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Bash executes first part of script but not second

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# 1  
Old 05-05-2016
Bash executes first part of script but not second
My bash below verifies the integrity of all .bam in a directory and writes the out output to a .txt file. That is part one of the script that works. The second part of the bash searches each one of the .txt files for a string "(SUCCESS)" and if found display a message and if it is not found displays a different message.process.log created in the first bash. Currently, the script executes the first bash but stalls and does not end, it never closes executing the second bash. I can not seem to fix it and need some expert help. Thank you very much Smilie.

Bash part one (working as expected)
Code:
logfile=/home/cmccabe/Desktop/NGS/API/5-4-2016/process.log
for f in /home/cmccabe/Desktop/NGS/API/5-4-2016/*.bam ; do
 echo "Start bam validation creation: $(date) - File: $f"
 bname=`basename $f`
 pref=${bname%%.bam}
 bam validate --in $f --verbose 2> /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/${pref}_validation.txt
 echo "End bam validation creation: $(date) - File: $f"
done >> "$logfile"

Bash part two (doesn't work as expected)
Code:
For file in /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/*.txt; do
echo "Start verifying $(date) - File: $file"
value=$( grep -ic "(SUCCESS)" )
if [ "$value" == 1 ]; then
 echo "bam file is verified and complete"
 else
 echo "bam is corrupt, check log for reason"
 echo "End bam verify: $(date) - File: $f"
 fi
 done >> "$logfile"

example of .txt file
Code:
Number of records read = 24723078
Number of valid records = 24723078

TotalReads(e6)  24.72
MappedReads(e6) 24.57
PairedReads(e6) 0.00
ProperPair(e6)  0.00
DuplicateReads(e6)  7.33
QCFailureReads(e6)  0.00

MappingRate(%)  99.38
PairedReads(%)  0.00
ProperPair(%)   0.00
DupRate(%)  29.66
QCFailRate(%)   0.00

TotalBases(e6)  4332.46
BasesInMappedReads(e6)  4325.68
Returning: 0 (SUCCESS)

Last edited by cmccabe; 05-05-2016 at 10:13 PM.. Reason: fixed format
# 2  
Old 05-05-2016
First, the line:
Code:
For file in /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/*.txt; do;

needs to be changed to:
Code:
for file in /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/*.txt; do

Then, note that the command:
Code:
value=$( grep -ic "(SUCCESS)" )

is reading standard input looking for the string (SUCCESS). Maybe you intended to use:
Code:
value=$( grep -ic "(SUCCESS)" "$file" )

This User Gave Thanks to Don Cragun For This Post:
cmccabe
# 3  
Old 05-06-2016
Quote:
Originally Posted by cmccabe
My [ICODE][...]

Bash part one (working as expected)
Code:
logfile=/home/cmccabe/Desktop/NGS/API/5-4-2016/process.log
for f in /home/cmccabe/Desktop/NGS/API/5-4-2016/*.bam ; do
 echo "Start bam validation creation: $(date) - File: $f"
 bname=`basename $f`
 pref=${bname%%.bam}
 bam validate --in $f --verbose 2> /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/${pref}_validation.txt
 echo "End bam validation creation: $(date) - File: $f"
done >> "$logfile"

Bash part two (doesn't work as expected)
Code:
For file in /home/cmccabe/Desktop/NGS/API/5-4-2016/bam_validation/*.txt; do
echo "Start verifying $(date) - File: $file"
value=$( grep -ic "(SUCCESS)" )
if [ "$value" == 1 ]; then
 echo "bam file is verified and complete"
 else
 echo "bam is corrupt, check log for reason"
 echo "End bam verify: $(date) - File: $f"
 fi
 done >> "$logfile"

[...]
Also, notice that in your working snippet $f was the name of the file in the loop. In your refactored version, the variable you chose for a file is file but the $f has not been substituted.

Another version could be:
Code:
    if $(grep -iq "(SUCCESS)" "${doc}"); then
        echo "The verification of the bam file is completed."
    else
        echo "The bam file is corrupted. Check log for reason."
        echo "End of bam file verification: $(date) - File: ${doc}"
    fi

This User Gave Thanks to Aia For This Post:
cmccabe
# 4  
Old 05-06-2016
You don't use your variable file. Shouldn't it be an argument for grep?

BTW, it doesn't make much sense if you just say "the script doesn't work". You need to explain, in which way it doesn't work.
This User Gave Thanks to rovf For This Post:
cmccabe
# 5  
Old 05-06-2016
I will try out those changes and I apologize for not explaining "the script doesn't work". The bash executes and creates the .txt files but when each .txt file is searched the bash stalls. There is no error it just does not finish completely. I will change the script, execute, and post back. Thank you very much Smilie.
# 6  
Old 05-06-2016
Quote:
Originally Posted by cmccabe
I will try out those changes and I apologize for not explaining "the script doesn't work". The bash executes and creates the .txt files but when each .txt file is searched the bash stalls. There is no error it just does not finish completely. I will change the script, execute, and post back. Thank you very much Smilie.
It probably stalls, because it is waiting for input from standard input, since you did not provide the file name in the grep command, per Don's note.
This User Gave Thanks to gandolf989 For This Post:
cmccabe
# 7  
Old 05-06-2016
Thank you all for your help, everything works now Smilie
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