I am running TELR on a tree genome which is ~ 830Mb and 12 chromosomes.
It is finishing successfully, however in my output files, it has only identified TE insertions on the first chromosome. This is the case for multiple sets of reads. I have separately assembled the reads and the genome assemblies are complete with all chromosomes present.
Do you know what could be causing this bias to the first chromosome?
Thank you in advance!
Lily
The .log is below
more barcode03/TELR.log
05/07/2024 04:47:43: INFO: CMD: /u/home/l/ldpeck/.conda/envs/TELR/bin/telr -i /u/project/vlsork/ldpeck/longreads/fastq/barcode03_ALLpass.fastq -r /u
/home/l/ldpeck/genome_resources/GCF_001633185.2_ValleyOak3.2_genomic.fna -l /u/home/l/ldpeck/genome_resources/Qlobata.v3.0.RepeatModeler-open-1.0.8.
consensi.fa.classified -x ont -t 12 -o barcode03
05/07/2024 04:47:43: INFO: Parsing input files...
05/07/2024 04:47:43: INFO: Raw reads are provided
05/07/2024 04:47:43: INFO: Start alignment...
05/07/2024 21:18:13: INFO: Sort and index BAM...
05/07/2024 22:00:28: INFO: First alignment finished in 17 hours 12 minutes 44 seconds
05/07/2024 22:00:28: INFO: Detecting SVs from BAM file...
05/07/2024 23:14:22: INFO: SV detection finished in 1 hours 13 minutes 54 seconds
05/07/2024 23:14:22: INFO: Parse structural variant VCF...
05/07/2024 23:27:14: INFO: Perform local assembly of non-reference TE loci...
05/07/2024 23:29:43: INFO: Local assembly finished in 2 minutes 27 seconds
05/07/2024 23:29:43: INFO: Annotate contigs...
05/07/2024 23:30:10: INFO: Estimating allele frequency...
05/07/2024 23:41:35: INFO: Perform local realignment...
05/07/2024 23:41:57: INFO: Local realignment finished in 22 seconds
05/07/2024 23:42:23: INFO: Allele frequency estimation finished in 48 seconds
05/08/2024 02:06:20: INFO: Map contigs to reference...
05/08/2024 02:11:03: INFO: Write output...
05/08/2024 02:11:21: INFO: TELR finished in 21 hours 23 minutes 38 seconds
There are 67 TE insertions in the .bed file, which are all on the first chromosome -
Hello
Thanks very much for this great tool.
I am running TELR on a tree genome which is ~ 830Mb and 12 chromosomes.
It is finishing successfully, however in my output files, it has only identified TE insertions on the first chromosome. This is the case for multiple sets of reads. I have separately assembled the reads and the genome assemblies are complete with all chromosomes present.
Do you know what could be causing this bias to the first chromosome?
Thank you in advance!
Lily
The
.logis belowThere are 67 TE insertions in the
.bedfile, which are all on the first chromosome -