From 9a15241fdf125cae7812eacd772d3292ad59e50b Mon Sep 17 00:00:00 2001 From: alipirani88 Date: Wed, 28 Jul 2021 15:17:19 -0400 Subject: [PATCH] Removing .snakemake folder and ignoring it in .gitignore --- .gitignore | 11 +++++++++++ .snakemake/log/.nfs000000000138e59d00025c9d | 0 .../RGVkdXBSZWFkcy9BX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= | 1 - .../metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFt | 1 - .../RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFtLmJhaQ== | 1 - .../RGVkdXBSZWFkcy9CX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= | 1 - .../metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFt | 1 - .../RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFtLmJhaQ== | 1 - .snakemake/metadata/bWFwcGVkL0FfYWxuLmJhbQ== | 1 - .snakemake/metadata/bWFwcGVkL0FfYWxuLnNhbQ== | 1 - .snakemake/metadata/bWFwcGVkL0FfYWxuX3NvcnQuYmFt | 1 - .snakemake/metadata/bWFwcGVkL0JfYWxuLmJhbQ== | 1 - .snakemake/metadata/bWFwcGVkL0JfYWxuLnNhbQ== | 1 - .snakemake/metadata/bWFwcGVkL0JfYWxuX3NvcnQuYmFt | 1 - .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZGljdA== | 1 - .../metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMS5idDI= | 1 - .../metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMi5idDI= | 1 - .../metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMy5idDI= | 1 - .../metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuNC5idDI= | 1 - .../metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuZmFp | 1 - .../cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjEuYnQy | 1 - .../cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjIuYnQy | 1 - .../cmVzdWx0cy90cmltbWVkL0FfUjFfMDAxLmZhc3RxLmd6 | 1 - ...VzdWx0cy90cmltbWVkL0FfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= | 1 - .../cmVzdWx0cy90cmltbWVkL0FfUjJfMDAxLmZhc3RxLmd6 | 1 - ...VzdWx0cy90cmltbWVkL0FfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= | 1 - .../cmVzdWx0cy90cmltbWVkL0JfUjFfMDAxLmZhc3RxLmd6 | 1 - ...VzdWx0cy90cmltbWVkL0JfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= | 1 - .../cmVzdWx0cy90cmltbWVkL0JfUjJfMDAxLmZhc3RxLmd6 | 1 - ...VzdWx0cy90cmltbWVkL0JfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= | 1 - .../cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0= | 1 - ...VzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0uYmFp | 1 - ...VzdWx0cy9EZWR1cFJlYWRzL0FfZGVwdGhfb2ZfY292ZXJhZ2U= | 1 - ...9EZWR1cFJlYWRzL0FfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== | 1 - .../cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0= | 1 - ...VzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0uYmFp | 1 - ...VzdWx0cy9EZWR1cFJlYWRzL0JfZGVwdGhfb2ZfY292ZXJhZ2U= | 1 - ...9EZWR1cFJlYWRzL0JfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== | 1 - .../metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQV9yYXcudmNm | 1 - .../metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQl9yYXcudmNm | 1 - .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uYmFt | 1 - .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uc2Ft | 1 - .../metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG5fc29ydC5iYW0= | 1 - .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uYmFt | 1 - .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uc2Ft | 1 - .../metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG5fc29ydC5iYW0= | 1 - .../metadata/dHJpbW1lZC9BX1IxX3VucGFpcmVkLmZhc3RxLmd6 | 1 - .../metadata/dHJpbW1lZC9BX1IxXzAwMS5mYXN0cS5neg== | 1 - .../metadata/dHJpbW1lZC9BX1IyX3VucGFpcmVkLmZhc3RxLmd6 | 1 - .../metadata/dHJpbW1lZC9BX1IyXzAwMS5mYXN0cS5neg== | 1 - .../metadata/dHJpbW1lZC9CX1IxX3VucGFpcmVkLmZhc3RxLmd6 | 1 - .../metadata/dHJpbW1lZC9CX1IxXzAwMS5mYXN0cS5neg== | 1 - .../metadata/dHJpbW1lZC9CX1IyX3VucGFpcmVkLmZhc3RxLmd6 | 1 - .../metadata/dHJpbW1lZC9CX1IyXzAwMS5mYXN0cS5neg== | 1 - 54 files changed, 11 insertions(+), 52 deletions(-) create mode 100644 .gitignore