list index out of range error in step1

[jamesc99]

svision-pro_germline_540201_4294967294.txt test_hg002_pacbio_vacmap.zip uniq_cigar_column_hg002_pacbio_vacmap_region_chr1_40000000_50000000.txt

Hi @songbowang125 ,

I am continuously getting same error when runing SVision-pro on VACmap aligned BAM files.

Errors look like:

2024-08-25 17:59:34,744 [ERROR]    [Collecting Error] pacbio_vacmap chr1_40000000_50000000. Error log: list index out of range. Locate At: [<FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/pytho
n3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/collect_op.py, line 43 in collect_and_detect_in_interval>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1
.8-py3.7.egg/src/cigar_op.py, line 479 in collect_cigars_from_bam>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/cigar_op.py, line 600 i
n collect_from_intra_align>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/cigar_op.py, line 178 in cigar_to_list>]
2024-08-25 17:59:34,745 [ERROR]    [Collecting Error] pacbio_vacmap chr1_220000000_230000000. Error log: list index out of range. Locate At: [<FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/pyt
hon3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/collect_op.py, line 43 in collect_and_detect_in_interval>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro
-1.8-py3.7.egg/src/cigar_op.py, line 479 in collect_cigars_from_bam>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/cigar_op.py, line 600
 in collect_from_intra_align>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/cigar_op.py, line 178 in cigar_to_list>]
2024-08-25 17:59:34,745 [ERROR]    [Collecting Error] pacbio_vacmap chr2_10000_10000000. Error log: list index out of range. Locate At: [<FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.
7/site-packages/SVision_pro-1.8-py3.7.egg/src/collect_op.py, line 43 in collect_and_detect_in_interval>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-
py3.7.egg/src/cigar_op.py, line 479 in collect_cigars_from_bam>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/cigar_op.py, line 600 in c
ollect_from_intra_align>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/cigar_op.py, line 178 in cigar_to_list>]
2024-08-25 17:59:34,745 [ERROR]    [Collecting Error] pacbio_vacmap chr2_80000000_90000000. Error log: list index out of range. Locate At: [<FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/pytho
n3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/collect_op.py, line 43 in collect_and_detect_in_interval>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1
.8-py3.7.egg/src/cigar_op.py, line 479 in collect_cigars_from_bam>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/cigar_op.py, line 600 i
n collect_from_intra_align>, <FrameSummary file /stornext/snfs4/next-gen/scratch/ryan/tools/miniconda3/envs/svision-pro-env/lib/python3.7/site-packages/SVision_pro-1.8-py3.7.egg/src/cigar_op.py, line 178 in cigar_to_list>]

SVision-pro version I am using: v1.8 It usually starts normally and begins to report errors like above. I have attached the full log file and test data for your debug.

Script for running SVision-pro:

#!/bin/bash
#SBATCH --job-name=svision-pro_germline
#SBATCH --output=%x_%A_%a.out
#SBATCH --error=%x_%A_%a.err
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32gb
#SBATCH --time=72:00:00
#SBATCH --partition=medium
#SBATCH -A proj-fs0002

source /users/u250191/.bashrc 
conda activate svision-pro-env

ref38="/users/u250191/ryan_scratch_ln/reference/human-grch38.fasta"
access_bed="/users/u250191/ryan_scratch_ln/tools/SVision-pro/src/pre_process/hg38.access.10M.bed"
WORK_DIR=$(pwd) 
default_model_path="/users/u250191/ryan_scratch_ln/tools/SVision-pro/src/pre_process/model_liteunet_256_8_16_32_32_32.pth"

input_bam=$1
#WARNING: absolute path of bam file is required!
samplename=$2
#datatype=$3

SVision-pro --out_path ${WORK_DIR} --target_path ${input_bam} \
        --genome_path ${ref38} --model_path ${default_model_path} --access_path ${access_bed} \
        --sample_name ${samplename} --detect_mode germline \
        --process_num 8

I am assuming the error is raised due to lack of information on CIGAR column required by SVision-pro. I attached the file of CIGAR column of pacbio_vacmap chr1_40000000_50000000, which corresponds to the first error.

Please let me know if there is anything I can do, thanks again for your time!

[jamesc99]

Hi @songbowang125

Is there any update regarding this issue?

Thank you!

[songbowang125]

Hi,

I will make some upgrades tomorrow.

I haven't test any BAM files produced by VACmap before, but I think CIGAR strings are very essential for SV detection. Why not using the commonly used aligners such as minimap2?

thanks

[songbowang125]

Hi, I have upgraded the codes and you can try the new version v1.9. If any new errors, please let me know.

[jamesc99]

@songbowang125

Thanks for your update. I have been able to run SVision-pro on VACmap BAMs.

Why not using the commonly used aligners such as minimap2?

VACmap shows better performance in complex variants detection than minimap2. As an example, in our test, SVision-pro can detect 30-60% more complex SVs in VACmap BAMs.

Best