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Full Discussion: Cp command works on command line but not in bash
Top Forums Shell Programming and Scripting Cp command works on command line but not in bash Post 302990896 by Corona688 on Thursday 2nd of February 2017 12:09:00 PM
Old 02-02-2017
You are not capturing the errors. Try:

Code:
logfile=/home/cmccabe/Desktop/test/process.log
for file in /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf ; do
     echo "Start annovar creation: $(date) - file: $file"
     echo ${file##*/} >> /home/cmccabe/Desktop/NGS/annovar/target.txt
     cp /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf /home/cmccabe/Desktop/NGS/annovar
     echo "End annovar file creation: $(date) - file: $file"
done 2>&1 >> "$logfile"

Also: Why are you copying every single file every loop? If you're trying to copy them one at a time, cp * destination/ isn't the way to do it.
This User Gave Thanks to Corona688 For This Post:
cmccabe
 

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LEARN ABOUT DEBIAN

vcf-annotate

VCF-ANNOTATE(1) 						   User Commands						   VCF-ANNOTATE(1)

NAME

       vcf-annotate - annotate VCF file, add filters or custom annotations

SYNOPSIS

       cat in.vcf | vcf-annotate [OPTIONS] > out.vcf

DESCRIPTION

       About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.

	      Currently annotates only the INFO column, but it will be extended on demand.

OPTIONS

       -a, --annotations <file.gz>
	      The tabix indexed file with the annotations: CHR	FROM[	TO][	VALUE]+.

       -c, --columns <list>
	      The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third
	      column should be ignored. If TO is not present, it is assumed that TO equals to FROM.

       -d, --description <file|string>
	      Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'.  The descriptions can be  read  from  a
	      file, one annotation per line.

       -f, --filter <list>
	      Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.

       -h, -?, --help
	      This help message.

   Filters:
       +      Apply all filters with default values (can be overridden, see the example below).

       -X     Exclude the filter X

       1, StrandBias
	      FLOAT		       Min P-value for strand bias (given PV4) [0.0001]

       2, BaseQualBias
	      FLOAT		     Min P-value for baseQ bias [1e-100]

       3, MapQualBias
	      FLOAT		      Min P-value for mapQ bias [0]

       4, EndDistBias
	      FLOAT		      Min P-value for end distance bias [0.0001]

       a, MinAB
	      INT			    Minimum number of alternate bases [2]

       c, SnpCluster
	      INT1,INT2 	       Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []

       D, MaxDP
	      INT			    Maximum read depth [10000000]

       d, MinDP
	      INT			    Minimum read depth [2]

       q, MinMQ
	      INT			    Minimum RMS mapping quality for SNPs [10]

       Q, Qual
	      INT			     Minimum value of the QUAL field [10]

       r, RefN
	      Reference base is N []

       W, GapWin
	      INT			   Window size for filtering adjacent gaps [10]

       w, SnpGap
	      INT			   SNP within INT bp around a gap to be filtered [10]

   Example:
	      zcat  in.vcf.gz  |  vcf-annotate	-a  annotations.gz  -d	descriptions.txt  |  bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f
	      +/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz

   Where descriptions.txt contains:
	      key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'

vcf-annotate 0.1.5						     July 2011							   VCF-ANNOTATE(1)
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