From 307393e13b0214c9504d0cb1725cc301fbfbffde Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 29 Jul 2021 14:17:33 -0400 Subject: [PATCH 1/5] with fixed taxonomy, unit test kraken1 --- ...steria.Kraken1.yml.bak => unit-testing.Listeria.Kraken1.yml} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename .github/workflows/{unit-testing.Listeria.Kraken1.yml.bak => unit-testing.Listeria.Kraken1.yml} (98%) diff --git a/.github/workflows/unit-testing.Listeria.Kraken1.yml.bak b/.github/workflows/unit-testing.Listeria.Kraken1.yml similarity index 98% rename from .github/workflows/unit-testing.Listeria.Kraken1.yml.bak rename to .github/workflows/unit-testing.Listeria.Kraken1.yml index 9c5d6fc..43d7a41 100644 --- a/.github/workflows/unit-testing.Listeria.Kraken1.yml.bak +++ b/.github/workflows/unit-testing.Listeria.Kraken1.yml @@ -81,7 +81,7 @@ jobs: cp -vf jellyfish1 $a_bin/jellyfish which kraken-build mkdir -pv kraken - cp -rv Kalamari/src/taxonomy_v3.9 kraken/taxonomy + cp -rv Kalamari/src/taxonomy kraken/taxonomy find ${{ env.OUTDIR }} -name '*.fasta' -exec kraken-build --db kraken --add-to-library {} \; tree kraken # Some super debugging here with -x From 74c3a020f0df570369a3e9631b92916cc4cbb363 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 29 Jul 2021 14:23:56 -0400 Subject: [PATCH 2/5] shortened the minimizer length to 9 --- .github/workflows/unit-testing.Listeria.Kraken1.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/unit-testing.Listeria.Kraken1.yml b/.github/workflows/unit-testing.Listeria.Kraken1.yml index 43d7a41..f8e9dfe 100644 --- a/.github/workflows/unit-testing.Listeria.Kraken1.yml +++ b/.github/workflows/unit-testing.Listeria.Kraken1.yml @@ -88,7 +88,7 @@ jobs: sed -i.bak 's/set -e/set -e; set -x/' $a_bin/build_kraken_db.sh grep -v '^#' -m 20 -C 2 $a_bin/build_kraken_db.sh echo ".....Building the database....." - kraken-build --rebuild --db kraken --threads 2 --work-on-disk + kraken-build --minimizer-len 9 --rebuild --db kraken --threads 2 --work-on-disk - name: Kraken1 view results run: | tree kraken From 51f766f6cd97551fc3613f4932337f1bf2798c92 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 29 Jul 2021 14:30:17 -0400 Subject: [PATCH 3/5] kraken1 query --- .github/workflows/unit-testing.Listeria.Kraken1.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/unit-testing.Listeria.Kraken1.yml b/.github/workflows/unit-testing.Listeria.Kraken1.yml index f8e9dfe..bc33e71 100644 --- a/.github/workflows/unit-testing.Listeria.Kraken1.yml +++ b/.github/workflows/unit-testing.Listeria.Kraken1.yml @@ -89,8 +89,15 @@ jobs: grep -v '^#' -m 20 -C 2 $a_bin/build_kraken_db.sh echo ".....Building the database....." kraken-build --minimizer-len 9 --rebuild --db kraken --threads 2 --work-on-disk + - name: Kraken1 query + run: | + QUERY=$(find ${{ env.OUTDIR }} -name '*.fasta' | head -n 1) + kraken --db kraken -o kraken.raw --fasta-input $QUERY - name: Kraken1 view results run: | tree kraken ls -lhSR kraken + echo + head kraken.raw + From 8b4bb5c7b9c778c4ffd466f3f199245f1de37dcf Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 29 Jul 2021 14:33:53 -0400 Subject: [PATCH 4/5] m --- .github/workflows/unit-testing.Listeria.Kraken1.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/unit-testing.Listeria.Kraken1.yml b/.github/workflows/unit-testing.Listeria.Kraken1.yml index bc33e71..3370e7f 100644 --- a/.github/workflows/unit-testing.Listeria.Kraken1.yml +++ b/.github/workflows/unit-testing.Listeria.Kraken1.yml @@ -92,7 +92,7 @@ jobs: - name: Kraken1 query run: | QUERY=$(find ${{ env.OUTDIR }} -name '*.fasta' | head -n 1) - kraken --db kraken -o kraken.raw --fasta-input $QUERY + kraken --db kraken -output kraken.raw --fasta-input $QUERY - name: Kraken1 view results run: | tree kraken From ae81434948844627a7ba2b491c88d6f561460797 Mon Sep 17 00:00:00 2001 From: Lee Katz - Aspen Date: Thu, 29 Jul 2021 14:37:05 -0400 Subject: [PATCH 5/5] adding a query is $query statement --- .github/workflows/unit-testing.Listeria.Kraken1.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/unit-testing.Listeria.Kraken1.yml b/.github/workflows/unit-testing.Listeria.Kraken1.yml index 3370e7f..dbb06cc 100644 --- a/.github/workflows/unit-testing.Listeria.Kraken1.yml +++ b/.github/workflows/unit-testing.Listeria.Kraken1.yml @@ -92,6 +92,7 @@ jobs: - name: Kraken1 query run: | QUERY=$(find ${{ env.OUTDIR }} -name '*.fasta' | head -n 1) + echo "Query is $QUERY" kraken --db kraken -output kraken.raw --fasta-input $QUERY - name: Kraken1 view results run: |