delete mode 100644 .snakemake/log/.nfs000000000138e59d00025c9d delete mode 100644 .snakemake/metadata/RGVkdXBSZWFkcy9BX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= delete mode 100644 .snakemake/metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFt delete mode 100644 .snakemake/metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFtLmJhaQ== delete mode 100644 .snakemake/metadata/RGVkdXBSZWFkcy9CX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= delete mode 100644 .snakemake/metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFt delete mode 100644 .snakemake/metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFtLmJhaQ== delete mode 100644 .snakemake/metadata/bWFwcGVkL0FfYWxuLmJhbQ== delete mode 100644 .snakemake/metadata/bWFwcGVkL0FfYWxuLnNhbQ== delete mode 100644 .snakemake/metadata/bWFwcGVkL0FfYWxuX3NvcnQuYmFt delete mode 100644 .snakemake/metadata/bWFwcGVkL0JfYWxuLmJhbQ== delete mode 100644 .snakemake/metadata/bWFwcGVkL0JfYWxuLnNhbQ== delete mode 100644 .snakemake/metadata/bWFwcGVkL0JfYWxuX3NvcnQuYmFt delete mode 100644 .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZGljdA== delete mode 100644 .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMS5idDI= delete mode 100644 .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMi5idDI= delete mode 100644 .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMy5idDI= delete mode 100644 .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuNC5idDI= delete mode 100644 .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuZmFp delete mode 100644 .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjEuYnQy delete mode 100644 .snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjIuYnQy delete mode 100644 .snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjFfMDAxLmZhc3RxLmd6 delete mode 100644 .snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= delete mode 100644 .snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjJfMDAxLmZhc3RxLmd6 delete mode 100644 .snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= delete mode 100644 .snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjFfMDAxLmZhc3RxLmd6 delete mode 100644 .snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= delete mode 100644 .snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjJfMDAxLmZhc3RxLmd6 delete mode 100644 .snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= delete mode 100644 .snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0= delete mode 100644 .snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0uYmFp delete mode 100644 .snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfZGVwdGhfb2ZfY292ZXJhZ2U= delete mode 100644 .snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== delete mode 100644 .snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0= delete mode 100644 .snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0uYmFp delete mode 100644 .snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfZGVwdGhfb2ZfY292ZXJhZ2U= delete mode 100644 .snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== delete mode 100644 .snakemake/metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQV9yYXcudmNm delete mode 100644 .snakemake/metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQl9yYXcudmNm delete mode 100644 .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uYmFt delete mode 100644 .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uc2Ft delete mode 100644 .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG5fc29ydC5iYW0= delete mode 100644 .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uYmFt delete mode 100644 .