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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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simreads can't be used in NGMLR #105

Open liufy11 opened 4 years ago

liufy11 commented 4 years ago

Hi fritzsedlazeck 1 I generate Pacbio long read successfully , but when I use these reads to map to the reference with NGMLR ,a long-read mapper. the screen says: Mapping reads... free(): invalid pointer Aborted (core dumped) my question is whether I can use the genereted read to map using NGMLR directly or I should revise the format first. by the way , I can map Pacbio long read download from NCBI with NGMLR.

fritzsedlazeck commented 4 years ago

Hi, thanks for reaching out. Can you show me the way you ran NGMLR? What is the reference genome? Thanks Fritz

liufy11 commented 4 years ago

[Thanks for your reply ! I download Pacbio read(sra_data.fastq) and reference sequence(TAIR10.1.fa) of arabidopsis thaliana from NCBI

get the bam and Tair_error_profile_bwa.txt file

~/bin/ngmlr -t 20 -r ~/Analysis/SURVIVOR/data/TAIR10.1.fa -q ~/Analysis/SURVIVOR/sra_data.fastq -o sra.bam ~/bin/samtools view -s 0.1 sra.bam | ~/bin/SURVIVOR scanreads 1000 Tair_error_profile_bwa.txt

genereate Pacbio reads (There is no problem up to this point)

~/bin/SURVIVOR simreads ~/Analysis/SURVIVOR/data/TAIR10.1.fa Tair_error_profile_bwa.txt 20 Tair.Pac.fa

map Pacbio reads to reference by ngmlr. the screen says "Segmentation fault (core dumped)"

~/bin/ngmlr -t 20 -r ~/Analysis/SURVIVOR/data/TAIR10.1.fa -q Tair.Pac.fa -o Tair.sam

I cut the first 10 lines of the Tair.Pac.fa. when mapped to TAIR10.1.fa , the same error occur. I offer the Tair.Pac.10.txt file ,maybe this can helps solving the problem. Tair.Pac.10.txt