hmmsearch output is now compressed while it's being generated

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@@ -197,14 +197,13 @@ fi
 
 # Run hmmsearch for each model of the library against the input sequences
 print_status "running hmmsearch against input sequences"
-HMMSEARCH_RESDIR="${PV_TMPDIR}"/hmmsearch
-mkdir -p "${HMMSEARCH_RESDIR}"
+HMMSEARCH_RESFILE="${PV_TMPDIR}"/hmmsearch.out.gz
 for hmm in "${PV_LIBDIR}"/hmm/*.hmm; do
     [ -e "${hmm}" ] || continue
     hmmBase=${hmm##*/}
     hmmName=${hmmBase%.hmm}
-    echo "hmmsearch -o ${HMMSEARCH_RESDIR}/${hmmName}.out ${hmm} ${INPUT_FASTA} 2>>${PV_LOGFILE}"
-done | ${PEXEC_CMD}
+    echo "hmmsearch ${hmm} ${INPUT_FASTA} 2>>${PV_LOGFILE}"
+done | ${PEXEC_CMD} | gzip -c >"${HMMSEARCH_RESFILE}"
 if [ $? -ne 0 ]; then
     print_error "error during hmmsearch jobs, see log: ${PV_LOGFILE}"
     exit 1
@@ -213,10 +212,7 @@ fi
 print_status "processing hmmsearch output files"
 PV_HMMLIB="${PV_LIBDIR}"/"${PV_LIBNAME}".hmmdict.pgz
 PV_SCOREFILE="${PV_TMPDIR}"/hmmsearch.scores
-for f in "${HMMSEARCH_RESDIR}"/*.out; do 
-    [ -e "${f}" ] || continue
-    cat "${f}"
-done | python3 "${SCRIPTS_DIR}"/parseHMMER.py --hmmer-dict "${PV_HMMLIB}" --seq-db "${PV_SEQDESC}" >"${PV_SCOREFILE}" 2>>"${PV_LOGFILE}"
+zcat "${HMMSEARCH_RESFILE}" | python3 "${SCRIPTS_DIR}"/parseHMMER.py --hmmer-dict "${PV_HMMLIB}" --seq-db "${PV_SEQDESC}" >"${PV_SCOREFILE}" 2>>"${PV_LOGFILE}"
 if [ $? -ne 0 ]; then
     print_error "error during processing of hmmsearch results, see log: ${PV_LOGFILE}"
     exit 1