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Unclear error when using BAM from Nanopore data #15

Open mcortes-lopez opened 3 years ago

mcortes-lopez commented 3 years ago

Hi, I am trying to use bamsnap with long read data from Nanopore aligned reads using minimap. I do not manage to get any output and the exit error is a number that I cannot debug (when I Google "KeyError: 28747748" it does not return any meaningful results). Here is the code that I am using and the output:

bamsnap -bam ../aln_bam/dRNA_aln.sorted.bam -pos chr16:28932034 -out ./test.png

2021-01-26 23:07:53,894 : [INFO] Total running time: 0.0 sec Process proc 1: Traceback (most recent call last): File "/home/mcortesl/.conda/envs/myenv/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/home/mcortesl/.conda/envs/myenv/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/home/mcortesl/.conda/envs/myenv/lib/python3.7/site-packages/bamsnap/bamsnap.py", line 229, in run_process_drawplot_bamlist imagefname = bsplot.drawplot_bamlist(pos1, image_w, bamlist, xscale, refseq) File "/home/mcortesl/.conda/envs/myenv/lib/python3.7/site-packages/bamsnap/bamsnap.py", line 467, in drawplot_bamlist ia_sub = self.get_bamplot_image(bam, pos1, image_w, xscale, refseq) File "/home/mcortesl/.conda/envs/myenv/lib/python3.7/site-packages/bamsnap/bamsnap.py", line 351, in get_bamplot_image rset.calculate_readmap(is_strand_group=True) File "/home/mcortesl/.conda/envs/myenv/lib/python3.7/site-packages/bamsnap/drawreadset.py", line 305, in calculate_readmap r = DrawRead(a, self.refseq) File "/home/mcortesl/.conda/envs/myenv/lib/python3.7/site-packages/bamsnap/drawread.py", line 66, in __init__ self.set_read_variant() File "/home/mcortesl/.conda/envs/myenv/lib/python3.7/site-packages/bamsnap/drawread.py", line 126, in set_read_variant refbase = self.refseq[gp].upper() KeyError: 28747748

Could this be a problem because of the formatting of the minimap2 aligned file?

yinshiyi commented 2 years ago

I have similar observation using nanopore data, it seems failed at Process proc 1: Traceback (most recent call last): File "/home/shiyi/miniconda3/lib/python3.9/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/shiyi/miniconda3/lib/python3.9/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/shiyi/miniconda3/lib/python3.9/site-packages/bamsnap/bamsnap.py", line 235, in run_process_drawplot_bamlist imagefname = bsplot.drawplot_bamlist(pos1, image_w, bamlist, xscale, refseq) File "/home/shiyi/miniconda3/lib/python3.9/site-packages/bamsnap/bamsnap.py", line 473, in drawplot_bamlist ia_sub = self.get_bamplot_image(bam, pos1, image_w, xscale, refseq) File "/home/shiyi/miniconda3/lib/python3.9/site-packages/bamsnap/bamsnap.py", line 357, in get_bamplot_image rset.calculate_readmap(is_strand_group=True) File "/home/shiyi/miniconda3/lib/python3.9/site-packages/bamsnap/drawreadset.py", line 305, in calculate_readmap r = DrawRead(a, self.refseq) File "/home/shiyi/miniconda3/lib/python3.9/site-packages/bamsnap/drawread.py", line 66, in init self.set_read_variant() File "/home/shiyi/miniconda3/lib/python3.9/site-packages/bamsnap/drawread.py", line 125, in set_read_variant base = self.readseq_with_softclipped[bidx] TypeError: 'NoneType' object is not subscriptable

lskatz commented 1 year ago

Has anyone solved this issue?

comery commented 11 months ago

Has anyone solved this issue?

This may be helpful for you. see Issue#26