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Old 09-12-2019, 05:48 AM   #7
Junior Member
Location: Brazil

Join Date: Aug 2019
Posts: 7

1.I opened the directory with the files in the terminal.
2. Then I used the following command: in=${i}.bam out=${i}.fa
3. I received the following message:
java -ea -Xms300m -cp /home/lucasmalzoni/anaconda3/opt/bbmap-38.67-0/current/ jgi.ReformatReads in=.bam out=.fa
Executing jgi.ReformatReads [in=.bam, out=.fa]

Exception in thread "main" java.lang.RuntimeException: Can't read file '.bam'
at shared.Tools.testInputFiles(
at jgi.ReformatReads.<init>(
at jgi.ReformatReads.main(
4.file extensions contained in the directory

I don't understand why it's not working.
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