salmon shell script to automate quant

Question

[amitpande74]

Hi, I have 56 fastq.gz file in a folder called SRR. The files are paired end data and their names are SRR8068516_1.fastq.gz to SRR8068543_1.fastq.gz. The other pair is named likewise SRR8068516_2.fastq.gz to SRR8068543_2.fastq.gz. I wrote a shell script:

#!/bin/bash
for fn in /media/usr/LaCie/data/SRR{SRR80685..SRR80685};
do
samp=`basename ${fn}`
echo "Processing sample ${samp}"
./bin/salmon quant -i /home/usr/Downloads/salmon-1.2.1_linux_x86_64/transcripts_index/ -l A -1 /media/usr/LaCie/data/SRR ${fn}/${samp}_1.fastq.gz -2 /media/usr/LaCie/data/SRR ${fn}/${samp}_2.fastq.gz -p 8 --validateMappings -o quants/${samp}_quant
done

But on executing it gives me an error:

(base) usr@usr-X705UDR:~/Downloads/salmon-1.2.1_linux_x86_64$ ./salmon.sh 
Processing sample SRR{SRR80685..SRR80685}
Version Info: This is the most recent version of salmon.
### salmon (mapping-based) v1.2.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /home/usr/Downloads/salmon-1.2.1_linux_x86_64/transcripts_index/ }
### [ libType ] => { A }
### [ mates1 ] => { /media/usr/LaCie/data/SRR /media/amit/LaCie/data/SRR{SRR80685..SRR80685}/SRR{SRR80685..SRR80685}_1.fastq.gz }
### [ mates2 ] => { /media/usr/LaCie/data/SRR /media/amit/LaCie/data/SRR{SRR80685..SRR80685}/SRR{SRR80685..SRR80685}_2.fastq.gz }
### [ threads ] => { 8 }
### [ validateMappings ] => { }
### [ output ] => { quants/SRR{SRR80685..SRR80685}_quant }
Logs will be written to quants/SRR{SRR80685..SRR80685}_quant/logs
[2020-05-02 14:03:57.281] [jointLog] [info] setting maxHashResizeThreads to 8
[2020-05-02 14:03:57.281] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-05-02 14:03:57.281] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-05-02 14:03:57.281] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-05-02 14:03:57.281] [jointLog] [info] parsing read library format
[2020-05-02 14:03:57.281] [jointLog] [info] There is 1 library.
Exception : [
The following errors were detected with the read files
======================================================
ERROR: file [/media/usr/LaCie/data/SRR{SRR80685..SRR80685}/SRR{SRR80685..SRR80685}_1.fastq.gz] does not appear to exist!

]
./bin/salmon quant was invoked improperly.
For usage information, try ./bin/salmon quant --help
Exiting.

Kindly help as to which step is not appropriate in the code.

Answer 1

[ATpoint]

IDX="/home/usr/Downloads/salmon-1.2.1_linux_x86_64/transcripts_index/"
for fn in /media/usr/LaCie/data/SRR/SRR{80685..80685}
  do
    samp=`basename ${fn}`
    echo "Processing sample ${samp}"
    ./bin/salmon quant -i $IDX -l A -1 ${fn}_1.fastq.gz -2 ${fn}_2.fastq.gz -p 8 --validateMappings -o quants/${samp}_quant
  done

1 ) {From..To} takes integers, therefore it must be SRR{From..To}.

2) There was also a / missing after SRR and before {SRR80685..SRR80685}

3) ${fn} did already include the entire path to the basenames, you were providing it twice, this is what this line indicated:

### [ mates1 ] => { /media/usr/LaCie/data/SRR /media/amit/LaCie/data/SRR{SRR80685..SRR80685}/SRR{SRR80685..SRR80685}_1.fastq.gz }