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Old 09-12-2019, 06:48 AM   #7
Manuelly
Junior Member
 
Location: Brazil

Join Date: Aug 2019
Posts: 7
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1.I opened the directory with the files in the terminal.
2. Then I used the following command:
reformat.sh 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(Tools.java:1157)
at jgi.ReformatReads.<init>(ReformatReads.java:337)
at jgi.ReformatReads.main(ReformatReads.java:50)
4.file extensions contained in the directory
/home/lucasmalzoni/Documentos/DOC/1-file_aligned_SortSam_MarkDuplicates.bai
/home/lucasmalzoni/Documentos/DOC/1-file_aligned_SortSam_MarkDuplicates.bam
/home/lucasmalzoni/Documentos/DOC/1-file_aligned_SortSam_MarkDuplicates.metrics.txt

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