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Errors in SURPI.sh are now all written to stderr #2

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40 changes: 20 additions & 20 deletions SURPI.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -335,19 +335,19 @@ then # use config file
#verify that config file version matches SURPI version
if [ "$config_file_version" != "$SURPI_version" ]
then
echo "The config file $config_file was created with SURPI $config_file_version."
echo "The current version of SURPI running is $SURPI_version."
echo "Please generate a new config file with SURPI $SURPI_version in order to run SURPI."
echo "The config file $config_file was created with SURPI $config_file_version." >&2
echo "The current version of SURPI running is $SURPI_version." >&2
echo "Please generate a new config file with SURPI $SURPI_version in order to run SURPI." >&2
exit 65
fi
else
echo "The config file specified: $config_file is not present."
echo "The config file specified: $config_file is not present." >&2
exit 65
fi
else # parameters must be specified
if [ ! -r $inputfile ]
then
echo "The inputfile specified: $inputfile is not present."
echo "The inputfile specified: $inputfile is not present." >&2
exit 65
fi
fi
Expand Down Expand Up @@ -384,8 +384,8 @@ fi

if [ "$run_mode" != "Comprehensive" -a "$run_mode" != "Fast" ]
then
echo "${bold}$run_mode${normal} is not a valid run mode - must be Comprehensive or Fast."
echo "Please specify a valid run mode using the -u switch."
echo "${bold}$run_mode${normal} is not a valid run mode - must be Comprehensive or Fast." >&2
echo "Please specify a valid run mode using the -u switch." >&2
exit 65
fi

Expand Down Expand Up @@ -421,15 +421,15 @@ fi

if [ "$adapter_set" != "Truseq" -a "$adapter_set" != "Nextera" -a "$adapter_set" != "NexSolB" ]
then
echo "${bold}$adapter_set${normal} is not a valid adapter_set - must be Truseq, Nextera, or NexSolB."
echo "Please specify a valid adapter set using the -a switch."
echo "${bold}$adapter_set${normal} is not a valid adapter_set - must be Truseq, Nextera, or NexSolB." >&2
echo "Please specify a valid adapter set using the -a switch." >&2
exit 65
fi

if [ "$quality" != "Sanger" -a "$quality" != "Illumina" ]
then
echo "${bold}$quality${normal} is not a valid quality - must be Sanger or Illumina."
echo "Please specify a valid quality using the -q switch."
echo "${bold}$quality${normal} is not a valid quality - must be Sanger or Illumina." >&2
echo "Please specify a valid quality using the -q switch." >&2
exit 65
fi
if [ $quality = "Sanger" ]
Expand Down Expand Up @@ -457,15 +457,15 @@ fi

if [ ! $length_cutoff ]
then
echo "${bold}length_cutoff${normal} was not specified."
echo "Please specify a valid length_cutoff using the -x switch."
echo "${bold}length_cutoff${normal} was not specified." >&2
echo "Please specify a valid length_cutoff using the -x switch." >&2
exit 65
fi

if [ "$rapsearch_database" != "Viral" -a "$rapsearch_database" != "NR" ]
then
echo "${bold}$rapsearch_database${normal} is not a valid RAPSearch database - must be Viral or NR."
echo "Please specify a valid rapsearch_database using the -r switch, or place one of the above options in your config file."
echo "${bold}$rapsearch_database${normal} is not a valid RAPSearch database - must be Viral or NR." >&2
echo "Please specify a valid rapsearch_database using the -r switch, or place one of the above options in your config file." >&2
exit 65
fi

Expand Down Expand Up @@ -583,7 +583,7 @@ else
fi
if [[ ($dependency_check = "FAIL" || $reference_check = "FAIL") ]]
then
echo -e "${red}There is an issue with one of the dependencies or reference databases above.${endColor}"
echo -e "${red}There is an issue with one of the dependencies or reference databases above.${endColor}" >&2
exit 65
else
echo -e "${green}All dependencies and reference data pass.${endColor}"
Expand Down Expand Up @@ -663,8 +663,8 @@ then
then
echo -e "${green}$FASTQ_file appears to be a valid FASTQ file. Check the quality.$basef.log file for details.${endColor}"
else
echo -e "${red}$FASTQ_file appears to be a invalid FASTQ file. Check the quality.$basef.log file for details.${endColor}"
echo -e "${red}You can bypass the quality check by not using the -v switch.${endColor}"
echo -e "${red}$FASTQ_file appears to be a invalid FASTQ file. Check the quality.$basef.log file for details.${endColor}" >&2
echo -e "${red}You can bypass the quality check by not using the -v switch.${endColor}" >&2
exit 65
fi
elif [ "$VERIFY_FASTQ" = 2 ]
Expand All @@ -674,8 +674,8 @@ then
then
echo -e "${green}$FASTQ_file appears to be a valid FASTQ file. Check the quality.$basef.log file for details.${endColor}"
else
echo -e "${red}$FASTQ_file appears to be a invalid FASTQ file. Check the quality.$basef.log file for details.${endColor}"
echo -e "${red}You can bypass the quality check by not using the -v switch.${endColor}"
echo -e "${red}$FASTQ_file appears to be a invalid FASTQ file. Check the quality.$basef.log file for details.${endColor}" >&2
echo -e "${red}You can bypass the quality check by not using the -v switch.${endColor}" >&2
exit 65
fi
elif [ "$VERIFY_FASTQ" = 3 ]
Expand Down