Fastdump and fastq to bam conversion is creating strange problem

[AnushaC]

Hi All,
Can any body explain me why it is going wrong
I am trying to convert sra to fastq and fastq to bam conversion but it is trying to open my destination file instead of righting to destination file can any body explain me why it is going like this way


#!/bin/bash
#PBS -l nodes=2pn=2
for files in /raid/development/anusha/python_test/shelltest/fetal_brain_sra/*.sra
do
OUT=(${files%.sra}.fastq)
#fastq-dump $files /raid/development/anusha/python_test/shelltest/ttbrianshell/$OUT
#fastq-dump $files > $1/$OUT
fastq-dump $files /raid/development/anusha/python_test/shelltest/ttbrianshell/$OUT
#fastq-dump $files /raid/development/anusha/python_test/shelltest/fb_fq_test/$OUT
#fastq-dump $files /raid/development/anusha/python_test/shelltest/fastqbwa/$OUT

script tried to open:

'/raid/development/anusha/python_test/shelltest/ttbrianshell//raid/development/anusha/python_test/shelltest/fetal_brain_sra/SRR203400.fastq'

same is the case with fastq to bam conversion
#!/bin/bash
#PBS -l nodes=2pn=2
#PATH="/raid/development/anusha/python_test/shelltest/fb_fq_test/"
#OPATH="raid/development/anusha/python_test/shelltest/fb_bam_test"
for files in /raid/development/anusha/python_test/shelltest/fastqbwa/*.fastq #/raid/development/anusha/python_test/shelltest/fb_fq_test/*.fastq
do
OUT=(${files%.fastq}.bam)
ref="/raid/references-and-indexes/hg19/bwa_new/hg19.fa"
#bwa aln -t 4 $1 $files |bwa samse $1 - $files |samtools view -bS - > $2 /$OUT #/raid/development/anusha/python_test/shelltest/fb_bam_test/$OUT
bwa aln -t 4 $ref $files |bwa samse $ref - $files > $1/$OUT #/raid/development/anusha/python_test/shelltest/fetalbrain_bwa_sam/$OUT
# bwa aln -t 4 $ref $files |bwa samse $ref - $files -|samtools view -bS - > /raid/development/anusha/python_test/shelltest/test_bwa_bam/$OUT

done



write to the disk... anusha@cn1:/raid/development/anusha/python_test/shelltest/fastqbwa> for files in "/raid/development/anusha/python_test/shelltest.fastq}.bam); ref="/raid/references-and-indexes/hg19/bwa_new/hg19.fa"; bwa aln -t 4 $ref $files |bwa samse $ref - $files > "raid/development/anusha/python_test/shelltest/ttbrianshell"/$OUT
> done
-bash: raid/development/anusha/python_test/shelltest/ttbrianshell//raid/development/anusha/python_test/shelltest/fastqbwa/*.bam: No such file or directory
[bwa_aln] 17bp reads: max_diff = 2

[dpryan]

Read the usage for fastq-dump, you're executing it wrong. You would have the same problem if you executed it manually (i.e., not via your cluster), which should tell you something. Further, the fact that it's trying to open the file you're specifying for output should also tell you something...

BTW, remember to strip the path off of a file if you're going to do scripting like this.

[AnushaC]

Hi ,
I read the SRA tool kit manual and fast dump syntax is
fastq-dump mySRA.sra
I am not understanding why it is trying to open which I am specifying for output . If problem with fastq dump it should file for that only. It is failing for BWA alignment also and could u explain me where I am going wrong and in what cases it will go like this

Thanks in advance ,
Anusha.ch

[dpryan]

Hi ,
I read the SRA tool kit manual and fast dump syntax is
fastq-dump mySRA.sra

Exactly! It should be obvious from that what you're doing wrong, since you're not doing that!

I should add that the more general syntax for fastq-dump is:

fastq-dump some_dataset.sra some_other_dataset.sra yet_another_dataset.sra ...

It should be apparent that what it and you are expecting are different things...