Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ERROR: Could not open alignment.bam #16

Open
Hulanyue opened this issue Jun 25, 2020 · 0 comments
Open

ERROR: Could not open alignment.bam #16

Hulanyue opened this issue Jun 25, 2020 · 0 comments

Comments

@Hulanyue
Copy link

Hi!
When I run ./hercules -2 -li long.fasta -ai alignment.bam -si preprocessing/short.fasta -t 30 -o corrected_long.fasta in Terminal,it's Okay!

And the result is:
Long Read: le.fa
Short read: preprocessing/short.fasta
Alignment File: bowtie/alignment.bam
Output file: corrected_long.fasta
Will output coverage?: No
Min mapping quality: 0
Max Coverage: 1
Filter size: 100
Maximum insertion: 3
Maximum deletion: 10
Match transition probability: 0.7
Insertion transition probability: 0.25
Deletion transition probability: 0.05
Deletion transition factor: 2.5
Match emission probability: 0.97
Mismatch emission probability: 0.01
Insertion emission probability: 0.333333
Max thread: 30
Correction has begun...

Results have been written under corrected_long.fasta

But when I debug code (the tool is Vs Code),I input command : "args": ["-2","-li" ,"le.fa","-ai","alignment.bam","-si","bin/preprocessing/short.fasta","-t","4","-o","corrected_long.fasta"],in launch.json and run ,it show me the error:
Long Read: le.fa
Short read: bin/preprocessing/short.fasta
Alignment File: alignment.bam
Output file: corrected_long.fasta
Will output coverage?: No
Min mapping quality: 0
Max Coverage: 1
Filter size: 100
Maximum insertion: 3
Maximum deletion: 10
Match transition probability: 0.7
Insertion transition probability: 0.25
Deletion transition probability: 0.05
Deletion transition factor: 2.5
Match emission probability: 0.97
Mismatch emission probability: 0.01
Insertion emission probability: 0.333333
Max thread: 4
ERROR: Could not open alignment.bam

I try to make it but I can't, so can you give me some advice?

Thank you !

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant