can't find rc_s.py

[macmanes]

Fresh clone of repo this AM:

python /share/Shannon/shannon.py -o shannon --left assembly_1P.cor.fq --right assembly_2P.cor.fq -p 48 -K 75
--------------------------------------------
Shannon: RNA Seq de novo Assembly
Version: 0.0.2
--------------------------------------------
Checking the various dependencies
--------------------------------------------
Using jellyfish in /home/macmanes/.linuxbrew/bin/jellyfish
Using GPMETIS in /usr/bin/gpmetis
OPTIONS -p: Running parallel with 48 jobs.
OPTIONS -K: Kmer size set to 75
OPTIONS: File extension detected as fastq.
--------------------------------------------
Wed May 10 08:54:46 2017: Starting Shannon run..
Using GNU Parallel in /home/macmanes/.linuxbrew/bin/parallel
Wed May 10 08:54:46 2017: Running Quorum for read error correction with quality scores..
python: can't open file 'rc_s.py': [Errno 2] No such file or directory
python: can't open file 'rc_s.py': [Errno 2] No such file or directory
....
python: can't open file 'rc_s.py': [Errno 2] No such file or directory
cat: /mnt/data3/macmanes/Mya/RNAseq/reads/assembly_reads/shannon/shannon_algo_input/rc_1.fasta_1: No such file or directory
cat: /mnt/data3/macmanes/Mya/RNAseq/reads/assembly_reads/shannon/shannon_algo_input/rc_1.fasta_2: No such file or directory
cat: /mnt/data3/macmanes/Mya/RNAseq/reads/assembly_reads/shannon/shannon_algo_input/rc_1.fasta_3: No such file or directory
...
rm: cannot remove '/mnt/data3/macmanes/Mya/RNAseq/reads/assembly_reads/shannon/shannon_algo_input/rc_1.fasta_*': No such file or directory
25214345
148
python: can't open file 'rc_s.py': [Errno 2] No such file or directory

rc_s.py is in fact in the Shannon home directory..

[shunfumao]

Hi Macmanes,

As a quick remedy, could you go to Shannon's directory as your current working directory and run again? We'll fix the bug related to the path issue and let you know. Thanks!

e.g.

cd /share/Shannon/ python shannon.py -o <path/to/output_dir> --left assembly_1P.cor.fq --right assembly_2P.cor.fq -p 48 -K 75

[shunfumao]

Hi MacManes,

I've fixed a bug regarding the shannon path issue. Now I think your original commant should run even if your current directory is not the Shannon code folder.

Thanks!

Shunfu