Loop stops after the 13th round in bash

Question

I have a folder fasta_files containing 500 files
Each file contains fasta sequence which is in this format

cat $file.fnn

>Fas1#66
EEYLKKFLMTSLVGFMYRMYKEYEVPDTDRNWTPKPSSAEFPGLKELKIKIDQLQLLLDTACSDESNTELTLLTLLEFIRAG
>Fas2#80
LQEWMPSYSKPTHTTKTLLSELITLVDTLKQETNDVPSESVVNTILSIADSCKTQTQKSKEAKTTIDSFLREH
.
.
.
>Fas3#87
VDTCASTCADTNVNTCASMCADTNVDTCASTCANTCASTEYTDLADPERIPLHIMQKTLNVPNELQADI

In addition, a got a blast file output which is in this format

Cat blastfile

Fas1#66 gi|1769046680|dbj|**BBO53957.1**|   100.000 0.0 1264    2654827 N/A N/A  
Fas1#66 gi|1769046681|dbj|**BBO53958.1**|   100.000 0.0 1117    2654827 N/A N/A  
Fas2#80 gi|1769046682|dbj|**BBO53959.1**|   100.000 0.0 1119    2654827 N/A N/A  
Fas3#87 gi|1769046683|dbj|**AWO53960.1**|   100.000 6.01e-118   339 2654827 N/A N/A

My aim is to make a connection between each of fasta.fnn with the blastfile in order to obtain the value after the third pipe (mentioned with bold) in the blastfile like the output below

Cat $file.list    
BBO53957.1
BBO53958.1
BBO53959.1
AWO53960.1

I wrote this script which works

mkdir  fasta_files/lists
mkdir  fasta_files/fnn
echo "1" >counter

    for file in $(ls fasta_files/*.fnn) ;do


        cat $file|grep ">" |sed 's/>//'g|grep -wf- /home/kgee/DATA/blastfile |awk '{print $2}'|cut -d\| -f4 |sort -u >$file.list 
        mv $file.list  fasta_files/lists
        mv $file  fasta_files/fnn

        echo  "**" $(tail -1 counter) "** LIST GENE FAMILIES FILES GENERATED"
        awk '{print $1+1}' counter >>counter 

    done 
mv *list* lists
rm counter

The screen output is this:

** 1 ** LIST GENE FAMILIES FILES GENERATED
** 2 ** LIST GENE FAMILIES FILES GENERATED
** 3 ** LIST GENE FAMILIES FILES GENERATED
** 4 ** LIST GENE FAMILIES FILES GENERATED
** 5 ** LIST GENE FAMILIES FILES GENERATED
** 6 ** LIST GENE FAMILIES FILES GENERATED
** 7 ** LIST GENE FAMILIES FILES GENERATED
** 8 ** LIST GENE FAMILIES FILES GENERATED
** 9 ** LIST GENE FAMILIES FILES GENERATED
** 10 ** LIST GENE FAMILIES FILES GENERATED
** 11 ** LIST GENE FAMILIES FILES GENERATED
** 12 ** LIST GENE FAMILIES FILES GENERATED
Cursor blinks for ever

All the 12 generated files $file.list in the folder file.list are exactly like I want.
My issue is that after the 13th time the loop brakes for a reason.
I removed the 13th file from the folder but again the loop "breaks" at the 13th time.
I removed all the files except 20 files and again "breaks" at the 13th time

Does anyone have any idea how to overcome this problem?

Loop stops after the 13th round in bash

0 Answers