I am so confused about the KeyError: 'M'. I've used it with the sam bam file, however, now it report the error.I tried few times and reinstall the git. The bug still exits.
DEBUG : Creating converter from 7 to 5
DEBUG : Creating converter from 5 to 7
DEBUG : Creating converter from 7 to 5
DEBUG : Creating converter from 5 to 7
INFO : Parameter list:
Sample = out
Reference annotation index = /home/data/xxxx/xxxxxx/scte/macFas5.exclusive.idx
Minimum number of genes required = 200
Minimum number of counts required = None
Number of threads = 1
INFO : Loading the genome annotation index... 2022-03-08 12:10:31
INFO : Loaded '/home/data/xxxxx/xxxxx/scte/macFas5.exclusive.idx' binary file with 4428688 items
['1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '3', '4', '5', '6', '7', '8', '9', 'X']
INFO : Finished loading the genome annotation index... 2022-03-08 12:11:28
INFO : Processing BAM/SAM files ...2022-03-08 12:11:28
INFO : Input SAM/BAM file appears to be valid
CR UR good
INFO : Done BAM/SAM files processing ...2022-03-08 13:26:22
INFO : Splitting ...2022-03-08 13:26:22
INFO : Executing single thread path
Traceback (most recent call last):
File "/home/data/xxxx/miniconda3/envs/xxxxxxx/bin/scTE", line 4, in import('pkg_resources').run_script('scTE==1.0', 'scTE')
File "/home/data/xx/miniconda3/envs/xxxxxx/lib/python3.8/site-packages/pkg_resources/init.py", line 651, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/data/xxx/miniconda3/envs/xxxxxx/lib/python3.8/site-packages/pkg_resources/init.py", line 1448, in run_script
exec(code, namespace, namespace)
File "/home/data/xxx/miniconda3/envs/xxxxx/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTE", line 169, in
main()
File "/home/data/xxxxx/miniconda3/envs/xxxxxx/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTE", line 129, in main
whitelist = splitAllChrs(chr_list, filename=outname, genenumber=args.genenumber, countnumber=args.countnumber, UMI=args.UMI)
File "/home/data/xxxxxxxx/miniconda3/envs/xxxxxx/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/scTE/base.py", line 260, in splitAllChrs
if line in uniques[chrom]:
KeyError: 'M'
Hi.
I am so confused about the KeyError: 'M'. I've used it with the sam bam file, however, now it report the error.I tried few times and reinstall the git. The bug still exits.
DEBUG : Creating converter from 7 to 5 DEBUG : Creating converter from 5 to 7 DEBUG : Creating converter from 7 to 5 DEBUG : Creating converter from 5 to 7 INFO : Parameter list: Sample = out Reference annotation index = /home/data/xxxx/xxxxxx/scte/macFas5.exclusive.idx Minimum number of genes required = 200 Minimum number of counts required = None Number of threads = 1
INFO : Loading the genome annotation index... 2022-03-08 12:10:31 INFO : Loaded '/home/data/xxxxx/xxxxx/scte/macFas5.exclusive.idx' binary file with 4428688 items ['1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '2', '20', '3', '4', '5', '6', '7', '8', '9', 'X'] INFO : Finished loading the genome annotation index... 2022-03-08 12:11:28
INFO : Processing BAM/SAM files ...2022-03-08 12:11:28 INFO : Input SAM/BAM file appears to be valid CR UR good
INFO : Done BAM/SAM files processing ...2022-03-08 13:26:22
INFO : Splitting ...2022-03-08 13:26:22 INFO : Executing single thread path Traceback (most recent call last): File "/home/data/xxxx/miniconda3/envs/xxxxxxx/bin/scTE", line 4, in
import('pkg_resources').run_script('scTE==1.0', 'scTE')
File "/home/data/xx/miniconda3/envs/xxxxxx/lib/python3.8/site-packages/pkg_resources/init.py", line 651, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/data/xxx/miniconda3/envs/xxxxxx/lib/python3.8/site-packages/pkg_resources/init.py", line 1448, in run_script
exec(code, namespace, namespace)
File "/home/data/xxx/miniconda3/envs/xxxxx/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTE", line 169, in
main()
File "/home/data/xxxxx/miniconda3/envs/xxxxxx/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTE", line 129, in main
whitelist = splitAllChrs(chr_list, filename=outname, genenumber=args.genenumber, countnumber=args.countnumber, UMI=args.UMI)
File "/home/data/xxxxxxxx/miniconda3/envs/xxxxxx/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/scTE/base.py", line 260, in splitAllChrs
if line in uniques[chrom]:
KeyError: 'M'
How can I fix it?
Thanks and best wishes, Chris