diff --git a/README.md b/README.md
index d9e2748..fa97335 100644
--- a/README.md
+++ b/README.md
@@ -113,7 +113,7 @@ outputs/                    service_info.json           workflow_engine_params.t
 run.pid                     start_time.txt              yevis-metadata.yml
 
 # Execute sapporo/ro_crate.py script
-$ docker run --rm -v $PWD:$PWD -w $PWD ghcr.io/sapporo-wes/sapporo-service:latest python3 /app/sapporo/ro_crate.py $PWD
+$ docker run --rm -v /var/run/docker.sock:/var/run/docker.sock -v $PWD:$PWD -w $PWD ghcr.io/sapporo-wes/sapporo-service:latest python3 /app/sapporo/ro_crate.py $PWD
 ```
 
 ## Development
diff --git a/tests/example_crate/gatk_1st.json b/tests/example_crate/gatk_1st.json
index b01b0b5..9a6e91c 100644
--- a/tests/example_crate/gatk_1st.json
+++ b/tests/example_crate/gatk_1st.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T15:58:25+00:00",
+            "datePublished": "2022-09-20T14:09:26+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -2529,7 +2529,7 @@
             ],
             "cpuArchitecture": "x86_64",
             "cpuCount": 4,
-            "freeDiskSpace": 138291744768,
+            "freeDiskSpace": 138369884160,
             "gid": 0,
             "inDocker": true,
             "os": "Linux",
@@ -4162,7 +4162,7 @@
                 }
             ],
             "pid": 12,
-            "runId": "work",
+            "runId": "gatk_1st",
             "startTime": "2022-09-08T09:30:03",
             "state": "COMPLETE",
             "stderr": {
@@ -4265,6 +4265,28 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/c71fb9c2-b6e8-48f4-9350-c9b6ab4647dc/data/outputs/G97753.NA12878.vcf.idx"
         },
+        {
+            "@id": "#samtools",
+            "@type": "SoftwareApplication",
+            "name": "samtools",
+            "version": "1.15.1--h1170115_0"
+        },
+        {
+            "@id": "#8a8cb096-c6ac-46ea-8da1-8818e562748c",
+            "@type": [
+                "FileStats"
+            ],
+            "duplicateRate": 0.3063459248661424,
+            "duplicateReads": 719878,
+            "generatedBy": {
+                "@id": "#samtools"
+            },
+            "mappedRate": 1.0,
+            "mappedReads": 2349886,
+            "totalReads": 2349886,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
+        },
         {
             "@id": "outputs/G97753.NA12878.bam",
             "@type": [
@@ -4281,6 +4303,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "5bb2600f09cdbb7847e2bac06ebf1323f97a9243a0323c5429c375ed262965334952f3e4eda904096aa7ea6f1f79a4c05f5443785257ee981bbaff65ce2d531c",
+            "stats": {
+                "@id": "#8a8cb096-c6ac-46ea-8da1-8818e562748c"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/c71fb9c2-b6e8-48f4-9350-c9b6ab4647dc/data/outputs/G97753.NA12878.bam"
         },
@@ -4331,6 +4356,24 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/c71fb9c2-b6e8-48f4-9350-c9b6ab4647dc/data/outputs/G97753.NA12878.vcf"
         },
+        {
+            "@id": "#vcftools",
+            "@type": "SoftwareApplication",
+            "name": "vcftools",
+            "version": "0.1.16--pl5321h9a82719_6"
+        },
+        {
+            "@id": "#c80f6b40-0f8e-4a32-96f4-8e4b3678f8e1",
+            "@type": [
+                "FileStats"
+            ],
+            "generatedBy": {
+                "@id": "#vcftools"
+            },
+            "indelsCount": 2,
+            "snpsCount": 16,
+            "variantCount": 18
+        },
         {
             "@id": "outputs/splitAndPassOnly.vcf",
             "@type": [
@@ -4348,6 +4391,9 @@
             "lineCount": 96,
             "mode": "-rw-r--r--",
             "sha512": "9278bb53e11183d0be5fcb45c5eea49235bbbc02da9d2181c4c32bd13550a8059f0348e3db4314de3778214dd584271063c97d60b89687328255a5c786ac3fa4",
+            "stats": {
+                "@id": "#c80f6b40-0f8e-4a32-96f4-8e4b3678f8e1"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/c71fb9c2-b6e8-48f4-9350-c9b6ab4647dc/data/outputs/splitAndPassOnly.vcf"
         },
@@ -4368,6 +4414,22 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/c71fb9c2-b6e8-48f4-9350-c9b6ab4647dc/data/outputs/per_base_coverage.tsv"
         },
+        {
+            "@id": "#fe047f14-c581-485e-823f-1150f5b9d4f4",
+            "@type": [
+                "FileStats"
+            ],
+            "duplicateRate": 0.3063243148927087,
+            "duplicateReads": 723304,
+            "generatedBy": {
+                "@id": "#samtools"
+            },
