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awk runs and produces output but with error

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# 1  
Old 08-02-2016
awk runs and produces output but with error
When I run the awk below, I get an error message

Code:
awk -v OFS='\t' '$(NF-1)=="Benign" || ($(NF-2) OFS $(NF-1))=="Likely Benign" {$(NF)=$(NF-2) OFS $(NF-1)} {print $0 }' input
awk: cmd. line:1: (FILENAME=VUS FNR=8) fatal: attempt to access field -1

input
Code:
Chr    Start    End    Ref    Alt    Func.refGene    AAChange.refGene    PopFreqMax    CLINSIG    Classification

The code ran with no error before I added $7 and I also used the below awk to see what NF equals, but am not able to correct the error:

Code:
awk 'NR==1{for(i=1;i<=NF;i++){print "Number of field in terms of NF is--> NF-" NF-i", value is-->" $i}}' file.txt
Number of field in terms of NF is--> NF-9, value is-->Chr
Number of field in terms of NF is--> NF-8, value is-->Start
Number of field in terms of NF is--> NF-7, value is-->End
Number of field in terms of NF is--> NF-6, value is-->Ref
Number of field in terms of NF is--> NF-5, value is-->Alt
Number of field in terms of NF is--> NF-4, value is-->Func.refGene
Number of field in terms of NF is--> NF-3, value is-->AAChange.refGene
Number of field in terms of NF is--> NF-2, value is-->PopFreqMax
Number of field in terms of NF is--> NF-1, value is-->CLINSIG
Number of field in terms of NF is--> NF-0, value is-->Classification

Thank you especially @RavinderSingh13 Smilie
# 2  
Old 08-02-2016
What does the next line of your input file look like?
This User Gave Thanks to Don Cragun For This Post:
cmccabe
# 3  
Old 08-02-2016
Empty line in input file. Try:
Code:
awk -v OFS='\t' 'NF && ($(NF-1)=="Benign" || ($(NF-2) OFS $(NF-1))=="Likely Benign") {$(NF)=$(NF-2) OFS $(NF-1)} {print $0 }' input

This User Gave Thanks to rdrtx1 For This Post:
cmccabe
# 4  
Old 08-02-2016
The below is what the data looks like. Thank you Smilie.

Code:
Chr    Start    End    Ref    Alt    Func.refGene    AAChange.refGene    PopFreqMax    CLINSIG    Classification
chr1    43395635    43395635    C    T    exonic        0.12    Benign    
chr1    43396414    43396414    G    A    exonic        0.14    Benign

# 5  
Old 08-02-2016
Quote:
Originally Posted by cmccabe
The below is what the data looks like. Thank you Smilie.

Code:
Chr    Start    End    Ref    Alt    Func.refGene    AAChange.refGene    PopFreqMax    CLINSIG    Classification
chr1    43395635    43395635    C    T    exonic        0.12    Benign    
chr1    43396414    43396414    G    A    exonic        0.14    Benign

That is strange. From your script, one would expect the error:
Code:
awk: cmd. line:1: (FILENAME=VUS FNR=8) fatal: attempt to access field -1

only if an input line is empty or only contains one field. You should not get that error from your script for any input line with two or more fields.

And, since it complains about line:1, it looks like awk is seeing a short or empty line before your heading line???
Last edited by Don Cragun; 08-02-2016 at 06:36 PM.. Reason: Add final note.
This User Gave Thanks to Don Cragun For This Post:
cmccabe
# 6  
Old 08-03-2016
Quote:
Originally Posted by cmccabe
When I run the awk below, I get an error message
Code:
awk -v OFS='\t' '$(NF-1)=="Benign" || ($(NF-2) OFS $(NF-1))=="Likely Benign" {$(NF)=$(NF-2) OFS $(NF-1)} {print $0 }' input
awk: cmd. line:1: (FILENAME=VUS FNR=8) fatal: attempt to access field -1

input
Code:
Chr    Start    End    Ref    Alt    Func.refGene    AAChange.refGene    PopFreqMax    CLINSIG    Classification

The code ran with no error before I added $7 and I also used the below awk to see what NF equals, but am not able to correct the error:

Code:
awk 'NR==1{for(i=1;i<=NF;i++){print "Number of field in terms of NF is--> NF-" NF-i", value is-->" $i}}' file.txt
Number of field in terms of NF is--> NF-9, value is-->Chr
Number of field in terms of NF is--> NF-8, value is-->Start
Number of field in terms of NF is--> NF-7, value is-->End
Number of field in terms of NF is--> NF-6, value is-->Ref
Number of field in terms of NF is--> NF-5, value is-->Alt
Number of field in terms of NF is--> NF-4, value is-->Func.refGene
Number of field in terms of NF is--> NF-3, value is-->AAChange.refGene
Number of field in terms of NF is--> NF-2, value is-->PopFreqMax
Number of field in terms of NF is--> NF-1, value is-->CLINSIG
Number of field in terms of NF is--> NF-0, value is-->Classification

Thank you especially @RavinderSingh13 Smilie
Hello cmccabe,

Glad that solution helped you. As Don mentioned here before too, there must be an empty line in your Input_file because it is saying FNR==8 so on 8th line it is trying to get value of $(NF-1) which is failing because there is NULL value of NF so it is complaining that attempting to access field -1. As usual please show complete Input_file with expected Output and all the requirements.

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
# 7  
Old 08-03-2016
I got the awk to run, there was a hidden space that was found using notepad++. Thank you very much Smilie.
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