Changeset 5476


Ignore:
Timestamp:
Jun 10, 2019, 9:50:39 AM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1142: Create MIPs flow cell and start sequencing

Updated the hiseq_status.sh script so that will check if a file or folder exists before trying to use it.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • other/pipeline/trunk/hiseq_status.sh

    r5474 r5476  
    5959# use this for progress reporting
    6060RUN_PARAMETERS=${DATA_FOLDER}/runParameters.xml
    61 RUN_INFO=${DATA_FOLDER}/RunInfo.xml
    6261if [ -f "${RUN_PARAMETERS}" ]; then
    6362  echo "RunParameters: `date +"${DATE_FORMAT}" -r "${RUN_PARAMETERS}"`"
    64   echo "BclCount: `find "${DATA_FOLDER}" -type f -name *.bcl | wc -l`"
    65   echo "LaneCount: `grep -o 'LaneCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
    66   echo "SurfaceCount: `grep -o 'SurfaceCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
    67   echo "SwathCount: `grep -o 'SwathCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
    68   echo "TileCount: `grep -o 'TileCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
    6963  echo "Read1: `grep '<Read1>' "${RUN_PARAMETERS}" | cut -d '>' -f 2 | cut -d '<' -f 1`"
    7064  echo "Read2: `grep '<Read2>' "${RUN_PARAMETERS}" | cut -d '>' -f 2 | cut -d '<' -f 1`"
     
    7468fi
    7569
     70# Count number of BCL files which gives us information about
     71# the progress of the sequencing
     72BCL_FOLDER=${DATA_FOLDER}/Data/Intensities/BaseCalls
     73if [ -d "${BCL_FOLDER}" ]; then
     74  echo "BclCount: `find "${BCL_FOLDER}" -type f -name *.bcl | wc -l`"
     75fi
     76
     77# RunInfo.xml contains information about the layout of the flowcell
     78# which we need to be able to compare the number of BCL files
     79RUN_INFO=${DATA_FOLDER}/RunInfo.xml
     80if [ -f "${RUN_PARAMETERS}" ]; then
     81  echo "LaneCount: `grep -o 'LaneCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
     82  echo "SurfaceCount: `grep -o 'SurfaceCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
     83  echo "SwathCount: `grep -o 'SwathCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
     84  echo "TileCount: `grep -o 'TileCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
     85fi
     86
     87
     88
    7689# RTAComplete.txt is created when everything is complete
    7790# This becomes the end date of the job and should trigger
Note: See TracChangeset for help on using the changeset viewer.