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Description
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 !