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  • able not found while opening manager within database module

    Hi All,
    I am trying converting sra to bam file using for group of sra files .
    I using following code
    #!/bin/bash

    while read line; do
    OUT=${line%.sra}.bam
    fastq-dump -Z $line | bowtie -v 3 -k 2 --sam $2 - | samtools view -bS -o $OUT -
    done < $1
    cat outputsra.txt
    SRR203400.sra
    SRR203401.sra
    SRR203402.sra
    SRR203403.sra
    SRR203404.sra
    SRR203405.sra
    SRR203406.sra
    SRR203407.sra
    SRR203408.sra
    SRR203409.sra
    It is working fine if it is a single sra file but it is very very long time to execute . And also if i run for the whole file

    it is giving me this error
    anusha@cn1:/raid/development/anusha/python_test/shelltest> ./readoutputsra1.sh SRX062364.output.txt /raid/references-and-indexes/hg19/bowtie-indexes/hg19
    2013-10-17T20:55:24 fastq-dump.2.1.12 err: table not found while opening manager within database module - failed to open 'SRR203400.sra'
    Written 0 spots total

    =============================================================
    An error occurred during processing.
    A report was generated into the file '/home/anusha/ncbi_error_report.xml'.
    If the problem persists, you may consider sending the file
    to '[email protected]' for assistance.
    =============================================================

    Warning: Could not find any reads in "-"
    # reads processed: 0
    # reads with at least one reported alignment: 0 (0.00%)
    # reads that failed to align: 0 (0.00%)
    No alignments
    [samopen] SAM header is present: 25 sequences.
    [sam_read1] reference 'ID:Bowtie VN:0.12.7 CL:"bowtie -v 3 -k 2 --sam /raid/references-and-indexes/hg19/bowtie-indexes/hg19 -"
    ' is recognized as '*'.
    [main_samview] truncated file.
    2013-10-17T20:55:30 fastq-dump.2.1.12 err: table not found while opening manager within database module - failed to open 'SRR203401.sra'
    Written 0 spots total

    =============================================================
    An error occurred during processing.
    A report was generated into the file '/home/anusha/ncbi_error_report.xml'.
    If the problem persists, you may consider sending the file
    to '[email protected]' for assistance.
    =============================================================
    I tried downlaoding new sra file but it did not work . Can anybody suggest what is happening

    Thanks in advance ,
    Anusha.Ch

  • #2
    Anusha,

    Make this easy on yourself and just download the fastq files for these data sets directly from ENA.

    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/S...03400.fastq.gz
    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/S...03401.fastq.gz
    ftp://ftp.sra.ebi.ac.uk/vol1/fastq/S...03402.fastq.gz

    and so on. You get the idea.

    *Devon Ryan gets thanks for providing this tip in a past fastq-dump related thread.

    That said: You could try providing path of the sra file (i.e. ./file.sra etc) when you run the fastq-dump. That seems to work for some errors.
    Last edited by GenoMax; 10-17-2013, 02:03 PM.

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