at-cg / raft Goto Github PK

I get a segmentation fault when I try to run the RAFT stage using the following command:

COVERAGE=$(grep "homozygous" "${OUTPUT_PATH}/1_HIFIASM_ASSEMBLIES/${SAMPLE_NAME}/${SAMPLE_NAME}.errorcorrect.log" | tail -1 | awk '{print $6}')

/var/lib/slurm/slurmd/job1460416/slurm_script: line 96: 3795738 Segmentation fault      (core dumped) 
raft -e ${COVERAGE} -o "${OUTPUT_PATH}/1_HIFIASM_ASSEMBLIES/${SAMPLE_NAME}/${SAMPLE_NAME}.fragmented" "${OUTPUT_PATH}/1_HIFIASM_ASSEMBLIES/${SAMPLE_NAME}/${SAMPLE_NAME}.errorcorrect.ec.fa" "${OUTPUT_PATH}/1_HIFIASM_ASSEMBLIES/${SAMPLE_NAME}/${SAMPLE_NAME}.overlaps.paf"

Tried to rerun it and got the same error again. I am using a node with 128 CPUs and 1500GB RAM.

I am running the pipeline with the new High Accuracy ONT Ultra long dataset that was released recently.

Hi!
I get the following error when trying to make

make
g++ -std=c++14 -O3 main.cpp -o raft -lz
g++: error: unrecognized command line option '-std=c++14'
make: *** [Makefile:6: all] Error 1

Thank you!

Hello,

First of all, thank you for this interesting tool. I've been using it to investigate the influence of read length on the contained read problem and I've ran into a problem. I can't seem to find the exact positions from which the cut read comes from in the original read. From looking at the code it seems that's only possible if the reads follow a specific naming scheme(if I understood your code correctly). Would it be possible to add this?
E.g. if I have a read named long_read_1 cut into 2 shorter ones, currently I would get reads with names: read=1,long_read_1 and read=2,long_read_1, my suggestion would be to name the reads let's say read=1,pos=0:15000,long_read_1 and read=2,pos=15000:27200,long_read_1. Hope I made it clear enough.

Thank you in advance and kind regards!