csbbcompbio / csbb-v3.0 Goto Github PK

Hello,
You may want to consider using the Anaconda python/r distribution and bioconda (https://bioconda.github.io) project to simplify installation of the tools used here. Regards

Hi I was trying CSBB. Install modules went OK. But when I try to run modules on the test files I run into problems.

Running BasicStats I get Excecution Stopped because of errors ... Contact Praneet Chaturvedi for bugs and issues on github. There is no error log.

For Process_RNASeq_SingleEnd I get
(base) nickwebster@nicks-imac-pro CSBB_Integrated_RNAseq_analysis % perl CSBB-v3.0_MacOS.pl Process-RNASeq_SingleEnd ~/CSBB/Test_Files/SingleEnd_RNA-seq.fastq xenopus-leavis ~/CSBB/test phred33

Operating System is darwin

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CSBB - Computational Suite For Bioinformaticians and Biologists

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Version_3.0

Developed and maintained by Praneet Chaturvedi!!

Please report issues and bugs on https://github.com/csbbcompbio/CSBB-v3.0

CSBB-v3.0 Last run : Mon Sep 26 12:36:48 2022

Current Run: Mon Sep 26 13:27:28 2022

/Users/nickwebster/CSBB/CSBB-v3.0_Logs directory is already present, CSBB will use the same to write module logs

Process-RNASeq_SingleEnd module loaded

CSBB is creating /Users/nickwebster/CSBB/test/Quality_Check_Reports for writing Quality Check results

CSBB will use Fastqc for Quality Check, RSEM for mapping and quantification and UCSC utilities for generating Bigwig Files
(base) nickwebster@nicks-imac-pro

It seems that my Mac is preventing some modules from running. Any ideas?