Needle error - cannot get second filename

Hi all,

I'm trying to loop through my sequence list for needle command below:

while IFS="," read -r c1 c2
do \  
echo ${c1} ${c2}; \
res=$(echo ${c1} | sed 's/_*.fasta//') \    
needle -asequence "${c1}" -bsequence "${c2}" -gapopen 10 -gapextend 0.5 -outfile ${res}.needle \    
done < <(tail -n +2 compare.txt)

compare.txt is comma-delimited file that contains list below:

list1,list2
Sample1.fasta,Sample6.fasta
Sample2.fasta,Sample7.fasta

But I got error that it cannot read the files for -bsequence although I have checked that file existed, and I can echo the second variable correctly.

Error:

Sample1.fasta Sample6.fasta
Needleman-Wunsch global alignment of two sequences
'rror: Failed to open filename 'Sample6.fasta
'rror: Unable to read sequence 'Sample6.fasta
Died: needle terminated: Bad value for '-bsequence' and no prompt
Sample2.fasta Sample7.fasta
Needleman-Wunsch global alignment of two sequences
'rror: Failed to open filename 'Sample7.fasta
'rror: Unable to read sequence 'Sample7.fasta
Died: needle terminated: Bad value for '-bsequence' and no prompt

I believe it is not error from needle command but actually from the scripting but I'm not sure what terms I can google for this error. Appreciate if anyone can help with this.

needle bash

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written 5.1 years ago by kaixas •

Looks like your code should work. Are the files not in the directory where you are running this from? Try adding relative or full paths to the file names.

$ while IFS="," read -r c1 c2; do echo ${c1} ${c2}; res=$(echo ${c1} | sed 's/_*.fasta//'); echo needle -asequence "${c1}" -bsequence "${c2}" -gapopen 10 -gapextend 0.5 -outfile ${res}.needle; done < <(tail -n +2 compare.txt)
Sample1.fasta Sample6.fasta
needle -asequence Sample1.fasta -bsequence Sample6.fasta -gapopen 10 -gapextend 0.5 -outfile Sample1.needle
Sample2.fasta Sample7.fasta
needle -asequence Sample2.fasta -bsequence Sample7.fasta -gapopen 10 -gapextend 0.5 -outfile Sample2.needle

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written 5.1 years ago by GenoMax

I did that too and it doesn't work. I tried to run the code manually like below and it worked so the files are definitely in the directory.

needle -asequence Sample1.fasta -bsequence Sample6.fasta -gapopen 10 -gapextend 0.5 -outfile t.needle

I did try add echo to check whether it prints correctly or not but in terminal it only printed this:

while IFS=$'\t' read -r c1 c2; do echo needle -asequence ${c1} -bsequence ${c2} -gapopen 10 -gapextend 0.5 -outfile t.needle; done < <(tail -n +2 compare.txt)

 -gapopen 10 -gapextend 0.5 -outfile t.needleence Sample6.fasta
 -gapopen 10 -gapextend 0.5 -outfile t.needleence Sample7.fasta

But if I added > text.txt at the end of the command, it can print correctly in the file so that is weird.

needle -asequence Sample1.fasta -bsequence Sample6.fasta
 -gapopen 10 -gapextend 0.5 -outfile t.needle
needle -asequence Sample2.fasta -bsequence Sample7.fasta
 -gapopen 10 -gapextend 0.5 -outfile t.needle

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written 5.1 years ago by kaixas •

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