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Invalid parameter passed to taxonomyreport in easy-taxonomy workflow

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milot-mirdita committed Oct 9, 2019
1 parent 076daa3 commit eb090882bbffd798eb8a41e92bee25a805d0e85a
Showing with 5 additions and 4 deletions.
  1. +3 −3 data/easytaxonomy.sh
  2. +2 −1 src/workflow/EasyTaxonomy.cpp
@@ -40,7 +40,7 @@ fi

if notExists "${TMP_PATH}/result_tophit1.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" filterdb "${TMP_PATH}/result" "${TMP_PATH}/result_top1" --extract-lines 1 ${THREADS_PAR} \
"$MMSEQS" filterdb "${TMP_PATH}/result" "${TMP_PATH}/result_top1" --extract-lines 1 ${THREADS_COMP_PAR} \
|| fail "filterdb died"
fi

@@ -52,13 +52,13 @@ fi

if notExists "${TMP_PATH}/result_top1_swapped_sum.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" summarizealis "${TMP_PATH}/result_top1_swapped" "${TMP_PATH}/result_top1_swapped_sum" ${THREADS_PAR} \
"$MMSEQS" summarizealis "${TMP_PATH}/result_top1_swapped" "${TMP_PATH}/result_top1_swapped_sum" ${THREADS_COMP_PAR} \
|| fail "filterdb died"
fi

if notExists "${TMP_PATH}/result_top1_swapped_sum_tax.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" addtaxonomy "${TARGET}" "${TMP_PATH}/result_top1_swapped_sum" "${TMP_PATH}/result_top1_swapped_sum_tax" ${THREADS_PAR} --pick-id-from 1 --tax-lineage \
"$MMSEQS" addtaxonomy "${TARGET}" "${TMP_PATH}/result_top1_swapped_sum" "${TMP_PATH}/result_top1_swapped_sum_tax" ${THREADS_COMP_PAR} --pick-id-from 1 --tax-lineage \
|| fail "filterdb died"
fi

@@ -61,7 +61,8 @@ int easytaxonomy(int argc, const char **argv, const Command& command) {
par.alignmentMode = alignmentMode;
cmd.addVariable("LCA_PAR", par.createParameterString(par.lca).c_str());
cmd.addVariable("CONVERT_PAR", par.createParameterString(par.convertalignments).c_str());
cmd.addVariable("THREADS_PAR", par.createParameterString(par.threadsandcompression).c_str());
cmd.addVariable("THREADS_COMP_PAR", par.createParameterString(par.threadsandcompression).c_str());
cmd.addVariable("THREADS_PAR", par.createParameterString(par.onlythreads).c_str());
cmd.addVariable("CREATETSV_PAR", par.createParameterString(par.createtsv).c_str());
par.evalThr = 100000000;
cmd.addVariable("SWAPRESULT_PAR", par.createParameterString(par.swapresult).c_str());

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