Question: Using FreeBayes in Exome Sequencing Analysis Tutorial
gravatar for pcm20
10 months ago by
pcm2010 wrote:

I have been attempting to work through the Exome Sequencing Analysis tutorial available on the wiki and in the FreeBayes step I am instructed to upload a human reference genome from the Data Libraries section of Shared Data, but the folder doesn't seem to exist anywhere. Is there now a different process to pulling out this reference genome from Shared Data?

I also tried to upload the reference genome from the USCS Main to work around the first problem, but after running FreeBayes with this reference and one of the files provided with the tutorial an error is reported saying, "Error running samtools faidx for FreeBayes." I am still new to using Galaxy so is there anyway to fix this error, meaning am I missing something obvious? Or is there an issue with the tutorial instructions?

This is a full readout of the error report:

Dataset generation errors Dataset 12: Call SNPS with Freebayes on data 1 and data 10

Tool execution generated the following error message: /galaxy-repl/main/jobdir/015/408/15408451/ line 9: 16225 Segmentation fault (core dumped) samtools faidx localref.fa 2>&1 Error running samtools faidx for FreeBayes unable to find FASTA index entry for 'chr22' The tool produced the following additional output: [fai_build_core] different line length in sequence '(null)'.

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