+            "mappedRate": 0.9999944944088605,
+            "mappedReads": 2361223,
+            "totalReads": 2361236,
+            "unmappedRate": 5.505591139555724e-06,
+            "unmappedReads": 13
+        },
         {
             "@id": "outputs/G97753.NA12878.realigned.bam",
             "@type": [
@@ -4384,6 +4446,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "057c8d8eeb508e0792e39fd45fbfab4eecb9c15b601a4d9fdc540ae21e55aaaddcb8079978fa97efe799db0fddfa6b792cac9db662bb0d121da403acceda8781",
+            "stats": {
+                "@id": "#fe047f14-c581-485e-823f-1150f5b9d4f4"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/c71fb9c2-b6e8-48f4-9350-c9b6ab4647dc/data/outputs/G97753.NA12878.realigned.bam"
         },
diff --git a/tests/example_crate/gatk_2nd.json b/tests/example_crate/gatk_2nd.json
index c36c575..1934b20 100644
--- a/tests/example_crate/gatk_2nd.json
+++ b/tests/example_crate/gatk_2nd.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T15:59:23+00:00",
+            "datePublished": "2022-09-20T14:10:50+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -2529,7 +2529,7 @@
             ],
             "cpuArchitecture": "x86_64",
             "cpuCount": 4,
-            "freeDiskSpace": 138291736576,
+            "freeDiskSpace": 138361393152,
             "gid": 0,
             "inDocker": true,
             "os": "Linux",
@@ -4162,7 +4162,7 @@
                 }
             ],
             "pid": 12,
-            "runId": "work",
+            "runId": "gatk_2nd",
             "startTime": "2022-09-08T08:59:34",
             "state": "COMPLETE",
             "stderr": {
@@ -4265,6 +4265,28 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/cc91b422-25a2-4721-8d66-477ef4e141a7/data/outputs/G97753.NA12878.vcf.idx"
         },
+        {
+            "@id": "#samtools",
+            "@type": "SoftwareApplication",
+            "name": "samtools",
+            "version": "1.15.1--h1170115_0"
+        },
+        {
+            "@id": "#74251a63-fbc5-4694-97d3-bed9a43c6a30",
+            "@type": [
+                "FileStats"
+            ],
+            "duplicateRate": 0.3063459248661424,
+            "duplicateReads": 719878,
+            "generatedBy": {
+                "@id": "#samtools"
+            },
+            "mappedRate": 1.0,
+            "mappedReads": 2349886,
+            "totalReads": 2349886,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
+        },
         {
             "@id": "outputs/G97753.NA12878.bam",
             "@type": [
@@ -4281,6 +4303,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "2ca1e340a4eec22d5d254d5e5c30bd7fea5215fd09f4b424553933b88a61f971b59049d550054fa911c4cc686b08e82a7106bab44a4ac7cadc8e4a525718be43",
+            "stats": {
+                "@id": "#74251a63-fbc5-4694-97d3-bed9a43c6a30"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/cc91b422-25a2-4721-8d66-477ef4e141a7/data/outputs/G97753.NA12878.bam"
         },
@@ -4331,6 +4356,24 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/cc91b422-25a2-4721-8d66-477ef4e141a7/data/outputs/G97753.NA12878.vcf"
         },
+        {
+            "@id": "#vcftools",
+            "@type": "SoftwareApplication",
+            "name": "vcftools",
+            "version": "0.1.16--pl5321h9a82719_6"
+        },
+        {
+            "@id": "#c2c735ed-405b-4ac6-aba1-eeaf31e2d3a6",
+            "@type": [
+                "FileStats"
+            ],
+            "generatedBy": {
+                "@id": "#vcftools"
+            },
+            "indelsCount": 2,
+            "snpsCount": 16,
+            "variantCount": 18
+        },
         {
             "@id": "outputs/splitAndPassOnly.vcf",
             "@type": [
@@ -4348,6 +4391,9 @@
             "lineCount": 96,
             "mode": "-rw-r--r--",
             "sha512": "e869e0002f11260c7e2573f11d84a67f281301ccc20744d84f11409552214154dddfad3acf09aacf2e9af3d985a41147ac64563fda64750767576dffaf343d67",
+            "stats": {
+                "@id": "#c2c735ed-405b-4ac6-aba1-eeaf31e2d3a6"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/cc91b422-25a2-4721-8d66-477ef4e141a7/data/outputs/splitAndPassOnly.vcf"
         },
@@ -4368,6 +4414,22 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/cc91b422-25a2-4721-8d66-477ef4e141a7/data/outputs/per_base_coverage.tsv"
         },
+        {
+            "@id": "#80c75c41-a993-4f09-a6cc-e11faa5f5581",
+            "@type": [
+                "FileStats"
+            ],
+            "duplicateRate": 0.3063243148927087,
