-rwxrwxrwx 1 nizai6a nizai6a     1255 10月 30 19:47 juicer_tools*
-rwxrwxrwx 1 nizai6a nizai6a 36188666 10月 30 19:48 juicer_tools_1.22.01.jar*
-rwxrwxrwx 1 nizai6a nizai6a 32048230 10月 30 19:48 juicer_tools.1.9.9_jcuda.0.8.jar*
-rwxrwxrwx 1 nizai6a nizai6a 32048230 10月 30 19:49 juicer_tools.jar*
-rwxrwxrwx 1 nizai6a nizai6a 25619398 10月 30 19:49 merge-stats.jar*
-rwxrwxrwx 1 nizai6a nizai6a     2276 10月 30 19:49 relaunch_prep.sh*
-rwxrwxrwx 1 nizai6a nizai6a      228 10月 30 19:47 sam_to_mnd.sh*
-rwxrwxrwx 1 nizai6a nizai6a     2135 10月 30 19:49 sam_to_pre.awk*
-rwxrwxrwx 1 nizai6a nizai6a     4682 10月 30 19:47 stats_sub.awk*

[wen10-git]

The error may be caused by a relative path (".") command.