You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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 !
The text was updated successfully, but these errors were encountered:
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 !
The text was updated successfully, but these errors were encountered: