BIONF/HaMStR

CAST not working

cagescudero opened this issue · 8 comments

cagescudero commented

Hello

I am manually creating a new data set. In the step 6 (Create the annotation files for your taxon with the provided perl script) I get the following error:

Can't exec "/home/ubuntu/annotation_fas/CAST/cast": No such file or directory at /home/ubuntu/anaconda3/envs/hamstr/lib/python3.8/site-packages/greedyFAS/annoFAS.pl line 909.
Use of uninitialized value $castOut in scalar chomp at /home/ubuntu/anaconda3/envs/hamstr/lib/python3.8/site-packages/greedyFAS/annoFAS.pl line 910.
Use of uninitialized value $castOut in concatenation (.) or string at /home/ubuntu/anaconda3/envs/hamstr/lib/python3.8/site-packages/greedyFAS/annoFAS.pl line 911.

I used the following command:

annoFAS --fasta=/home/ubuntu/tools/HaMStR/genome_dir/TEST@00001@1/TEST@00001@1.fa --path=/home/ubuntu/tools/HaMStR/weight_dir --name=TEST@00001@1

It seems that CAST is not compiled to work with our system. I couldn't find the CAST v1.0 on their webpage.

Best,
Cata

trvinh commented

Hi Cata,
can you check if you have the folder cast at /home/ubuntu/annotation_fas/ and if that folder contains any things or just empty? If it is not empty, please try to run cast directly from there to see if it works.
Let me know more after you checked those points. Many thanks 😊

cagescudero commented

Hello,

The folder is there and the executable of cast too. However, when I try to tun the code alone is not working.

~/annotation_fas/CAST/$ ./cast 
-bash: ./cast: No such file or directory

Also, I tried to use the cast.zip (after unzipping) that is located in the same directory but I get the same error.

~/annotation_fas/CAST/cast-linux$ ./cast 
-bash: ./cast: No such file or directory

Best,
Cata

trvinh commented

@Cataescuderoo
could you please go to the CAST folder and do

ls -la

then send me the screen shot?

cagescudero commented

@trvinh
Here it is.

~/annotation_fas/CAST$ ls -la
total 428
drwxr-xr-x 4 ubuntu ubuntu   4096 Feb  7 13:48 .
drwxrwxr-x 9 ubuntu ubuntu   4096 Jan 21 16:41 ..
-rwxr-xr-x 1 ubuntu ubuntu  18009 May  3  2017 LICENSE
-rwxr-xr-x 1 ubuntu ubuntu   1405 May  3  2017 README
-rwxr-xr-x 1 ubuntu ubuntu  22892 May  3  2017 cast
drwxr-x--- 2 ubuntu ubuntu   4096 Feb  7 13:38 cast-linux
-rw-r--r-- 1 ubuntu ubuntu 370555 May  3  2017 cast.zip
drwxr-xr-x 2 ubuntu ubuntu   4096 Feb  7 17:01 tmp
trvinh commented

can you also do

file cast

to see if it is executable?

cagescudero commented 
~/annotation_fas/CAST$ file cast
cast: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked, interpreter /lib/ld-, for GNU/Linux 2.0.0, not stripped
trvinh commented

Probably your computer system (is it a ubuntu 64 bit?) doesn't have the libraries for running 32-bit tools. Please check this link https://askubuntu.com/questions/454253/how-to-run-32-bit-app-in-ubuntu-64-bit to see if it can solve this problem.

cagescudero commented

CAST is working now after installing the 32 bit libraries. Thanks!

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