failed at step 3

[e-lerat]

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]

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]

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

[xunchen85]

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