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Bash script jumping too quickly to the next command - crash

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Top Forums Shell Programming and Scripting Bash script jumping too quickly to the next command - crash
# 15  
Old 05-24-2016
You posted code which you didn't actually run. Naturally I spotted an error which didn't actually happen. In the future, post your code very exactly: Word for word, letter for letter, keystroke for keystroke. The quoting for that line is seriously wonky no matter how you cut it though. Try

Code:
echo -e "#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tInputFileName\t${custom}\tDescription" > "${metadata}/metadata.tsv"

And once again, run it with set -x so we can see what actually happens. Without that we're only wild guessing.
Last edited by Corona688; 05-24-2016 at 02:43 PM..
# 16  
Old 05-24-2016
Hi, iam really sorry about the mis-communication.
I really appreciate your help.
This is the line and its set -x output;


Code:
[CFIA-ACIA+tremblaye@biocomp-0-12 ~]$ echo -e "#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tInputFileName\t${custom}\tDescription" > "${metadata}/metadata.tsv"
+ echo -e '#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tInputFileName\tTrapType\tLure\tCollectionDate\tProvince\tCity\tDescription'
[

# 17  
Old 05-24-2016
How about the lines after it?
# 18  
Old 05-24-2016
Code:
#create Metadata file for QIIME
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$ custom=$(echo "${customFields[@]}" | sed -e 's/ /\\t/g')
++ echo TrapType Lure CollectionDate Province City
++ sed -e 's/ /\\t/g'
+ custom='TrapType\tLure\tCollectionDate\tProvince\tCity'
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$ echo -e "#SampleID\tBarcodeSequence\tLinkerPrimerSeq
> 
> for g in $(find "$trimmed" -type f | grep "
> do
>   name=$(basename "$g")
>   nameNoExt="
>   #create array: a=(1 2 3 4)
>   #show
>   #t="${nameNoExt//-/ }"
>   #params=("${nam
>   #echo "${params[@]}"
>   param1=$(cut <<< "$na
>   param2=$(cut <<< "$nameNoExt" -d "-" -f 
>   param3=$(cut <<< "$nameNoExt" 
> 
>   tempLine=$(cat "$barcode" | grep "$param1" | grep "$param2" | grep "$param3")
>   echo "$tempLine" | awk -v fileName="$name" -v sampleName="$its" -F $'\t' 'BEGIN {OFS = FS} {print $1, $3, $4, fileName, $6, $7, $8, $9, 
> done
> 
> 
> ##########

---------- Post updated at 04:23 PM ---------- Previous update was at 04:22 PM ----------

ok, it seems like from my black box some info is lost with copy/âste.

The command I ran was this
Code:
#create Metadata file for QIIME
custom=$(echo "${customFields[@]}" | sed -e 's/ /\\t/g') #add custom
echo -e "#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tInputFileName\t${custom}\tDescription" > "${metadata}/metadata.tsv"

for g in $(find "$trimmed" -type f | grep "fasta" | grep -v "scrap") # -v -> exclude
do
  name=$(basename "$g")
  nameNoExt="${name%.*}"
  #create array: a=(1 2 3 4)
  #show content of array: echo "${a[@]}"
  #t="${nameNoExt//-/ }"
  #params=("${nameNoExt//-/ }") #${string//substring/replacement}
  #echo "${params[@]}"
  param1=$(cut <<< "$nameNoExt" -d "-" -f 1) #equals $(echo "$nameNoExt" | cut -d "-" -f 1)
  param2=$(cut <<< "$nameNoExt" -d "-" -f 2)
  param3=$(cut <<< "$nameNoExt" -d "-" -f 3 | sed -e 's/Run//') #only keep the number of the run

  tempLine=$(cat "$barcode" | grep "$param1" | grep "$param2" | grep "$param3")
  echo "$tempLine" | awk -v fileName="$name" -v sampleName="$its" -F $'\t' 'BEGIN {OFS = FS} {print $1, $3, $4, fileName, $6, $7, $8, $9, $10, $1"-"sampleName}' >> "${metadata}/metadata.tsv"
done


#######################
#                     #

# 19  
Old 05-24-2016
...and what does it show with set -x ? One or the other by itself is not useful! We need both!
# 20  
Old 05-25-2016
The command was this:
Code:
#create Metadata file for QIIME
custom=$(echo "${customFields[@]}" | sed -e 's/ /\\t/g') #add custom
echo -e "#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tInputFileName\t${custom}\tDescription" > "${metadata}/metadata.tsv"

for g in $(find "$trimmed" -type f | grep "fasta" | grep -v "scrap") # -v -> exclude
do
  name=$(basename "$g")
  nameNoExt="${name%.*}"
  #create array: a=(1 2 3 4)
  #show content of array: echo "${a[@]}"
  #t="${nameNoExt//-/ }"
  #params=("${nameNoExt//-/ }") #${string//substring/replacement}
  #echo "${params[@]}"
  param1=$(cut <<< "$nameNoExt" -d "-" -f 1) #equals $(echo "$nameNoExt" | cut -d "-" -f 1)
  param2=$(cut <<< "$nameNoExt" -d "-" -f 2)
  param3=$(cut <<< "$nameNoExt" -d "-" -f 3 | sed -e 's/Run//') #only keep the number of the run

  tempLine=$(cat "$barcode" | grep "$param1" | grep "$param2" | grep "$param3")
  echo "$tempLine" | awk -v fileName="$name" -v sampleName="$its" -F $'\t' 'BEGIN {OFS = FS} {print $1, $3, $4, fileName, $6, $7, $8, $9, $10, $1"-"sampleName}' >> "${metadata}/metadata.tsv"
done

The ouput, with set -x was that:
Code:
custom=$(echo "${customFields[@]}" | sed -e 's/ /\\t/g')
++ echo TrapType Lure CollectionDate Province City
++ sed -e 's/ /\\t/g'
+ custom='TrapType\tLure\tCollectionDate\tProvince\tCity'
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$ echo -e "#SampleID\tBarcodeSequence\tLinkerPrimerSeq
> 
> for g in $(find "$trimmed" -type f | grep "
> do
>   name=$(basename "$g")
>   nameNoExt="
>   #create array: a=(1 2 3 4)
>   #show
>   #t="${nameNoExt//-/ }"
>   #params=("${nam
>   #echo "${params[@]}"
>   param1=$(cut <<< "$na
>   param2=$(cut <<< "$nameNoExt" -d "-" -f 
>   param3=$(cut <<< "$nameNoExt" 
> 
>   tempLine=$(cat "$barcode" | grep "$param1" | grep "$param2" | grep "$param3")
>   echo "$tempLine" | awk -v fileName="$name" -v sampleName="$its" -F $'\t' 'BEGIN {OFS = FS} {print $1, $3, $4, fileName, $6, $7, $8, $9, 
> done
> 
> 
> ##########

# 21  
Old 05-25-2016
How exactly are you running this code? I see prompts and such appearing in it, it doesn't look like its being run from a shell script.
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