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uc2Ft delete mode 100644 .snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG5fc29ydC5iYW0= delete mode 100644 .snakemake/metadata/dHJpbW1lZC9BX1IxX3VucGFpcmVkLmZhc3RxLmd6 delete mode 100644 .snakemake/metadata/dHJpbW1lZC9BX1IxXzAwMS5mYXN0cS5neg== delete mode 100644 .snakemake/metadata/dHJpbW1lZC9BX1IyX3VucGFpcmVkLmZhc3RxLmd6 delete mode 100644 .snakemake/metadata/dHJpbW1lZC9BX1IyXzAwMS5mYXN0cS5neg== delete mode 100644 .snakemake/metadata/dHJpbW1lZC9CX1IxX3VucGFpcmVkLmZhc3RxLmd6 delete mode 100644 .snakemake/metadata/dHJpbW1lZC9CX1IxXzAwMS5mYXN0cS5neg== delete mode 100644 .snakemake/metadata/dHJpbW1lZC9CX1IyX3VucGFpcmVkLmZhc3RxLmd6 delete mode 100644 .snakemake/metadata/dHJpbW1lZC9CX1IyXzAwMS5mYXN0cS5neg== diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..4b0c955 --- /dev/null +++ b/.gitignore @@ -0,0 +1,11 @@ +.snakemake +# Compiled source # +################### +*.com +*.class +*.dll +*.exe +*.o +*.so + +*.log diff --git a/.snakemake/log/.nfs000000000138e59d00025c9d b/.snakemake/log/.nfs000000000138e59d00025c9d deleted file mode 100644 index e69de29..0000000 diff --git a/.snakemake/metadata/RGVkdXBSZWFkcy9BX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= b/.snakemake/metadata/RGVkdXBSZWFkcy9BX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= deleted file mode 100644 index 7a97487..0000000 --- a/.snakemake/metadata/RGVkdXBSZWFkcy9BX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_MarkDuplicates", "input": ["mapped/A_aln_sort.bam"], "log": ["logs/gatk/A_GATK_MarkDuplicates.log"], "params": [], "shellcmd": "picard MarkDuplicates REMOVE_DUPLICATES=true I=mapped/A_aln_sort.bam O=DedupReads/A_aln_marked.bam M=DedupReads/A_marked_dup_metrics.txt 2>logs/gatk/A_GATK_MarkDuplicates.log", "incomplete": false, "starttime": 1627483891.617179, "endtime": 1627483946.173071, "job_hash": 2957219239524, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFt b/.snakemake/metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFt deleted file mode 100644 index 5555fe6..0000000 --- a/.snakemake/metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFt +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_MarkDuplicates", "input": ["mapped/A_aln_sort.bam"], "log": ["logs/gatk/A_GATK_MarkDuplicates.log"], "params": [], "shellcmd": "picard MarkDuplicates REMOVE_DUPLICATES=true I=mapped/A_aln_sort.bam O=DedupReads/A_aln_marked.bam M=DedupReads/A_marked_dup_metrics.txt 2>logs/gatk/A_GATK_MarkDuplicates.log", "incomplete": false, "starttime": 1627483891.614159, "endtime": 1627483946.172118, "job_hash": 2957219239524, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFtLmJhaQ== b/.snakemake/metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFtLmJhaQ== deleted file mode 100644 index d577818..0000000 --- a/.snakemake/metadata/RGVkdXBSZWFkcy9BX2Fsbl9tYXJrZWQuYmFtLmJhaQ== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "samtools_index", "input": ["DedupReads/A_aln_marked.bam"], "log": ["logs/samtools/A_samtools.log"], "params": [], "shellcmd": "samtools index DedupReads/A_aln_marked.bam", "incomplete": false, "starttime": 1627483946.25299, "endtime": 1627483950.059112, "job_hash": 2957219239508, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/RGVkdXBSZWFkcy9CX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= b/.snakemake/metadata/RGVkdXBSZWFkcy9CX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= deleted file mode 100644 index 5001942..0000000 --- a/.snakemake/metadata/RGVkdXBSZWFkcy9CX21hcmtlZF9kdXBfbWV0cmljcy50eHQ= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_MarkDuplicates", "input": ["mapped/B_aln_sort.bam"], "log": ["logs/gatk/B_GATK_MarkDuplicates.log"], "params": [], "shellcmd": "picard MarkDuplicates REMOVE_DUPLICATES=true I=mapped/B_aln_sort.bam O=DedupReads/B_aln_marked.bam M=DedupReads/B_marked_dup_metrics.txt 2>logs/gatk/B_GATK_MarkDuplicates.log", "incomplete": false, "starttime": 1627483891.636179, "endtime": 1627483946.203063, "job_hash": 2957219239604, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFt b/.snakemake/metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFt deleted file