empty "host_bp_seqs.fa"

[WenjinGudaisy]

Hi,

I tried your tool on one of our sample that has HPV integrations. But I found errors when running it. May I have your help to look at it?

Here are the error messages in the error file:

[M::bwa_idx_load_from_disk] read 0 ALT contigs
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -t 8 -h 1000 /home/wenjingu/scratch/HPV_fusion/ref_hg19/
hs37d5.fa /home/wenjingu/scratch/HPV_fusion/cell_line_RNAseq_res/Sample_8137
8_call_ins/host_bp_seqs.fa
[main] Real time: 5.174 sec; CPU: 2.673 sec
[E::idx_find_and_load] Could not retrieve index file for '/home/wenjingu/scr
atch/HPV_fusion/cell_line_RNAseq_res/Sample_81378_call_ins/host_bp_seqs.bam'

I think the tool interrupted at this command:
bwa mem -t 8 -h 1000 /home/wenjingu/scratch/HPV_fusion/ref_hg19/h s37d5.fa /home/wenjingu/scratch/HPV_fusion/cell_line_RNAseq_res/Sample_81378 _call_ins/host_bp_seqs.fa | samtools view -b -F 2308 > /home/wenjingu/scratc h/HPV_fusion/cell_line_RNAseq_res/Sample_81378_call_ins/host_bp_seqs.bam

Because the "host_bp_seqs.fa" file is empty.

Here is my outputs list:
bam_0 host_bp_seqs.masked.bed results.remapped.t1.txt
cigars-map host-regions results.remapped.txt
config.txt host-side.cs.bam results.t1.txt
contig_map log.txt results.txt
head_1.fq qnames-map virus_bp_seqs.fa
head_2.fq reads.scores.bin virus_bp_seqs.masked.bed
head.sam readsx virus-side.cs.bam
host_bp_seqs.bam results.alternative.txt
host_bp_seqs.fa results.discarded.txt

All the files start with "results" are empty. The "host_bp_seqs.fa" and "virus_bp_seqs.fa" are empty as well.

The error, log and "environment.yaml" files for this job were attached.

https://drive.google.com/drive/folders/1Pv4jkfHKFYINxa7lIRtZmXhmVMuwtJeA?usp=sharing

Thanks,
Wenjin

---

Wenjin Gu
PhD candidate
Department of Computational Medicine & Bioinformatics,
University of Michigan,
Mills Lab, Room 2055, Palmer Commons, 100 Washtenaw Ave, Ann Arbor, 48109

[v-mukhina]

Hi @Mesh89 , I have the same issue on a sample with a known and well supported viral integration. There are no errors, but virus_clips.fa, host_bp_seqs.fa and other resulting files are also empty. it looks like this issue has similar symptoms to #6

[Nihir Patel]

@v-mukhina @Mesh89 , not sure if this is still useful, but I've had the exact same issues, turned out that sdust (implementation of DUST) was not in the environment. After installing (alternatively, you can provide path for --dust, --bwa and --samtools), it worked fine.
Hopefully that helps.