+            "duplicateReads": 723304,
+            "generatedBy": {
+                "@id": "#samtools"
+            },
+            "mappedRate": 0.9999944944088605,
+            "mappedReads": 2361223,
+            "totalReads": 2361236,
+            "unmappedRate": 5.505591139555724e-06,
+            "unmappedReads": 13
+        },
         {
             "@id": "outputs/G97753.NA12878.realigned.bam",
             "@type": [
@@ -4384,6 +4446,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "2b818b96876ccceae64a715f4ce08a0254265598c98f20130dec8e3fed7b241f8cb4ef3bed3da611f59460b55744ebb6b137c4e31806e48f3232a105eb180ab7",
+            "stats": {
+                "@id": "#80c75c41-a993-4f09-a6cc-e11faa5f5581"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/cc91b422-25a2-4721-8d66-477ef4e141a7/data/outputs/G97753.NA12878.realigned.bam"
         },
diff --git a/tests/example_crate/gatk_mac.json b/tests/example_crate/gatk_mac.json
index 63b34eb..0d46a0a 100644
--- a/tests/example_crate/gatk_mac.json
+++ b/tests/example_crate/gatk_mac.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T16:01:36+00:00",
+            "datePublished": "2022-09-20T14:13:10+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -637,7 +637,7 @@
             ],
             "cpuArchitecture": "x86_64",
             "cpuCount": 4,
-            "freeDiskSpace": 138291724288,
+            "freeDiskSpace": 138361294848,
             "gid": 0,
             "inDocker": true,
             "os": "Linux",
@@ -1323,7 +1323,7 @@
             ],
             "name": "Sapporo test result",
             "pid": 615,
-            "runId": "work",
+            "runId": "gatk_mac",
             "startTime": "2022-09-14T05:42:22",
             "state": "EXECUTOR_ERROR",
             "stderr": {
diff --git a/tests/example_crate/jga_1st.json b/tests/example_crate/jga_1st.json
index dae81a0..d646dbe 100644
--- a/tests/example_crate/jga_1st.json
+++ b/tests/example_crate/jga_1st.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T16:03:06+00:00",
+            "datePublished": "2022-09-20T14:15:05+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -795,7 +795,7 @@
             ],
             "cpuArchitecture": "x86_64",
             "cpuCount": 4,
-            "freeDiskSpace": 138291556352,
+            "freeDiskSpace": 138361159680,
             "gid": 0,
             "inDocker": true,
             "os": "Linux",
@@ -1541,7 +1541,7 @@
                 }
             ],
             "pid": 12,
-            "runId": "work",
+            "runId": "jga_1st",
             "startTime": "2022-09-10T13:33:40",
             "state": "COMPLETE",
             "stderr": {
@@ -1697,6 +1697,24 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/79027d00-d40c-4d25-b71d-3c07afc9ac86/data/outputs/NA19023.cram.idxstats"
         },
+        {
+            "@id": "#vcftools",
+            "@type": "SoftwareApplication",
+            "name": "vcftools",
+            "version": "0.1.16--pl5321h9a82719_6"
+        },
+        {
+            "@id": "#1a960c73-e6b2-42a5-ba81-06634a7fef68",
+            "@type": [
+                "FileStats"
+            ],
+            "generatedBy": {
+                "@id": "#vcftools"
+            },
+            "indelsCount": 1,
+            "snpsCount": 14,
+            "variantCount": 1061
+        },
         {
             "@id": "outputs/NA19023.autosome_PAR_ploidy_2.g.vcf.gz",
             "@type": [
@@ -1713,6 +1731,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "58b1ed78251ababa6dc48d8f1e51d07fc1c551e2e0382cd4e593bd790d33a7141c6d45816a2c2c4e57c70b8d067b7fe736cf795f9e88974eb8aba8f31ec0bde6",
+            "stats": {
+                "@id": "#1a960c73-e6b2-42a5-ba81-06634a7fef68"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/79027d00-d40c-4d25-b71d-3c07afc9ac86/data/outputs/NA19023.autosome_PAR_ploidy_2.g.vcf.gz"
         },
@@ -1804,6 +1825,18 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/79027d00-d40c-4d25-b71d-3c07afc9ac86/data/outputs/NA19023.cram.collect_base_dist_by_cycle"
         },
+        {
+            "@id": "#6f6dd093-3a4d-4f77-9b6a-dec713436eb5",
+            "@type": [
+                "FileStats"
+            ],
+            "generatedBy": {
+                "@id": "#vcftools"
+            },
+            "indelsCount": 0,
+            "snpsCount": 4,
+            "variantCount": 42
+        },
         {
             "@id": "outputs/NA19023.chrY_nonPAR_ploidy_1.g.vcf.gz",
             "@type": [