mode 100644 index 6ca987f..0000000 --- a/.snakemake/metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFt +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_MarkDuplicates", "input": ["mapped/B_aln_sort.bam"], "log": ["logs/gatk/B_GATK_MarkDuplicates.log"], "params": [], "shellcmd": "picard MarkDuplicates REMOVE_DUPLICATES=true I=mapped/B_aln_sort.bam O=DedupReads/B_aln_marked.bam M=DedupReads/B_marked_dup_metrics.txt 2>logs/gatk/B_GATK_MarkDuplicates.log", "incomplete": false, "starttime": 1627483891.632171, "endtime": 1627483946.202083, "job_hash": 2957219239604, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFtLmJhaQ== b/.snakemake/metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFtLmJhaQ== deleted file mode 100644 index 8a46188..0000000 --- a/.snakemake/metadata/RGVkdXBSZWFkcy9CX2Fsbl9tYXJrZWQuYmFtLmJhaQ== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "samtools_index", "input": ["DedupReads/B_aln_marked.bam"], "log": ["logs/samtools/B_samtools.log"], "params": [], "shellcmd": "samtools index DedupReads/B_aln_marked.bam", "incomplete": false, "starttime": 1627483946.32507, "endtime": 1627483950.083013, "job_hash": 2957219239588, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/bWFwcGVkL0FfYWxuLmJhbQ== b/.snakemake/metadata/bWFwcGVkL0FfYWxuLmJhbQ== deleted file mode 100644 index ad22c24..0000000 --- a/.snakemake/metadata/bWFwcGVkL0FfYWxuLmJhbQ== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "trimmed/A_R1_001.fastq.gz", "trimmed/A_R1_unpaired.fastq.gz", "trimmed/A_R2_001.fastq.gz", "trimmed/A_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/A.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2 -x resources/Aus0004.fasta -1 trimmed/A_R1_001.fastq.gz -2 trimmed/A_R2_001.fastq.gz -U trimmed/A_R1_unpaired.fastq.gz -U trimmed/A_R2_unpaired.fastq.gz -S mapped/A_aln.sam -t -p 8 --non-deterministic --end-to-end && samtools view -Sb mapped/A_aln.sam > mapped/A_aln.bam && samtools sort -O BAM -o mapped/A_aln_sort.bam mapped/A_aln.bam", "incomplete": false, "starttime": 1627483771.835069, "endtime": 1627483891.173165, "job_hash": 2957219239540, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/bWFwcGVkL0FfYWxuLnNhbQ== b/.snakemake/metadata/bWFwcGVkL0FfYWxuLnNhbQ== deleted file mode 100644 index b2e48da..0000000 --- a/.snakemake/metadata/bWFwcGVkL0FfYWxuLnNhbQ== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "trimmed/A_R1_001.fastq.gz", "trimmed/A_R1_unpaired.fastq.gz", "trimmed/A_R2_001.fastq.gz", "trimmed/A_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/A.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2 -x resources/Aus0004.fasta -1 trimmed/A_R1_001.fastq.gz -2 trimmed/A_R2_001.fastq.gz -U trimmed/A_R1_unpaired.fastq.gz -U trimmed/A_R2_unpaired.fastq.gz -S mapped/A_aln.sam -t -p 8 --non-deterministic --end-to-end && samtools view -Sb mapped/A_aln.sam > mapped/A_aln.bam && samtools sort -O BAM -o mapped/A_aln_sort.bam mapped/A_aln.bam", "incomplete": false, "starttime": 1627483771.832067, "endtime": 1627483891.172172, "job_hash": 2957219239540, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/bWFwcGVkL0FfYWxuX3NvcnQuYmFt b/.snakemake/metadata/bWFwcGVkL0FfYWxuX3NvcnQuYmFt deleted file mode 100644 index 6d0b71c..0000000 --- a/.snakemake/metadata/bWFwcGVkL0FfYWxuX3NvcnQuYmFt +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "trimmed/A_R1_001.fastq.gz", "trimmed/A_R1_unpaired.fastq.gz", "trimmed/A_R2_001.fastq.gz", "trimmed/A_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/A.