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Bash script jumping too quickly to the next command - crash

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# 8  
Old 05-20-2016
Hi rbatte1,

I just ran this:
Code:
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$  echo $trimmed
/home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed

[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$ custom=$(echo "${customFields[@]}" | sed -e 's/ /\\t/g') #add custom
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$ echo -e "#SampleID\tBarcodeSequence\tLinkerPrimerSequence\tInputFileName\t"${custom}"\tDescription" > "${metadata}"/metadata.tsv
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$ 
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$ 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
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$ 
[CFIA-ACIA+tremblaye@biocomp-0-9 ~]$

And, it works. I do get the desired output file. (I don't when looping)..
I can't understand why it works only when ran separately.

Any idea..?
# 9  
Old 05-20-2016
What shell is your login shell?

What shell does your script file have at the top after #!
# 10  
Old 05-20-2016
Code:
#!/bin/bash

# 11  
Old 05-20-2016
We've seen what happens when it does work.

We haven't seen what happens when it doesn't work.

Add this to the line below #!/bin/bash

set -x
...and run it again, and post the output.
# 12  
Old 05-20-2016
Hi,
Thanks a lot;
here is the output with set -x:

Code:
for f in $(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta") # -v -> exclude
> do
>   sed -i 's/%[^:]*//' "$f"
> done
++ find /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed -type f
++ grep -F .fasta
++ grep -v -F .scrap.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S18-ITS2_BC18-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S05-ITS2_BC05-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S40-ITS2_BC40-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S01-ITS2_BC01-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S42-ITS2_BC42-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S02-ITS2_BC02-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S34-ITS2_BC34-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S11-ITS2_BC11-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S07-ITS2_BC07-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S09-ITS2_BC09-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S43-ITS2_BC43-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S32-ITS2_BC32-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S37-ITS2_BC37-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S26-ITS2_BC26-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S44-ITS2_BC44-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S31-ITS2_BC31-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S30-ITS2_BC30-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S22-ITS2_BC22-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S45-ITS2_BC45-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S25-ITS2_BC25-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S17-ITS2_BC17-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S06-ITS2_BC06-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S16-ITS2_BC16-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S21-ITS2_BC21-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S39-ITS2_BC39-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S27-ITS2_BC27-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S24-ITS2_BC24-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S10-ITS2_BC10-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S41-ITS2_BC41-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S35-ITS2_BC35-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S14-ITS2_BC14-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S08-ITS2_BC08-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S03-ITS2_BC03-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S23-ITS2_BC23-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S28-ITS2_BC28-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S38-ITS2_BC38-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S29-ITS2_BC29-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S12-ITS2_BC12-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S36-ITS2_BC36-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S33-ITS2_BC33-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S15-ITS2_BC15-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S20-ITS2_BC20-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S13-ITS2_BC13-Run9.fasta
+ for f in '$(find "$trimmed" -type f | grep -F ".fasta" | grep -v -F ".scrap.fasta")'
+ sed -i 's/%[^:]*//' /home/CFIA-ACIA/tremblaye/2016-05-10_run9-its2/trimmed/EM15S19-ITS2_BC19-Run9.fasta
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ 
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ #######################
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ #                     #
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ #      Metadata #
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ #                     #
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ #######################
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ 
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ 
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ #create Metadata file for QIIME
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ 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-0-13 2016-05-10_run9-its2]$ 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
> 
>

This User Gave Thanks to tremblayemilie9 For This Post:
Corona688
# 13  
Old 05-20-2016
Code:
[CFIA-ACIA+tremblaye@biocomp-0-13 2016-05-10_run9-its2]$ 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
> 
>

A missing double-quote has caused BASH to consider that entire code block as inside those double quotes. That's what the > at the beginning of the line is warning you about, it's telling you it's a continuation of something inside quotes. I'm a bit surprised BASH didn't warn you about 'premature end of file' or some such.
# 14  
Old 05-24-2016
Hello,
so I put the missing quote where I think you meant and launched my pipeline as 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

and the same problem occured...
Did I misunderstand what you meant?
Thanks
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