@@ -1820,6 +1853,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "a4876258fd697980a3a7ed678f3d3923049b68b4e2058293b6f4d3d55d12b583f4e701971c33ca9078a8f1b6951a177b07e9019a6b6928dfe4c507909a7c0e96",
+            "stats": {
+                "@id": "#6f6dd093-3a4d-4f77-9b6a-dec713436eb5"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/79027d00-d40c-4d25-b71d-3c07afc9ac86/data/outputs/NA19023.chrY_nonPAR_ploidy_1.g.vcf.gz"
         },
@@ -2019,6 +2055,18 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/79027d00-d40c-4d25-b71d-3c07afc9ac86/data/outputs/NA19023.chrX_nonPAR_ploidy_1.g.vcf.gz.bcftools-stats.log"
         },
+        {
+            "@id": "#b66fcc34-d00c-4937-809a-fb3f943485dd",
+            "@type": [
+                "FileStats"
+            ],
+            "generatedBy": {
+                "@id": "#vcftools"
+            },
+            "indelsCount": 0,
+            "snpsCount": 0,
+            "variantCount": 2
+        },
         {
             "@id": "outputs/NA19023.chrX_nonPAR_ploidy_2.g.vcf.gz",
             "@type": [
@@ -2035,6 +2083,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "28387445db7849fa2957130d2979e11e2329adeb3c80dc38cabd2e8dc07c71a425f26160ee8fb313315db4c8343be52475591b889ecbf61645cec3d18b0c0cf3",
+            "stats": {
+                "@id": "#b66fcc34-d00c-4937-809a-fb3f943485dd"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/79027d00-d40c-4d25-b71d-3c07afc9ac86/data/outputs/NA19023.chrX_nonPAR_ploidy_2.g.vcf.gz"
         },
@@ -2367,6 +2418,18 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/79027d00-d40c-4d25-b71d-3c07afc9ac86/data/outputs/NA19023.cram.collect_base_dist_by_cycle.chart.pdf"
         },
+        {
+            "@id": "#6a0909e9-431c-4301-8460-1fbfd21d69b9",
+            "@type": [
+                "FileStats"
+            ],
+            "generatedBy": {
+                "@id": "#vcftools"
+            },
+            "indelsCount": 0,
+            "snpsCount": 0,
+            "variantCount": 2
+        },
         {
             "@id": "outputs/NA19023.chrX_nonPAR_ploidy_1.g.vcf.gz",
             "@type": [
@@ -2383,6 +2446,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "2eac577b0626787c8e1b8546f42310cf9dcbea882292516cdbd8a75a05166653abffb75551eaaebf3a0c9cde31a3d54a481b5f1360b5205ec2d8dc73854192cc",
+            "stats": {
+                "@id": "#6a0909e9-431c-4301-8460-1fbfd21d69b9"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/79027d00-d40c-4d25-b71d-3c07afc9ac86/data/outputs/NA19023.chrX_nonPAR_ploidy_1.g.vcf.gz"
         },
diff --git a/tests/example_crate/jga_2nd.json b/tests/example_crate/jga_2nd.json
index 39d9bd1..b5df3cf 100644
--- a/tests/example_crate/jga_2nd.json
+++ b/tests/example_crate/jga_2nd.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T16:08:53+00:00",
+            "datePublished": "2022-09-20T14:21:16+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -795,7 +795,7 @@
             ],
             "cpuArchitecture": "x86_64",
             "cpuCount": 4,
-            "freeDiskSpace": 138291490816,
+            "freeDiskSpace": 138361094144,
             "gid": 0,
             "inDocker": true,
             "os": "Linux",
@@ -1541,7 +1541,7 @@
                 }
             ],
             "pid": 12,
-            "runId": "work",
+            "runId": "jga_2nd",
             "startTime": "2022-09-10T20:40:42",
             "state": "COMPLETE",
             "stderr": {
@@ -1697,6 +1697,24 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/7e91fa2d-09b8-4887-ab7c-5391aa2787d1/data/outputs/NA19023.cram.idxstats"
         },
+        {
+            "@id": "#vcftools",
+            "@type": "SoftwareApplication",
+            "name": "vcftools",
+            "version": "0.1.16--pl5321h9a82719_6"
+        },
+        {
+            "@id": "#fbbf2633-4e5d-41f1-9639-a0a00cc027d9",
+            "@type": [
+                "FileStats"
+            ],
+            "generatedBy": {
+                "@id": "#vcftools"
+            },
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@@ -1713,6 +1731,9 @@
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@@ -1820,6 +1853,9 @@
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@@ -2367,6 +2418,18 @@
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@@ -2383,6 +2446,9 @@
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diff --git a/tests/example_crate/jga_mac.json b/tests/example_crate/jga_mac.json
index 7d45b09..207d456 100644
--- a/tests/example_crate/jga_mac.json
+++ b/tests/example_crate/jga_mac.json
