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  • the hell

    Hi people. I am having a problem with bwa. I am trying to align fastq file to a reference genome. I've also indexed the reference genome. I went to the directory where my fastq files are and when I " bwa aln reference_genome.fna my_file.fastq" i got the following warning.

    [bwa_seq_open] fail to open file my_file.fastq : No such file or directory

    The file is in the directory, it exist for true and I am seeing it there, and I am calling it from the correct path.

    What's the problem, could you guys give an answer?

  • #2
    Originally posted by alebueno View Post
    The file is in the directory, it exist for true and I am seeing it there, and I am calling it from the correct path.
    Well, we don't see it. How about an 'ls -l' and perhaps a 'pwd' for us to chew on.

    Comment


    • #3
      Also, try using an absolute path to the file.

      Comment


      • #4
        Ok. The file I am trying to align has the name "Bac5_S5_L001_R1_001.fastq" and is not being recognized.

        The ls -l has the following output


        lgmmicrorganismo@lgmmicrorganismo-To-be-filled-by-O-E-M:~/Projeto_Cviolaceum/2015/fechamento_gap$ ls -l
        total 2200020
        -rwxrwxrwx 1 lgmmicrorganismo lgmmicrorganismo 1120717011 Nov 4 16:28 Bac5_S5_L001_R1_001.fastq
        -rwxrwxrwx 1 lgmmicrorganismo lgmmicrorganismo 1118949615 Nov 4 16:29 Bac5_S5_L001_R2_001.fastq
        -rw-rw-r-- 1 lgmmicrorganismo lgmmicrorganismo 4810547 Jan 14 15:32 GCF_000007705.1_ASM770v1_genomic.fna (2)
        -rw-rw-r-- 1 lgmmicrorganismo lgmmicrorganismo 12 Jan 14 15:33 GCF_000007705.1_ASM770v1_genomic.fna (2).amb
        -rw-rw-r-- 1 lgmmicrorganismo lgmmicrorganismo 104 Jan 14 15:33 GCF_000007705.1_ASM770v1_genomic.fna (2).ann
        -rw-rw-r-- 1 lgmmicrorganismo lgmmicrorganismo 4751164 Jan 14 15:33 GCF_000007705.1_ASM770v1_genomic.fna (2).bwt
        -rw-rw-r-- 1 lgmmicrorganismo lgmmicrorganismo 1187772 Jan 14 15:33 GCF_000007705.1_ASM770v1_genomic.fna (2).pac
        -rw-rw-r-- 1 lgmmicrorganismo lgmmicrorganismo 2375592 Jan 14 15:33 GCF_000007705.1_ASM770v1_genomic.fna (2).sa
        -rw-rw-r-- 1 lgmmicrorganismo lgmmicrorganismo 73 Jan 9 13:03 library_bac5.txt~

        Comment


        • #5
          Yes. After I giving the full path it worked. Thank you.

          Comment

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