able not found while opening manager within database module

[AnushaC]

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

[GenoMax]

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.