@@ -84,7 +84,7 @@
             "author": {
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-            "datePublished": "2022-09-17T16:14:56+00:00",
+            "datePublished": "2022-09-20T14:27:17+00:00",
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@@ -373,7 +373,7 @@
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@@ -518,7 +518,7 @@
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-            "runId": "work",
+            "runId": "jga_mac",
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diff --git a/tests/example_crate/rnaseq_1st.json b/tests/example_crate/rnaseq_1st.json
index f199a27..f466b7c 100644
--- a/tests/example_crate/rnaseq_1st.json
+++ b/tests/example_crate/rnaseq_1st.json
@@ -84,7 +84,7 @@
             "author": {
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@@ -28054,7 +28054,7 @@
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@@ -42606,6 +42606,28 @@
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@@ -42622,6 +42644,9 @@
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@@ -42675,6 +42716,9 @@
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@@ -42712,6 +42772,9 @@
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@@ -42863,9 +42942,28 @@
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@@ -42882,6 +42980,9 @@
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diff --git a/tests/example_crate/rnaseq_2nd.json b/tests/example_crate/rnaseq_2nd.json
index 8b026f1..6e0c451 100644
--- a/tests/example_crate/rnaseq_2nd.json
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@@ -84,7 +84,7 @@
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@@ -28054,7 +28054,7 @@
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             "url": "http://localhost:1122/runs/7db408c0-b88d-485a-97b0-7a42add17e9b/data/outputs/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam"
         },
+        {
+            "@id": "#c789d4c7-4b59-47bf-bc93-0f870e5fe4af",
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+            "totalReads": 94419,
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+            "unmappedReads": 0
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         {
             "@id": "outputs/star_salmon/WT_REP2.markdup.sorted.bam",
             "@type": [
@@ -42882,6 +42980,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
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             "url": "http://localhost:1122/runs/7db408c0-b88d-485a-97b0-7a42add17e9b/data/outputs/star_salmon/WT_REP2.markdup.sorted.bam"
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diff --git a/tests/example_crate/rnaseq_mac.json b/tests/example_crate/rnaseq_mac.json
index 24b98d2..7d6e2be 100644
--- a/tests/example_crate/rnaseq_mac.json
+++ b/tests/example_crate/rnaseq_mac.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T16:39:35+00:00",
+            "datePublished": "2022-09-20T16:50:38+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -4435,7 +4435,7 @@
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             "cpuCount": 4,
-            "freeDiskSpace": 138289729536,
+            "freeDiskSpace": 138676137984,
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             "inDocker": true,
             "os": "Linux",
diff --git a/tests/example_crate/rnaseq_only_sapporo.json b/tests/example_crate/rnaseq_only_sapporo.json
index c84164e..1ba28cc 100644
--- a/tests/example_crate/rnaseq_only_sapporo.json
+++ b/tests/example_crate/rnaseq_only_sapporo.json
@@ -81,7 +81,7 @@
             "about": {
                 "@id": "#sapporo-test-suite"
             },
-            "datePublished": "2022-09-17T16:39:45+00:00",
+            "datePublished": "2022-09-20T16:50:48+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
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@@ -28018,7 +28018,7 @@
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             "cpuCount": 4,
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+            "freeDiskSpace": 138676137984,
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@@ -42550,6 +42550,28 @@
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             "name": "BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data."
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+        {
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+            "@type": "SoftwareApplication",
+            "name": "samtools",
+            "version": "1.15.1--h1170115_0"
