What is the output of fixchr?

[Surbhigrewal]

Hi @mnshgl0110

I ran fixchr on a sam file using the command

fixchr -c ref.query.sam -r ref.fasta -q query.fasta -F S

The st.out says:
�[0;49;32m2025-03-06 09:21:43,680 - fixchr - INFO - Reading alignments (fixchr.py:68)�[0m
�[0;49;32m2025-03-06 10:44:24,660 - fixchr - INFO - Selecting homologous chromosomes (fixchr.py:80)�[0m
�[0;49;93m2025-03-06 10:44:25,239 - homchr - WARNING - Chromosomes IDs do not match in the two genomes (func.py:664)�[0m
�[0;49;32m2025-03-06 11:45:25,688 - fixchr - INFO - Checking chromosome direction (fixchr.py:87)�[0m
�[0;49;93m2025-03-06 11:45:27,529 - fixchr - WARNING - Inverting query chromosomes: ['Chr1', 'Chr2', 'Chr3', 'Chr4', 'Chr6'] (fixchr.py:90)�[0m
�[0;49;32m2025-03-06 11:45:35,014 - fixchr - INFO - Writing output files (fixchr.py:104)�[0m
�[0;49;32m2025-03-06 12:46:18,284 - fixchr - INFO - Finished (fixchr.py:119)�[0m

But the only new files I see are
homologous.pdf
input_alignments.txt

Should there be modified query sequence fasta too?

Not sure what should be the input for syri from this result.

[octpalacios]

Hi,

In your terminal, run the following command:
ls -alth

This will display the files, including .fixchr.qry.filtered.fa and .fixchr.ref.filtered.fa, and others.