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2 -x resources/Aus0004.fasta -1 trimmed/A_R1_001.fastq.gz -2 trimmed/A_R2_001.fastq.gz -U trimmed/A_R1_unpaired.fastq.gz -U trimmed/A_R2_unpaired.fastq.gz -S mapped/A_aln.sam -t -p 8 --non-deterministic --end-to-end && samtools view -Sb mapped/A_aln.sam > mapped/A_aln.bam && samtools sort -O BAM -o mapped/A_aln_sort.bam mapped/A_aln.bam", "incomplete": false, "starttime": 1627483771.839068, "endtime": 1627483891.174148, "job_hash": 2957219239540, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/bWFwcGVkL0JfYWxuLmJhbQ== b/.snakemake/metadata/bWFwcGVkL0JfYWxuLmJhbQ== deleted file mode 100644 index eeac792..0000000 --- a/.snakemake/metadata/bWFwcGVkL0JfYWxuLmJhbQ== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "trimmed/B_R1_001.fastq.gz", "trimmed/B_R1_unpaired.fastq.gz", "trimmed/B_R2_001.fastq.gz", "trimmed/B_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/B.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2 -x resources/Aus0004.fasta -1 trimmed/B_R1_001.fastq.gz -2 trimmed/B_R2_001.fastq.gz -U trimmed/B_R1_unpaired.fastq.gz -U trimmed/B_R2_unpaired.fastq.gz -S mapped/B_aln.sam -t -p 8 --non-deterministic --end-to-end && samtools view -Sb mapped/B_aln.sam > mapped/B_aln.bam && samtools sort -O BAM -o mapped/B_aln_sort.bam mapped/B_aln.bam", "incomplete": false, "starttime": 1627483652.011061, "endtime": 1627483771.381062, "job_hash": 2957219239620, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/bWFwcGVkL0JfYWxuLnNhbQ== b/.snakemake/metadata/bWFwcGVkL0JfYWxuLnNhbQ== deleted file mode 100644 index a941ddc..0000000 --- a/.snakemake/metadata/bWFwcGVkL0JfYWxuLnNhbQ== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "trimmed/B_R1_001.fastq.gz", "trimmed/B_R1_unpaired.fastq.gz", "trimmed/B_R2_001.fastq.gz", "trimmed/B_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/B.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2 -x resources/Aus0004.fasta -1 trimmed/B_R1_001.fastq.gz -2 trimmed/B_R2_001.fastq.gz -U trimmed/B_R1_unpaired.fastq.gz -U trimmed/B_R2_unpaired.fastq.gz -S mapped/B_aln.sam -t -p 8 --non-deterministic --end-to-end && samtools view -Sb mapped/B_aln.sam > mapped/B_aln.bam && samtools sort -O BAM -o mapped/B_aln_sort.bam mapped/B_aln.bam", "incomplete": false, "starttime": 1627483652.007047, "endtime": 1627483771.380064, "job_hash": 2957219239620, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/bWFwcGVkL0JfYWxuX3NvcnQuYmFt b/.snakemake/metadata/bWFwcGVkL0JfYWxuX3NvcnQuYmFt deleted file mode 100644 index f100162..0000000 --- a/.snakemake/metadata/bWFwcGVkL0JfYWxuX3NvcnQuYmFt +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "trimmed/B_R1_001.fastq.gz", "trimmed/B_R1_unpaired.fastq.gz", "trimmed/B_R2_001.fastq.gz", "trimmed/B_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/B.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2 -x resources/Aus0004.fasta -1 trimmed/B_R1_001.fastq.gz -2 trimmed/B_R2_001.fastq.gz -U trimmed/B_R1_unpaired.fastq.gz -U trimmed/B_R2_unpaired.fastq.gz -S mapped/B_aln.sam -t -p 8 --non-deterministic --end-to-end && samtools view -Sb mapped/B_aln.sam > mapped/B_aln.bam && samtools sort -O BAM -o mapped/B_aln_sort.bam mapped/B_aln.bam", "incomplete": false, "starttime": 1627483652.015038, "endtime": 1627483771.382058, "job_hash": 2957219239620, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZGljdA== b/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZGljdA== deleted file mode 100644 index f8466f7..0000000 --- a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZGljdA== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "picard_SeqDict", "input": ["resources/Aus0004.fasta"], "log": [], "params": [], "shellcmd": "picard CreateSequenceDictionary R=resources/Aus0004.fasta O=resources/Aus0004.dict", "incomplete": false, "starttime": 1627483382.657054, "endtime": 1627483383.418029, "job_hash": 2957219315220, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMS5idDI= b/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMS5idDI= deleted file mode 100644 index 8c7aef3..0000000 --- a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMS5idDI= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Build", "input": ["resources/Aus0004.fasta"], "log": [], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2-build