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+            "totalReads": 98338,
+            "unmappedRate": 0.0,
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         {
             "@id": "outputs/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam",
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@@ -42566,6 +42588,9 @@
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             "url": "http://localhost:1122/runs/1c5a197b-2f76-4bf2-a75e-cab7e43fbfeb/data/outputs/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam"
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@@ -42603,6 +42628,22 @@
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+        {
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@@ -42619,6 +42660,9 @@
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             "url": "http://localhost:1122/runs/1c5a197b-2f76-4bf2-a75e-cab7e43fbfeb/data/outputs/star_salmon/WT_REP1.markdup.sorted.bam"
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@@ -42640,6 +42684,22 @@
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         },
+        {
+            "@id": "#f1f3bec4-4f01-4880-898f-b9edc01024b9",
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+            "totalReads": 49040,
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         {
             "@id": "outputs/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam",
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@@ -42656,6 +42716,9 @@
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             "url": "http://localhost:1122/runs/1c5a197b-2f76-4bf2-a75e-cab7e43fbfeb/data/outputs/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam"
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@@ -42791,6 +42854,22 @@
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             "url": "http://localhost:1122/runs/1c5a197b-2f76-4bf2-a75e-cab7e43fbfeb/data/outputs/star_salmon/salmon.merged.gene_counts_length_scaled.rds"
         },
+        {
+            "@id": "#1a583f03-4702-4ec5-ad58-307b569c9c1c",
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+            "mappedReads": 94912,
+            "totalReads": 94912,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
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         {
             "@id": "outputs/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam",
             "@type": [
@@ -42807,9 +42886,28 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
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             "uid": 1000,
             "url": "http://localhost:1122/runs/1c5a197b-2f76-4bf2-a75e-cab7e43fbfeb/data/outputs/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam"
         },
+        {
+            "@id": "#b9399956-e2f4-4045-ab49-d36d0288f505",
+            "@type": [
+                "FileStats"
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+            "duplicateRate": 0.1288405935246084,
+            "duplicateReads": 12165,
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+            "totalReads": 94419,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
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         {
             "@id": "outputs/star_salmon/WT_REP2.markdup.sorted.bam",
             "@type": [
@@ -42826,6 +42924,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "421c71af8f6c530ccf55e5bb926c1a5bdda67cdbeca1e34226e1c51f4de928e43cca24dfa6cce5007e8c11ec1964ed57f0a14c6c85664932c52369e0b3b30074",
+            "stats": {
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             "uid": 1000,
             "url": "http://localhost:1122/runs/1c5a197b-2f76-4bf2-a75e-cab7e43fbfeb/data/outputs/star_salmon/WT_REP2.markdup.sorted.bam"
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diff --git a/tests/example_crate/rnaseq_small.json b/tests/example_crate/rnaseq_small.json
index 5180766..12aecb3 100644
--- a/tests/example_crate/rnaseq_small.json
+++ b/tests/example_crate/rnaseq_small.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T16:43:06+00:00",
+            "datePublished": "2022-09-20T16:53:59+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -24106,7 +24106,7 @@
             ],
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             "cpuCount": 4,
-            "freeDiskSpace": 138289643520,
+            "freeDiskSpace": 138676047872,
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@@ -36267,6 +36267,28 @@
             ],
             "name": "BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data."
