Chromosome names

[Liverworks]

Hi!

I am trying to use Aquila_stLFR for an animal species. My reference fasta has chromosome names like Scaffold_[number], not chr[number].

Preprocessing was OK, but on step1 I get errors:

4799941
36.012870783203375
21.0
389026.0
3.0
Traceback (most recent call last):
  File "/home/aglushkevich/.conda/envs/anpython3/lib/python3.7/site-packages/bin/Run_h5_all_multithreads.py", line 148, in save_variant_dict
    chr_num = int(data[0][3:])
ValueError: invalid literal for int() with base 10: 'ffold_2'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/aglushkevich/.conda/envs/anpython3/lib/python3.7/site-packages/bin/Run_h5_all_multithreads.py", line 591, in <module>
    variant_dict = save_variant_dict(vcf_file,mbq_threshold,avg_depth,out_dir)
  File "/home/aglushkevich/.conda/envs/anpython3/lib/python3.7/site-packages/bin/Run_h5_all_multithreads.py", line 190, in save_variant_dict
    variant_dict[(chr_num,pos)] = [ref,alt,GT]
UnboundLocalError: local variable 'chr_num' referenced before assignment
[main_samview] region "chr16" specifies an unknown reference name. Continue anyway.
[main_samview] region "chr1" specifies an unknown reference name. Continue anyway.
[main_samview] region "chr2" specifies an unknown reference name. Continue anyway.
samtools depth: can't parse region "chr16"
samtools depth: can't parse region "chr2"
samtools depth: can't parse region "chr1"

Can it be fixed, or should I change my reference contig names?

[maiziex]

Hi, Aquila_stLFR only uses regular reference fasta file and the contig name needs to be "chr1", "chr2", etc.

[maiziex]

Hi, Aquila_stLFR only uses regular reference fasta file and the contig name needs to be "chr1", "chr2", etc. Maizie (Xin) Zhou, Ph.D. Assistant Professor Biomedical Engineering, Computer Science, and Data Science Institute Vanderbilt University 5919 Stevenson Center Nashville, TN 37235 Phone: 615-343-6843 https://lab.vanderbilt.edu/maizie-zhou-lab/<https://lab.vanderbilt.edu/maizie-zhou-lab/> <https://lab.vanderbilt.edu/maizie-zhou-lab/>

…

________________________________ From: Liverworks ***@***.***> Sent: Friday, October 7, 2022 3:53 AM To: maiziex/Aquila_stLFR ***@***.***> Cc: Subscribed ***@***.***> Subject: [maiziex/Aquila_stLFR] Chromosome names (Issue #5) Hi! I am trying to use Aquila_stLFR for an animal species. My reference fasta has chromosome names like Scaffold_[number], not chr[number]. Preprocessing was OK, but on step1 I get errors: `4799941 36.012870783203375 21.0 389026.0 3.0 Traceback (most recent call last): File "/home/aglushkevich/.conda/envs/anpython3/lib/python3.7/site-packages/bin/Run_h5_all_multithreads.py", line 148, in save_variant_dict chr_num = int(data[0][3:]) ValueError: invalid literal for int() with base 10: 'ffold_2' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/aglushkevich/.conda/envs/anpython3/lib/python3.7/site-packages/bin/Run_h5_all_multithreads.py", line 591, in variant_dict = save_variant_dict(vcf_file,mbq_threshold,avg_depth,out_dir) File "/home/aglushkevich/.conda/envs/anpython3/lib/python3.7/site-packages/bin/Run_h5_all_multithreads.py", line 190, in save_variant_dict variant_dict[(chr_num,pos)] = [ref,alt,GT] UnboundLocalError: local variable 'chr_num' referenced before assignment [main_samview] region "chr16" specifies an unknown reference name. Continue anyway. [main_samview] region "chr1" specifies an unknown reference name. Continue anyway. [main_samview] region "chr2" specifies an unknown reference name. Continue anyway. samtools depth: can't parse region "chr16" samtools depth: can't parse region "chr2" samtools depth: can't parse region "chr1" ` Can it be fixed, or should I change my reference contig names? — Reply to this email directly, view it on GitHub<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmaiziex%2FAquila_stLFR%2Fissues%2F5&data=05%7C01%7Cmaizie.zhou%40vanderbilt.edu%7C52b565bf07a24d3043ae08daa8415d6c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C638007295938601171%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LnrVKN4f4uhy8SS%2BI62TWrnlunzbeLkebZuTpbIfwJI%3D&reserved=0>, or unsubscribe<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FABMOIQ4ZQIR4KUGJGOJZX5LWB7QHPANCNFSM6AAAAAAQ7MIE7Y&data=05%7C01%7Cmaizie.zhou%40vanderbilt.edu%7C52b565bf07a24d3043ae08daa8415d6c%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C638007295938601171%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Mqb%2F%2BLCW3w0RvMVOKRb1vdfa6yLZ5LhKcy7KEjuRPJE%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>