search

M-Mysara / CATCh

Chimera Detection Algorithm
GNU General Public License v3.0
0 stars 0 forks source link

Running CATCh #2

Open montedeletras opened 5 years ago

montedeletras commented 5 years ago

Dear Mohamed,

Thanks for the examples, but I'm still running into some problem to run CATCh. Perhaps you could point me to new tests? I am running some samples in my desktop, but the Databases are in an external HD, so paths are long. As far as I could understand CATCh seems to be having problems interfacing with the detectors, but the instructions provided said I did not need to install any of them except DECIPHER. Could you offer a new suggestion? Commands below: reference mode in the first block and Denovo mode in the second.

Thanks!

PS: De novo mode seems to run into a similar error...

REFERENCE $ perl CATCh.pl _f 9S9reps.fasta _m r _o z _h /home/microbiologia/Desktop/Amostrasteste/Flavia/CATCh_V1 _w ../../../../../../media/microbiologia/Seagate\ Expansion\ Drive/Databases/RDP-10.28_SSU_rRNA_Reference_Database.sqlite -p 4 _r ../../../../../../media/microbiologia/Seagate\ Expansion\ Drive/Databases/Silva.nr_v132/silva.nr_v132.align _u ../../../../../../media/microbiologia/Seagate\ Expansion\ Drive/Databases/gold.fa _I ../../../../../../media/microbiologia/Seagate\ Expansion\ Drive/Databases/Silva.nr_v132/silva.nr_v132.align #########Running Uchime Program########### Using ../../../../../../media/microbiologia/Seagate Expansion Drive/Databases/gold.fa as Uchime reference cp: cannot stat './seq.uchime.chimeras': No such file or directory #########Finished Uchime Program########### #########Running ChimeraSlayer Program########### Using ../../../../../../media/microbiologia/Seagate Expansion Drive/Databases/Silva.nr_v132/silva.nr_v132.align as ChimerSlayer reference sh: 1: ./mothur: not found sh: 1: ./mothur: not found cp: cannot stat './seq.cs.slayer.chimeras': No such file or directory #########Finished ChimeraSlayer Program########### #########Running Pintail Program########### Using default reference sh: 1: ./mothur: not found sh: 1: ./mothur: not found cp: cannot stat './seq.pin.pintail.chimeras': No such file or directory #########Finished Pintail Program########### #########Running Perseus Program########### #########Finished Perseus Program########### #########Running DECIPHER Program########### Using ../../../../../../media/microbiologia/Seagate Expansion Drive/Databases/RDP-10.28_SSU_rRNA_Reference_Database.sqlite as DECIPHER reference sh: 1: cannot open ChimeraFinder.R: No such file Done #########Finished DECIPHER Program########### #########Running CATCH Reference Model########### Error: Could not find or load main class weka.classifiers.functions.SMOreg #########Finished CATCH Reference Model###########

DENOVO $ perl CATCh.pl _f 9S9reps.fasta _m d _n 9S9reps.names _h /home/microbiologia/Desktop/Amostrasteste/Flavia/CATCh_V1 _w ../../../../../../media/microbiologia/Seagate\ Expansion\ Drive/Databases/RDP-10.28_SSU_rRNA_Reference_Database.sqlite -p 4 #########Running Uchime Program########### cp: cannot stat './seq.uchime.chimeras': No such file or directory #########Finished Uchime Program########### #########Running ChimeraSlayer Program########### Using default reference as ChimeraSlayer reference sh: 1: ./mothur: not found sh: 1: ./mothur: not found cp: cannot stat './seq.cs.slayer.chimeras': No such file or directory #########Finished ChimeraSlayer Program########### #########Running Perseus Program########### sh: 1: ./mothur: not found cp: cannot stat './seq.perseus.chimeras': No such file or directory #########Finished Perseus Program########### #########Running CATCH de novo Model########### Error: Could not find or load main class weka.classifiers.functions.SMOreg #########Finished CATCH de novo Model###########

M-Mysara commented 4 years ago

Dear,

The problem is that the script is not able to locate mothur executable, I would do the following:

a) Download CATCh from: https://github.com/M-Mysara/CATCh/releases b) Unzip it and run it as following: ./CATCh_v1.run --target /PATH/WHERE/YOU/WANT/TO/UNZIP c) run the program using the new script within the extracted foder (CATCh.pl), as you did above, bearing in mind that you should use the absolute path (i.e. instead of ../../../../../../media/microbiologia/Seagate Expansion Drive/Databases/RDP-10.28_SSU_rRNA_Reference_Database.sqlite, you should use /something/something/media/microbiologia/Seagate Expansion Drive/Databases/RDP-10.28_SSU_rRNA_Reference_Database.sqlite)

You may also want to try running CATCh using the test data first, to make sure it is working properly and if you have already done that, fixing the path issue would -most likely- resolve the problem).

Also you can find a lot of info in the other link: https://science.sckcen.be/en/Institutes/EHS/MCB/MIC/Bioinformatics/CATCh

I will try to make this more clear in the future.

Sincerely Mohamed

P.S. CATCh was also included in another package, named OCToPUS that can properly save you some of this headache (https://github.com/M-Mysara/OCToPUS)

Sincerely Mohamed