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xunchen85 / ERVcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.
http://www.uvm.edu/genomics/software/ERVcaller.html
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failed at step 3 #16

Open e-lerat opened 2 years ago

e-lerat commented 2 years ago

Hi, I am not sure about what is happening here. I use the program on my data (which are non human) and everything seems fine until this step. Then the vcf output file at the end is empty.

Step 3: Validation...

Converting SAM to BAM file, and then Sort and index the BAM file......

[bam_sort_core] merging from 0 files and 11 in-memory blocks... [bwa_index] Pack FASTA... 0.00 sec [bwa_index] Construct BWT for the packed sequence... [E::bwa_idx_load_from_disk] fail to locate the index files [E::bwa_idx_load_from_disk] fail to locate the index files

Here is my command line to launch the program

perl /home/ubuntu/ERVcaller-1.4/ERVcaller_v1.4.pl -i Dmel_chr2L_sim_100X_150 -f .fq.gz -H /home/ubuntu/genome_Del_1.fasta -T /home/ubuntu/ref_TE.fasta -t 12 -S 20 -BWA_MEM -I /home/ubuntu/ -O /home/ubuntu/Dmel_100X_sim/ -r 150

Thank you in advance for you help!

xunchen85 commented 2 years ago

Hi, it should be because no TEs were detected in the earlier step. We currently make the tools to run with human genome. Maybe you could check the reference coordinates, is it named "chr1-24,X,Y"?

Xun

e-lerat commented 2 years ago

Actually, it is not a human organism. I thought that using my own genome reference (-H) it would work.

xunchen85 commented 2 years ago

I see, it could also be used for other genomes with a bit changes to the code. Let me know if I could further help.

Xun