search

korem-lab / SGVFinder2

Other
5 stars 1 forks source link

An error in svfinder work_on_collection step #7

Closed jiushao12345 closed 9 months ago

jiushao12345 commented 9 months ago

Hello, I have already generated smp file and no errors were reported. Then, I run svfinder work_on_collection command and found the error svfinder work_on_collection --samp_to_map_dir ./Rep_result/ \

--output_dsgv ./Rep_SVs/ \
--output_vsgv ./Rep_SVs/

Running SGVFinder work_on_collection... Found 629 finished samples... Traceback (most recent call last): File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/bin/svfinder", line 8, in sys.exit(run()) File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/lib/python3.10/site-packages/SGVFinder2/cli/svfinder_cli.py", line 113, in run if args.csv_output: AttributeError: 'Namespace' object has no attribute 'csv_output' I try to run the python file: from SGVFinder2 import work_on_collection vsgv, dsgv = work_on_collection( samp_to_map='./Rep_result/', max_spacing=10, min_samp_cutoff=2, delsdetectthresh=0.25, real_del_thresh=0.95, dels_cooc_thresh=0.25, vsgv_dissim_thresh=0.125, vsgv_clip_quantile=0.02, vsgv_fit_interval=0.95, vsgv_fit_method='betaprime', x_coverage=0.01, rate_param=10, vsgv_dense_perc=85, browser_path=None, frames_path=None ) vsgv.to_csv('./vsgv_test.csv') dsgv.to_csv(.'/dsgv_test.csv') I did get two csv file with nothing.(The file only has two quotes, just like "") Looks for your help, thank you. I also found my smp , jspi and jsdel files were too small (less than 1 kb): 13922522014 Jan 22 17:48 re_478180_1_kneaddata_paired.bam 69 Jan 22 20:29 re_478180_1_kneaddata_paired.jsdel 62 Jan 22 20:29 re_478180_1_kneaddata_paired.jspi 10740445117 Jan 22 20:18 re_478180_1_kneaddata_paired.pmp 5 Jan 22 20:29 re_478180_1_kneaddata_paired.smp I try to use several bowtie2 reference database and have the similar results (less than 1 kb). I wonder if this is right.

ym2877 commented 9 months ago

My apologies for the delay @jiushao12345! I just updated with a fix.

jiushao12345 commented 9 months ago

hi, @ym2877, thanks for your reply. I reinstall svfinder2. And I found another question. I use the command "svfinder work_on_collection --help" and found the errors: Traceback (most recent call last): File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/bin/svfinder", line 5, in from SGVFinder2.cli.svfinder_cli import run File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/lib/python3.10/site-packages/SGVFinder2/init.py", line 3, in from .createdb import create_db_from_reps File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/lib/python3.10/site-packages/SGVFinder2/createdb.py", line 10, in from ICRAUtils import _open_gz_indif, _set_logging_handlers ModuleNotFoundError: No module named 'ICRAUtils' And I use the command "icra --help" there was also the same error. Traceback (most recent call last): File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/bin/icra", line 5, in from SGVFinder2.cli.icra_cli import run File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/lib/python3.10/site-packages/SGVFinder2/init.py", line 3, in from .createdb import create_db_from_reps File "/storage/zhenghoufengLab/guanpenglin/minicoda3/envs/sgvfinder2/lib/python3.10/site-packages/SGVFinder2/createdb.py", line 10, in from ICRAUtils import _open_gz_indif, _set_logging_handlers ModuleNotFoundError: No module named 'ICRAUtils'

ym2877 commented 9 months ago

@jiushao12345 my apologies- fixed this issue as well.