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Predicted sample export failed in GUI #50
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Hi Aniruddh, Off hand, the one issue I see is that all files have "_001" at the end. Can you remove "_001"? I believe the software thinks these are all read 1, which is overriding its detection of R1 and R2. If it fails, please look in log files I mentioned above. Best, |
Hi Aniruddh, If no files are produced in the Kallisto directory, then Kallisto ends up not being called. In such cases there are two options:
I would suggest #2 first, but before this, I recommend running again, but this time, do not select the ICGS option, denote at least two biological groups and set comparisons in the GUI. When doing so, please send the screen shot of how the samples show up to ensure it is not some hidden character naming that is a problem. Will be also good to see if the same issue occurs. Otherwise, to proceed with number 2, see the below instructions provided with the software: Input Files for Kallisto-Splice Analysis The latest version of AltAnalyze introduces a new method to quickly process raw sequencing data (FASTQ files) to directly produce gene expression and alternative splicing estimates, without any additional software on your desktop or laptop computer. Demo Files The Breast Cancer dataset was downsampled from the original fast files as described here: https://www.synapse.org/#!Synapse:syn7286377/files/ Running Kallisto-Splice through the Graphical User Interface
Outputs of Kallisto-Splice There are a large array of results from this workflow which can be found in the below described folders. Note, a separate PDF file is saved to the root directory describing the files in each of these folders. Please refer to those PDFs for details.
Below is an example command similar to the above analysis: python AltAnalyze.py --platform "RNASeq" --species Mm —fastq_dir /Users/altanalyze/DemoData/Mm-FASTQ-GSE70245-DownSampled/ --groupdir /Users/altanalyze/DemoData/Mm-FASTQ-GSE70245-DownSampled/groups.Breast_cancer.txt --compdir /Users/altanalyze/DemoData/Mm-FASTQ-GSE70245-DownSampled/comp.Breast_cancer.txt --output /Users/altanalyze/DemoData/Mm-FASTQ-GSE70245-DownSampled/output --expname Breast_cancer --runGOElite yes --returnPathways all |
Hello,
I am trying to map a list of fastq files to reference mus musculus for my research. My system has 32GB ram and i7 processor. But when i start running i get the following error. I don't have any idea how to solve this. I would be highly obliged if you help me solve this .
I have attached the image for your reference. Thanking you for your time.
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