resources/Aus0004.fasta resources/Aus0004.fasta", "incomplete": false, "starttime": 1627398712.183181, "endtime": 1627398715.631871, "job_hash": 2969579874180, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMi5idDI= b/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMi5idDI= deleted file mode 100644 index c10f052..0000000 --- a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMi5idDI= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Build", "input": ["resources/Aus0004.fasta"], "log": [], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2-build resources/Aus0004.fasta resources/Aus0004.fasta", "incomplete": false, "starttime": 1627398712.187169, "endtime": 1627398715.632869, "job_hash": 2969579874180, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMy5idDI= b/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMy5idDI= deleted file mode 100644 index 70b922f..0000000 --- a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuMy5idDI= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Build", "input": ["resources/Aus0004.fasta"], "log": [], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2-build resources/Aus0004.fasta resources/Aus0004.fasta", "incomplete": false, "starttime": 1627398712.191163, "endtime": 1627398715.633863, "job_hash": 2969579874180, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuNC5idDI= b/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuNC5idDI= deleted file mode 100644 index 685336b..0000000 --- a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuNC5idDI= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Build", "input": ["resources/Aus0004.fasta"], "log": [], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2-build resources/Aus0004.fasta resources/Aus0004.fasta", "incomplete": false, "starttime": 1627398712.194178, "endtime": 1627398715.633893, "job_hash": 2969579874180, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuZmFp b/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuZmFp deleted file mode 100644 index f4376c3..0000000 --- a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEuZmFp +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "gASVawEAAAAAAAAoQxJ0AGQBfA58EWQCjQMBAGQAUwCUKIwFaW5wdXSUjAZvdXRwdXSUjAZwYXJhbXOUjAl3aWxkY2FyZHOUjAd0aHJlYWRzlIwJcmVzb3VyY2VzlIwDbG9nlIwHdmVyc2lvbpSMBHJ1bGWUjAljb25kYV9lbnaUjA1jb250YWluZXJfaW1nlIwQc2luZ3VsYXJpdHlfYXJnc5SMD3VzZV9zaW5ndWxhcml0eZSMC2Vudl9tb2R1bGVzlIwMYmVuY2hfcmVjb3JklIwFam9iaWSUjAhpc19zaGVsbJSMD2JlbmNoX2l0ZXJhdGlvbpSMD2NsZWFudXBfc2NyaXB0c5SMCnNoYWRvd19kaXKUjA1lZGl0X25vdGVib29rlIwPY29uZGFfYmFzZV9wYXRolIwHYmFzZWRpcpR0lF2UKE6MFnNhbXRvb2xzIGZhaWR4IHtpbnB1dH2UaA9oEoaUZYwFc2hlbGyUhZR0lC4=", "rule": "samtools_faidx", "input": ["resources/Aus0004.fasta"], "log": [], "params": [], "shellcmd": "samtools faidx resources/Aus0004.fasta", "incomplete": false, "starttime": 1627398712.218163, "endtime": 1627398712.361164, "job_hash": 2969579874260, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjEuYnQy b/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjEuYnQy deleted file mode 100644 index 1676517..0000000 --- a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjEuYnQy +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Build", "input": ["resources/Aus0004.fasta"], "log": [], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2-build resources/Aus0004.fasta resources/Aus0004.fasta", "incomplete": false, "starttime": 1627398712.199163, "endtime": 1627398715.634886, "job_hash": 2969579874180, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjIuYnQy b/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjIuYnQy deleted file mode 100644 index 3775f51..0000000 --- a/.snakemake/metadata/cmVzb3VyY2VzL0F1czAwMDQuZmFzdGEucmV2LjIuYnQy +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Build", "input": ["resources/Aus0004.fasta"], "log": [], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "bowtie2-build resources/Aus0004.fasta resources/Aus0004.fasta", "incomplete": false, "starttime": 1627398712.203166, "endtime": 1627398715.635865, "job_hash": 2969579874180, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjFfMDAxLmZhc3RxLmd6 b/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjFfMDAxLmZhc3RxLmd6 deleted file mode 100644 index aa72e7c..0000000 --- a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjFfMDAxLmZhc3RxLmd6 +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz"], "log": ["logs/trimmomatic/A.