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+            "@type": "SoftwareApplication",
+            "name": "samtools",
+            "version": "1.15.1--h1170115_0"
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+        {
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+            "duplicateRate": 0.737013184893241,
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+            "totalReads": 49223,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
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         {
             "@id": "outputs/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam",
             "@type": [
@@ -36283,6 +36305,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
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             "url": "http://localhost:1122/runs/eaaae8dc-b00f-4b9c-8862-506f310f79fc/data/outputs/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam"
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@@ -36320,6 +36345,22 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/eaaae8dc-b00f-4b9c-8862-506f310f79fc/data/outputs/star_salmon/salmon.merged.transcript_tpm.tsv"
         },
+        {
+            "@id": "#f05b74cc-1045-488f-8aea-cc9bd5c3b72d",
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+            "unmappedReads": 0
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         {
             "@id": "outputs/star_salmon/WT_REP1.markdup.sorted.bam",
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@@ -36336,6 +36377,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
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             "url": "http://localhost:1122/runs/eaaae8dc-b00f-4b9c-8862-506f310f79fc/data/outputs/star_salmon/WT_REP1.markdup.sorted.bam"
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@@ -36357,6 +36401,22 @@
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         },
+        {
+            "@id": "#66032d5a-1043-4d53-b544-1221e3568bc8",
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+            "totalReads": 49040,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
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         {
             "@id": "outputs/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam",
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@@ -36373,6 +36433,9 @@
             "gid": 1000,
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             "url": "http://localhost:1122/runs/eaaae8dc-b00f-4b9c-8862-506f310f79fc/data/outputs/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam"
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@@ -36492,6 +36555,22 @@
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@@ -36508,6 +36587,9 @@
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diff --git a/tests/example_crate/rnaseq_v3.6.json b/tests/example_crate/rnaseq_v3.6.json
index d8f4147..69d39d5 100644
--- a/tests/example_crate/rnaseq_v3.6.json
+++ b/tests/example_crate/rnaseq_v3.6.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T16:45:45+00:00",
+            "datePublished": "2022-09-20T16:56:29+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
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@@ -28922,7 +28922,7 @@
             ],
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@@ -43468,6 +43468,28 @@
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             "name": "BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data."
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         {
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@@ -43484,6 +43506,9 @@
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@@ -43521,6 +43546,22 @@
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@@ -43537,6 +43578,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "5814285668e232e4f372a6ec0a3f3f4c8c0e29d6f504ea1983ff9e5e1bf3f892847fa391347fa944c0bca43aa25d9452b0b66f3e9c2a15e27604f301e24c4fbe",
+            "stats": {
+                "@id": "#b2e090cb-74c0-450a-a120-b6cf2322cd57"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/e2de879b-2525-4de8-a57c-d92e8aa10128/data/outputs/star_salmon/WT_REP1.markdup.sorted.bam"
         },
@@ -43558,6 +43602,22 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/e2de879b-2525-4de8-a57c-d92e8aa10128/data/outputs/star_salmon/salmon.merged.gene_counts_scaled.tsv"
         },
+        {
+            "@id": "#1d3b9ae9-e1e5-408d-8d3c-9bd854a788d5",
+            "@type": [
+                "FileStats"
+            ],
+            "duplicateRate": 0.7400081566068516,
+            "duplicateReads": 36290,
+            "generatedBy": {
