Open mdAdnn opened 2 years ago
Hi @mdAdnn
The manifest should be a text file where each line gives the path to a bam file. Additionally, the test data included with the program is for unit testing. You will need a WGS bam file as input to the program.
Thanks, Xiao
Hi,
I have WGS bam file. And also added the path in text file but I'm getting this error:
python3 star_caller.py --manifest '/media/sf_Shared/Cyrius-master/caller/tests/test_data/Path.txt' --genome 19 --prefix cyr --outDir test_output
WARNING:root:Input file for sample NA12878_hg19 does not exist.
INFO:root:Writing to json at 2022-09-28 19:24:37.329075
INFO:root:Writing to tsv at 2022-09-28 19:24:37.331685
What's in your Path.txt? Does it contain the absolute path to your NA12878_hg19.bam?
yes
'/media/sf_Shared/Cyrius-master/NA12878_hg19.bam'
'/media/sf_Shared/Cyrius-master/NA12878_hg19.bam.bai'
now its showing the following error when I reistalled the file: python star_caller.py --manifest '/media/sf_Shared/Cyrius-master/caller/tests/test_data/Path.txt' --genome 19 --prefix cyr --outDir test_output
WARNING:root:Input file for sample NA12878_hg19 does not exist.
WARNING:root:Input file for sample NA12878_hg19.bam does not exist.
INFO:root:Writing to json at 2022-09-29 13:04:01.454385
INFO:root:Writing to tsv at 2022-09-29 13:04:01.455826
Could you remove the quotes and retry? Also, no need to have a line for the .bai file.
hi I got output file from someone else but when I'm runing the lmpgx code its showing the following error python3 src/pgx.py -b BAM/CRAM -s NA18632 -o '/media/sf_Shared/PGx-master' -c lib/config.yml
Traceback (most recent call last):
File "/home/adnan/PGx-master/src/pgx.py", line 9, in
from discover_variants import _annotate_genotypes
File "/home/adnan/PGx-master/src/discover_variants.py", line 1, in
import vcf
File "/home/adnan/anaconda3/lib/python3.9/site-packages/vcf/init.py", line 166, in
from parser import Reader, Writer
ImportError: cannot import name 'Reader' from 'parser' (/home/adnan/anaconda3/lib/python3.9/lib-dynload/parser.cpython-39-x86_64-linux-gnu.so)
Hi @mdAdnn this does not seem to be related to Cyrius. Please send this question to lmpgx authors. Thanks.
Hi, what are the genes cyrius deals with? Like is it specifically for CYP2D6 and CYP2D7 or some other genes as well?
Cyrius is a caller for CYP2D6.
Hi,
Im getting this error despite everything properly, such as WGS bam file.
python3 star_caller.py --manifest /media/sf_Shared/Cyrius-master/caller/tests/test_data/NA23275.bam --genome 37 --prefix cyr --outDir test_output
Traceback (most recent call last):
File "/media/sf_Shared/Cyrius-master/star_caller.py", line 562, in
File "/media/sf_Shared/Cyrius-master/star_caller.py", line 513, in main
File "/home/adnan/anaconda3/lib/python3.9/codecs.py", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte