detect integration sites in human cancer cells from RNA-seq data (L526401A )

[solmarsab]

Hello,

I would like to use Survirus to detect integration sites in human cancer cells from RNA-seq data. I'am currently testing the tool on the sample L526401A for which viral integration site have been identified (https://academic.oup.com/bioinformatics/article/29/2/266/202055) unfortunately, I don't manage to detect any integration site with Survirus. I noticed the virus-anchors.bam and virus-clips.bam are empty whereas the host-clips.bam and host-anchors.bam are not. moreover I have the following error :

thank you very much for your help

[Mesh89]

Hi,

May I see the full output?

[solmarsab]

Hello,

Please find attached a file which contains the full log Survirus_log.txt

and see below all the output files created in my workdir thanks for your help.

[Mesh89]

The problem seems to be a segfault in the remapping step. May I know where you downloaded the data and the virus database from? It will be helpful to have the exact same data in order to find the cause.

[priyatolani]

Hi, I am trying to find viral integration sites in RNA-seq data. I am using Survirus but getting this error:

('Executing:', '/priya/software/SurVirus-master/reads_categorizer /priya2/common/NCBI_virus-refseq/viral_1_1/viral.1.1.genomic.fna /priya/common/survirus /priya/common/survirus/bam_0/') Killed ('Executing:', 'bwa mem -t 12 -h 9137 /priya2/common/NCBI_virus-refseq/hostgenome_viral/hostgenome_viral.1.1.fa /priya/common/survirus/bam_0//virus-side.fq | samtools view -b -F 2308 > /priya/common/survirus/bam_0//virus-side.bam') [M::bwa_idx_load_from_disk] read 0 ALT contigs [E::main_mem] fail to open file /priya/common/survirus/bam_0//virus-side.fq'. ('Executing:', 'bwa mem -t 12 -h 100 /priya2/common/NCBI_virus-refseq/hostgenome_viral/hostgenome_viral.1.1.fa /priya/common/survirus/bam_0//host-side.fq | samtools view -b -F 2308 > /priya/common/survirus/bam_0//host-side.bam') [M::bwa_idx_load_from_disk] read 0 ALT contigs [E::main_mem] fail to open file/priya/common/survirus/bam_0//host-side.fq'. ('Executing:', '/priya/software/SurVirus-master/merge_retained_reads /priya/common/survirus /priya/common/survirus/bam_0/') Segmentation fault (core dumped) ('Executing:', '/priya/software/SurVirus-master/build_region-reads_associations /priya/common/host_sequence/host_sequences/hostgenome/hostgenome.fa /priya2/common/NCBI_virus-refseq/viral_1_1/viral.1.1.genomic.fna /priya/common/survirus /priya/common/survirus/bam_0/') [E::hts_open_format] Failed to open file "/priya/common/survirus/host-side.cs.bam" : No such file or directory terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >' Aborted (core dumped) ('Executing:', '/priya/software/SurVirus-master/remapper /priya/common/host_sequence/host_sequences/hostgenome/hostgenome.fa /priya2/common/NCBI_virus-refseq/viral_1_1/viral.1.1.genomic.fna /priya/common/survirus /priya/common/survirus/bam_0/ > /priya/common/survirus/results.txt 2> /priya/common/survirus/log.txt') ('Executing:', '/priya/software/SurVirus-master/bp_region_consensus_builder /priya/common/host_sequence/host_sequences/hostgenome/hostgenome.fa /priya2/common/NCBI_virus-refseq/viral_1_1/viral.1.1.genomic.fna /priya/common/survirus /priya/common/survirus/bam_0/') ('Executing:', '/priya/software/sdust-master/sdust /priya/common/survirus/host_bp_seqs.fa > /priya/common/survirus/host_bp_seqs.masked.bed') ('Executing:', '/priya/software/sdust-master/sdust /priya/common/survirus/virus_bp_seqs.fa > /priya/common/survirus/virus_bp_seqs.masked.bed') ('Executing:', '/priya/software/SurVirus-master/filter /priya/common/survirus > /priya/common/survirus/results.t1.txt') ('Executing:', '/priya/software/SurVirus-master/filter /priya/common/survirus --remapped > /priya/common/survirus/results.remapped.t1.txt') ('Executing:', '/priya/software/SurVirus-master/filter /priya/common/survirus --print-rejected > /priya/common/survirus/results.discarded.txt') Finding alternative locations... ('Executing:', 'bwa mem -t 12 -h 1000 /priya/common/host_sequence/host_sequences/hostgenome/hostgenome.fa /priya/common/survirus/host_bp_seqs.fa | samtools view -b -F 2308 > /priya/common/survirus/host_bp_seqs.bam') [M::bwa_idx_load_from_disk] read 0 ALT contigs [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -t 12 -h 1000 /priya/common/host_sequence/host_sequences/hostgenome/hostgenome.fa /priya/common/survirus/host_bp_seqs.fa [main] Real time: 51.921 sec; CPU: 9.147 sec [E::idx_find_and_load] Could not retrieve index file for '/priya/common/survirus/host_bp_seqs.bam'

Thank you very much for your help

[Mesh89]

The problem is here:

('Executing:', '/priya/software/SurVirus-master/reads_categorizer /priya2/common/NCBI_virus-refseq/viral_1_1/viral.1.1.genomic.fna /priya/common/survirus /priya/common/survirus/bam_0/') Killed

Every other error is a consequence of that. You should contact your system administrator to find out why the process is being killed.