+                "@id": "#samtools"
+            },
+            "mappedRate": 1.0,
+            "mappedReads": 49040,
+            "totalReads": 49040,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
+        },
         {
             "@id": "outputs/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam",
             "@type": [
@@ -43574,6 +43634,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "84f09d7013d1d42c1aed472a017e979c82ba191fff6d1d683bc53a9316f58b37b275cb57aa820c0c3744245b87208680019b454ab6e35669fa667e92b93e4ef0",
+            "stats": {
+                "@id": "#1d3b9ae9-e1e5-408d-8d3c-9bd854a788d5"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/e2de879b-2525-4de8-a57c-d92e8aa10128/data/outputs/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam"
         },
@@ -43709,6 +43772,22 @@
             "uid": 1000,
             "url": "http://localhost:1122/runs/e2de879b-2525-4de8-a57c-d92e8aa10128/data/outputs/star_salmon/salmon.merged.gene_counts_length_scaled.rds"
         },
+        {
+            "@id": "#d112f6d2-6797-4ca5-9e77-14627e0f1fb6",
+            "@type": [
+                "FileStats"
+            ],
+            "duplicateRate": 0.12314565070802427,
+            "duplicateReads": 11688,
+            "generatedBy": {
+                "@id": "#samtools"
+            },
+            "mappedRate": 1.0,
+            "mappedReads": 94912,
+            "totalReads": 94912,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
+        },
         {
             "@id": "outputs/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam",
             "@type": [
@@ -43725,9 +43804,28 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "35069423b2c059f0a125f6774da5ec3b9aa391a51fae8dfb38a5f09fde56c48f3134983bc3b424bb7db7eb3624020eeb31b6edf8672364ca301bc359ea4da4ac",
+            "stats": {
+                "@id": "#d112f6d2-6797-4ca5-9e77-14627e0f1fb6"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/e2de879b-2525-4de8-a57c-d92e8aa10128/data/outputs/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam"
         },
+        {
+            "@id": "#3ac7b43f-716a-4ec6-9818-c3f0f081baf7",
+            "@type": [
+                "FileStats"
+            ],
+            "duplicateRate": 0.1288405935246084,
+            "duplicateReads": 12165,
+            "generatedBy": {
+                "@id": "#samtools"
+            },
+            "mappedRate": 1.0,
+            "mappedReads": 94419,
+            "totalReads": 94419,
+            "unmappedRate": 0.0,
+            "unmappedReads": 0
+        },
         {
             "@id": "outputs/star_salmon/WT_REP2.markdup.sorted.bam",
             "@type": [
@@ -43744,6 +43842,9 @@
             "gid": 1000,
             "mode": "-rw-r--r--",
             "sha512": "064ab3727a72532dbd2c6473f79262fc1b434ad91df05c4991453f78b739ded45f66c26b6021582874dcfeef256ea6ac5b383ab1a48bbbfa9b01b8a288a5ec3c",
+            "stats": {
+                "@id": "#3ac7b43f-716a-4ec6-9818-c3f0f081baf7"
+            },
             "uid": 1000,
             "url": "http://localhost:1122/runs/e2de879b-2525-4de8-a57c-d92e8aa10128/data/outputs/star_salmon/WT_REP2.markdup.sorted.bam"
         },
diff --git a/tests/example_crate/trimming.json b/tests/example_crate/trimming.json
index 1b4b24b..de2acb5 100644
--- a/tests/example_crate/trimming.json
+++ b/tests/example_crate/trimming.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T16:49:28+00:00",
+            "datePublished": "2022-09-20T14:44:20+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -474,7 +474,7 @@
             ],
             "cpuArchitecture": "x86_64",
             "cpuCount": 4,
-            "freeDiskSpace": 138289438720,
+            "freeDiskSpace": 138360713216,
             "gid": 0,
             "inDocker": true,
             "os": "Linux",
diff --git a/tests/example_crate/trimming_mac.json b/tests/example_crate/trimming_mac.json
index 00cec05..8cbba50 100644
--- a/tests/example_crate/trimming_mac.json
+++ b/tests/example_crate/trimming_mac.json
@@ -84,7 +84,7 @@
             "author": {
                 "@id": "https://orcid.org/0000-0003-2765-0049"
             },
-            "datePublished": "2022-09-17T16:49:33+00:00",
+            "datePublished": "2022-09-20T14:44:25+00:00",
             "description": "RO-Crate of Sapporo's run execution results.",
             "hasPart": [
                 {
@@ -474,7 +474,7 @@
             ],
             "cpuArchitecture": "x86_64",
             "cpuCount": 4,
-            "freeDiskSpace": 138289430528,
+            "freeDiskSpace": 138360705024,
             "gid": 0,
             "inDocker": true,
             "os": "Linux",