search

pauline-ng / SIFT4G_Create_Genomic_DB

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.jar to annotate VCF files.
GNU General Public License v3.0
21 stars 7 forks source link

I can not creat database #76

Closed NiklausMikaelson12138 closed 9 months ago

NiklausMikaelson12138 commented 1 year ago

Hi，while I creat a database，i recieve the massage said ‘’Unable to read from /home/zyi/program/sift/SIFT4G_Create_Genomic_DB/test_files/covid_19/singleRecords/MN908947.3.singleRecords_noncoding‘’，please how can i go through. The issue come from the script named make_regions_file.py

NiklausMikaelson12138 commented 1 year ago

Unable to read from /home/zyi/program/sift/SIFT4G_Create_Genomic_DB/test_files/covid_19/singleRecords/MN908947.3.singleRecords_noncoding Traceback (most recent call last): File "/home/zyi/program/sift/SIFT4G_Create_Genomic_DB/make_regions_file.py", line 69, in get_regions (chrom_file, out_file) File "/home/zyi/program/sift/SIFT4G_Create_Genomic_DB/make_regions_file.py", line 32, in get_regions pos = get_pos (first_line) File "/home/zyi/program/sift/SIFT4G_Create_Genomic_DB/make_regions_file.py", line 8, in get_pos return int (fields[0]) ValueError: invalid literal for int() with base 10: ''

pauline-ng commented 9 months ago

I just released a Dockerfile to help users with installation problems. Please see if this helps.

NiklausMikaelson12138 commented 9 months ago

你好，我已收到您的来信，我会尽快回复，谢谢