unix - For loop for sequence alignment using STAR

Question

I am trying to run a sequence alignment with STAR. I have a total of 28 files paired-end files, 14 R1 and 14 R2. My files are called like this:

mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam_R2.fq
mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam_R2.fq
mapped_trimmed.LLC1b_Aligned.sortedByCoord.out.bam_R2.fq
mapped_trimmed.LLC1a_Aligned.sortedByCoord.out.bam_R2.fq
mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC1b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC1a_Aligned.sortedByCoord.out.bam_R1.fqq

The code I have written to run star so far is this one:

#!/bin/bash --login
#$ -cwd
#$ -l short
#$ -pe smp.pe 12

module load apps/intel-18.0/star/2.7.2b

#get only files names
for i in *R1.fq; do name=$(basename ${i} _R1.fq);

  STAR --genomeDir /scratch/2021.01.25_salmon_transcripts/Genome  #Path to the index generated previously
  --runThreadN 12  #Number of cores
  --readFilesIn ${name}_R1.fq ${name}_R2.fq  #Path to the input files (forward and reverse)
  --outFileNamePrefix ${name}_aligned_transcriptome  #Prefix to the output files
  --outSAMtype BAM SortedByCoordinate  
  --limitBAMsortRAM 31000000000
done

Yet I keep getting this error

/opt/site/sge/default/spool/node403/job_scripts/1635775: line 17: syntax error near unexpected token `('
/opt/site/sge/default/spool/node403/job_scripts/1635775: line 17: `  --readFilesIn ${name}_R1.fq ${name}_R2.fq  #Path to the input files (forward and reverse)'

This is the output of the part of the code that should feed into line 17

for i in *R1.fq; do name=$(basename ${i} _R1.fq); echo $name
> done
mapped_trimmed.LLC1a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC1b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC2a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC2b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC3a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC3b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC4a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC4b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC5a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC5b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC6a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC6b_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam
mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam

And this is line 17 itself and it looks alright. So, I don't understand why this loop is not working

for i in *R1.fq; do name=$(basename ${i} _R1.fq); echo ${name}_R1.fq; done
mapped_trimmed.LLC1a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC1b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC2a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC2b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC3a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC3b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC4a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC4b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC5a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC5b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC6a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC6b_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC7a_Aligned.sortedByCoord.out.bam_R1.fq
mapped_trimmed.LLC7b_Aligned.sortedByCoord.out.bam_R1.fq

Which is exactly how the files are called in my folder.

question from:https://stackoverflow.com/questions/65903688/for-loop-for-sequence-alignment-using-star

Answer 1

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