Closed 23Niklas closed 2 months ago
Thanks for the detailed report!
It looks like pbmm2 gets upset if you give it a gzipped reference fasta. I made so that if pbmm2 is the chosen aligner that it now aligns to a decompressed copy of the reference instead. Could you pull the latest commit (2156e1185bae7218fa2683710eb684365afa8a42) and try running it again?
Thanks for your quick reply! Indeed just gunzipping the ref file resolved the alignment error. I will re-run telogator and let you know if it completes successfully this time. Speaking of, is it expected that telogator 2 takes ~8 hours for the test files, since they're quit small?
The test files in the repository may look small because I removed everything aside from the telomere reads, but they're actually full-sized datasets (with the PacBio data actually being combined from 3 separate runs combined). I've thought it might be useful to add a smaller set that users could run just to make check that the software works, but yeah, that kind of runtime is generally expected.
I'm typically running Telogator2 in an HPC environment with 16 processes (-p 16
, the default is 4), which for ~30x WGS data takes about 6hrs wall time and ~12GB of memory. There are a few options for speeding runs up that I used during development, such as -d
for downsampling reads, --fast-aln
for using a faster pairwise alignment algorithm, and --init-filt
which can be used to immediately prune interstitial telomere reads earlier on in the workflow (--init-filt 500 200
is a fairly safe starting point that should reduce runtime by ~50%). Though these are all somewhat-experimental features that I haven't throughly tested or documented.
This time it worked flawlessly, thank you!
One last question, I tried out my own reference file with -t
(CHM13_v2) and encountered the error below
aligning subtels to reference... (132 sec) getting anchors from alignment...Traceback (most recent call last): File "/n/data1/hms/dbmi/park/niklas/analysis/telomere_mosaicism/config/envs/telogator2/telogator2.py", line 1089, in <module> main() File "/n/data1/hms/dbmi/park/niklas/analysis/telomere_mosaicism/config/envs/telogator2/telogator2.py", line 948, in main my_chr = n.split('_')[1] IndexError: list index out of range
Do I need to adjust other reference files in a certain way to work for telogator?
Did you have a specific need for trying to anchor reads to contigs other than those in the default reference? In most cases you shouldn't need to include the -t
input option, as the default telogator-ref.fa contains all the subtelomeres of T2T_v2, for example.
The specific reason for the error is that the code is expecting that contigs are named like:
>referencebuild_chr#arm
e.g. >t2t-chm13_chr1p
I see, that explains the error. Thanks a lot for your help!
I was curious to see if this would work with other T2T references as well.
Hi, I am trying the telogator2 tutorial with the test data and am encountering an error in the alignment step. The error I am encountering is
Error: alignment command returned an error: 1
and results from the error in the subtel_aln.log file>|> 20240618 15:03:19.626 -|- WARN -|- CheckPositionalArgs -|- 0x7eff948f3780|| -|- Input is FASTA. Output BAM file cannot be used for polishing with GenomicConsensus! >|> 20240618 15:03:19.626 -|- FATAL -|- CheckPositionalArgs -|- 0x7eff948f3780|| -|- pbmm2 align ERROR: Could not determine read input type(s). Please do not mix data types, such as BAM+FASTQ. File of files may only contain BAMs or datasets.
The command I'm running is `#!/bin/bash
SBATCH -J telogator2
SBATCH -c 8
SBATCH -t 12:00:00
SBATCH -p short
SBATCH --mem=10G
SBATCH -o telogator2_%j.out
python telogator2.py \ -i test_data/hg002-telreads_pacbio.fa.gz \ -o results/ \ -p 8 \ --muscle /home/miniconda3/envs/telogator2/bin/muscle \ --pbmm2 /home/miniconda3/envs/telogator2/bin/pbmm2 \ -r hifi -tt 0.400 -ts 0.250 -n 4`
And I can also reproduce the same pbmm2 align ERROR form above using
pbmm2 align resources/telogator-ref.fa.gz results/temp/unanchored_subtels.fa.gz results/temp/subtel_aln.bam --preset HiFi --sort
I tried version 1.14.99 and 1.13.1 of pbmm2 and below is my full telogator2 env (I generated it from the respective yaml file). Thanks in advance for your help!
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