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz results/trimmed/A_R1_001.fastq.gz results/trimmed/A_R1_unpaired.fastq.gz results/trimmed/A_R2_001.fastq.gz results/trimmed/A_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/A.log", "incomplete": false, "starttime": 1627494536.566298, "endtime": 1627494804.678362, "job_hash": 2951726625668, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= b/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= deleted file mode 100644 index 52d0476..0000000 --- a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz"], "log": ["logs/trimmomatic/A.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz results/trimmed/A_R1_001.fastq.gz results/trimmed/A_R1_unpaired.fastq.gz results/trimmed/A_R2_001.fastq.gz results/trimmed/A_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/A.log", "incomplete": false, "starttime": 1627494536.576301, "endtime": 1627494804.679369, "job_hash": 2951726625668, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjJfMDAxLmZhc3RxLmd6 b/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjJfMDAxLmZhc3RxLmd6 deleted file mode 100644 index 8e3a841..0000000 --- a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjJfMDAxLmZhc3RxLmd6 +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz"], "log": ["logs/trimmomatic/A.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz results/trimmed/A_R1_001.fastq.gz results/trimmed/A_R1_unpaired.fastq.gz results/trimmed/A_R2_001.fastq.gz results/trimmed/A_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/A.log", "incomplete": false, "starttime": 1627494536.570302, "endtime": 1627494804.678381, "job_hash": 2951726625668, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= b/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= deleted file mode 100644 index 03f648a..0000000 --- a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0FfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz"], "log": ["logs/trimmomatic/A.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz results/trimmed/A_R1_001.fastq.gz results/trimmed/A_R1_unpaired.fastq.gz results/trimmed/A_R2_001.fastq.gz results/trimmed/A_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/A.log", "incomplete": false, "starttime": 1627494536.581302, "endtime": 1627494804.680367, "job_hash": 2951726625668, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjFfMDAxLmZhc3RxLmd6 b/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjFfMDAxLmZhc3RxLmd6 deleted file mode 100644 index 8eeb394..0000000 --- a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjFfMDAxLmZhc3RxLmd6 +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz"], "log": ["logs/trimmomatic/B.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz results/trimmed/B_R1_001.fastq.gz results/trimmed/B_R1_unpaired.fastq.gz results/trimmed/B_R2_001.fastq.gz results/trimmed/B_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/B.log", "incomplete": false, "starttime": 1627494536.53431, "endtime": 1627494806.681419, "job_hash": 2951726625748, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= b/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= deleted file mode 100644 index fb29d71..0000000 --- a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjFfdW5wYWlyZWQuZmFzdHEuZ3o= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz"], "log": ["logs/trimmomatic/B.