Hi everyone,
I have a question regarding the haplotype reconstruction algorithm PredictHaplo-1.0 (http://bmda.cs.unibas.ch/HivHaploTyper/)
I've been using this tool to run Roche 454 RLX data and it works well. However, when I switched to Illumina TruSeq, I keep getting the below segmentation fault errors.
I've had a brief look at the .sam file, but I don't see anything that seems out of the ordinary. What I don't understand is it fails to retrieve average read length when I have 2m+ reads inside the .sam file. I tried sorting and not sort the .sam file to see if it's confused about reads positioning, but I still get the same error message.
I've tried with another TruSeq data set, and the same error message appears. Might this be a TruSeq thing? I managed to borrow some Nextera XT data to see if the algorithm runs on Illumina data, that set worked.
I'm very confused, any help would be greatly appreciated.
I have a question regarding the haplotype reconstruction algorithm PredictHaplo-1.0 (http://bmda.cs.unibas.ch/HivHaploTyper/)
I've been using this tool to run Roche 454 RLX data and it works well. However, when I switched to Illumina TruSeq, I keep getting the below segmentation fault errors.
After parsing the reads in file /home/DataFiles/PredictHaplo_Files/087.sam: average read length= -nan
First read considered in the analysis starts at position 100000. Last read ends at position 0
There are 0 reads
Average read length: -nan
Local window size: -2147483648
min_overlap : -2083059138
Reconstruction starts at position 100000 and stops at position 0
Segmentation fault (core dumped)
First read considered in the analysis starts at position 100000. Last read ends at position 0
There are 0 reads
Average read length: -nan
Local window size: -2147483648
min_overlap : -2083059138
Reconstruction starts at position 100000 and stops at position 0
Segmentation fault (core dumped)
I've tried with another TruSeq data set, and the same error message appears. Might this be a TruSeq thing? I managed to borrow some Nextera XT data to see if the algorithm runs on Illumina data, that set worked.
I'm very confused, any help would be greatly appreciated.
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