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Old 09-11-2019, 07:44 AM   #5
Manuelly
Junior Member
 
Location: Brazil

Join Date: Aug 2019
Posts: 7
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I tried to execute the command and the following message appeared. Do you know how I can solve this?
/media/lucasmalzoni/Seagate Backup Plus Drive1/Joao/MT/02-Bam$ reformat.sh in=${i}.bam out=${i}.fa
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(Tools.java:1157)
at jgi.ReformatReads.<init>(ReformatReads.java:337)
at jgi.ReformatReads.main(ReformatReads.java:50)
(base) lucasmalzoni@galton:/media/lucasmalzoni/Seagate Backup Plus Drive1/Joao/MT/02-Bam$
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