TELR only finds TE insertions on first chromosome

[lilypeck]

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 .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 -

barcode03/barcode03_ALLpass.telr.bed 
NC_044904.1	1032836	1032841	rnd-5_family-4302	.	-
NC_044904.1	1053999	1054003	rnd-1_family-226	.	-
NC_044904.1	1099869	1099869	rnd-1_family-135	.	-
NC_044904.1	1115738	1115742	rnd-1_family-28|rnd-1_family-414|rnd-1_family-44|rnd-1_family-936|rnd-5_family-3646	.	-
NC_044904.1	1237003	1237006	rnd-1_family-27|rnd-1_family-275|rnd-1_family-29|rnd-3_family-1127|rnd-3_family-172	.	-
NC_044904.1	1317284	1317284	rnd-1_family-12|rnd-1_family-4	.	-
NC_044904.1	1344949	1344950	rnd-1_family-268	.	+
NC_044904.1	1453483	1453485	rnd-1_family-239|rnd-1_family-452|rnd-5_family-394	.	-
NC_044904.1	1477501	1477504	rnd-1_family-429|rnd-5_family-2250	.	-
NC_044904.1	1560954	1560969	rnd-1_family-358	.	+
NC_044904.1	1564438	1564447	rnd-5_family-1540	.	-
NC_044904.1	1770139	1770141	rnd-1_family-43	.	-
NC_044904.1	1784603	1784608	rnd-4_family-269	.	-
NC_044904.1	1843359	1843359	rnd-1_family-22|rnd-1_family-24	.	+
NC_044904.1	1856666	1856666	rnd-1_family-66|rnd-5_family-3370	.	-
NC_044904.1	1858066	1858066	rnd-1_family-1	.	-
NC_044904.1	1878004	1878007	rnd-4_family-366|rnd-6_family-4077	.	-
NC_044904.1	1900780	1900782	rnd-1_family-11|rnd-1_family-254|rnd-1_family-3|rnd-1_family-7	.	-
NC_044904.1	1917028	1917038	rnd-1_family-90	.	-
NC_044904.1	1961400	1961400	rnd-1_family-38	.	-
NC_044904.1	2058100	2058100	rnd-5_family-2523	.	-
NC_044904.1	2096028	2096031	rnd-1_family-19|rnd-1_family-20|rnd-1_family-58|rnd-3_family-369	.	-
NC_044904.1	2125712	2125750	rnd-3_family-626|rnd-5_family-3531	.	-
NC_044904.1	2152823	2152823	rnd-1_family-364	.	-
NC_044904.1	2332827	2332835	rnd-1_family-365|rnd-1_family-588	.	-
NC_044904.1	2340392	2340392	rnd-1_family-96	.	+
NC_044904.1	2409243	2409243	rnd-1_family-239	.	-
NC_044904.1	2445982	2445984	rnd-1_family-45	.	-
NC_044904.1	2451032	2451039	rnd-1_family-1	.	-
NC_044904.1	2463943	2463949	rnd-1_family-219	.	-
NC_044904.1	2566660	2566665	rnd-1_family-259|rnd-1_family-715|rnd-1_family-84|rnd-6_family-1302	.	-
NC_044904.1	2622522	2622531	rnd-1_family-43	.	-
NC_044904.1	2639432	2639440	rnd-1_family-119	.	-
NC_044904.1	2776399	2776498	rnd-5_family-2229	.	-
NC_044904.1	2778531	2778542	rnd-1_family-117	.	-
NC_044904.1	2831119	2831169	rnd-1_family-34	.	-
NC_044904.1	2899997	2900109	rnd-1_family-268|rnd-1_family-43|rnd-4_family-366	.	-
NC_044904.1	2950908	2950966	rnd-1_family-139	.	-
NC_044904.1	2982105	2982124	rnd-1_family-288	.	-
NC_044904.1	3030509	3030509	rnd-1_family-60	.	-
NC_044904.1	3162939	3162942	rnd-1_family-35	.	-
NC_044904.1	3183111	3183126	rnd-1_family-147	.	-
NC_044904.1	3221638	3221638	rnd-1_family-870|rnd-1_family-941|rnd-5_family-2523	.	+
NC_044904.1	3308754	3308754	rnd-1_family-43	.	-
NC_044904.1	3310630	3310630	rnd-1_family-515|rnd-5_family-1170	.	-
NC_044904.1	3447794	3447794	rnd-1_family-58	.	-
NC_044904.1	3448551	3448559	rnd-1_family-365|rnd-1_family-588	.	+
NC_044904.1	346059	346064	rnd-4_family-1862	.	+
NC_044904.1	3547476	3547480	rnd-1_family-239|rnd-1_family-452|rnd-5_family-394	.	-
NC_044904.1	3611549	3611559	rnd-1_family-358	.	+
NC_044904.1	3635277	3635282	rnd-1_family-226	.	-
NC_044904.1	3645400	3645400	rnd-1_family-37	.	-
NC_044904.1	3723532	3723541	rnd-1_family-35	.	-
NC_044904.1	3766267	3766267	rnd-1_family-246	.	-
NC_044904.1	3770943	3770950	rnd-5_family-6424	.	+
NC_044904.1	3878453	3878466	rnd-1_family-147	.	-
NC_044904.1	3886041	3886041	rnd-1_family-1|rnd-1_family-11|rnd-1_family-3	.	-
NC_044904.1	3963150	3963153	rnd-4_family-840	.	-
NC_044904.1	3973117	3973117	rnd-5_family-1212	.	-
NC_044904.1	427826	427831	rnd-1_family-718|rnd-1_family-883|rnd-5_family-1227|rnd-5_family-2674	.	-
NC_044904.1	430013	430013	rnd-1_family-116	.	-
NC_044904.1	431298	431298	rnd-1_family-365|rnd-1_family-588	.	-
NC_044904.1	445112	445121	rnd-1_family-214|rnd-3_family-730	.	-
NC_044904.1	450130	450137	rnd-1_family-45	.	-
NC_044904.1	689931	689934	rnd-1_family-61	.	-
NC_044904.1	782394	782395	rnd-4_family-840	.	-
NC_044904.1	885492	885497	rnd-1_family-1|rnd-1_family-11	.	-