Segmentation fault: SurVirus-master/remapper
agupta52 opened this issue · comments
Hello,
I would like to use Survirus to detect HPV integration sites in human WGS data. I am getting "Segmentation fault (core dumped) /data/ngsc4data/NGSC_softwares/SurVirus-master/remapper" error and would really appreciate the help. I have attached the standard error and standard output file for diagnosis. Here are some other details that might help:
Reference: hg38 human genome and HPV sequences provided as part of another HPV integration sites detector software (http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html)
Software: htslib v1.11, sparsehash v2.0.3, python v2.7.15, numpy v1.16.5, pyfaidx v0.7.0, pysam v0.17.0, samtools v1.10, bwa-v0.7.17 & sdust 0.1-r2
Command: python /data/ngsc4data/NGSC_softwares/SurVirus-master/surveyor.py \
58_R1_trimmed.fastq,58_R2_trimmed.fastq \
58 \
/data/ngsc4data/NGSC_reference/Human/hg38/bwaindex/hg38.fa \
/data/ngsc4data/NGSC_reference/HPV_index_files/HPV_143types_EBVref.fa \
/data/ngsc4data/NGSC_reference/Human_HPV/hg38/hg38_HPV.fa \
--threads 24 \
--wgs \
--fq \
--bwa /home/agupta/miniconda3/bin/bwa \
--samtools /home/agupta/miniconda3/bin/samtools \
--dust /home/agupta/miniconda3/bin/sdust
Please let me know if you need any other details. Looking forward to hearing from you.
Thanks,
Anuj