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz results/trimmed/B_R1_001.fastq.gz results/trimmed/B_R1_unpaired.fastq.gz results/trimmed/B_R2_001.fastq.gz results/trimmed/B_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/B.log", "incomplete": false, "starttime": 1627494536.542313, "endtime": 1627494806.68245, "job_hash": 2951726625748, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjJfMDAxLmZhc3RxLmd6 b/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjJfMDAxLmZhc3RxLmd6 deleted file mode 100644 index d866783..0000000 --- a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjJfMDAxLmZhc3RxLmd6 +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz"], "log": ["logs/trimmomatic/B.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz results/trimmed/B_R1_001.fastq.gz results/trimmed/B_R1_unpaired.fastq.gz results/trimmed/B_R2_001.fastq.gz results/trimmed/B_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/B.log", "incomplete": false, "starttime": 1627494536.539307, "endtime": 1627494806.682409, "job_hash": 2951726625748, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= b/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= deleted file mode 100644 index 8bb59cc..0000000 --- a/.snakemake/metadata/cmVzdWx0cy90cmltbWVkL0JfUjJfdW5wYWlyZWQuZmFzdHEuZ3o= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz"], "log": ["logs/trimmomatic/B.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz results/trimmed/B_R1_001.fastq.gz results/trimmed/B_R1_unpaired.fastq.gz results/trimmed/B_R2_001.fastq.gz results/trimmed/B_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/B.log", "incomplete": false, "starttime": 1627494536.546306, "endtime": 1627494806.683429, "job_hash": 2951726625748, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0= b/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0= deleted file mode 100644 index cff9e21..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_MarkDuplicates", "input": ["results/mapped/A_aln_sort.bam"], "log": ["logs/gatk/A_GATK_MarkDuplicates.log"], "params": [], "shellcmd": "picard MarkDuplicates REMOVE_DUPLICATES=true I=results/mapped/A_aln_sort.bam O=results/DedupReads/A_aln_marked.bam M=results/DedupReads/A_marked_dup_metrics.txt 2>logs/gatk/A_GATK_MarkDuplicates.log", "incomplete": false, "starttime": 1627497376.155157, "endtime": 1627497433.418374, "job_hash": 2940385042020, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0uYmFp b/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0uYmFp deleted file mode 100644 index b63d0d1..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfYWxuX21hcmtlZC5iYW0uYmFp +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "samtools_index", "input": ["results/DedupReads/A_aln_marked.bam"], "log": ["logs/samtools/A_samtools.log"], "params": [], "shellcmd": "samtools index results/DedupReads/A_aln_marked.bam", "incomplete": false, "starttime": 1627497433.53236, "endtime": 1627497437.458131, "job_hash": 2940385042004, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfZGVwdGhfb2ZfY292ZXJhZ2U= b/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfZGVwdGhfb2ZfY292ZXJhZ2U= deleted file mode 100644 index bcdd7be..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfZGVwdGhfb2ZfY292ZXJhZ2U= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_DepthofCoverage", "input": ["resources/Aus0004.dict", "resources/Aus0004.fasta", "results/DedupReads/A_aln_marked.bam"], "log": ["logs/gatk/A_GATK_DepthofCoverage.log"], "params": [], "shellcmd": "java -Xmx5G -jar ./bin/GenomeAnalysisTK.jar -T DepthOfCoverage -R resources/Aus0004.fasta -o results/DedupReads/A_depth_of_coverage -I results/DedupReads/A_aln_marked.bam --summaryCoverageThreshold 1 --summaryCoverageThreshold 2 --summaryCoverageThreshold 3 --summaryCoverageThreshold 4 --summaryCoverageThreshold 5 --summaryCoverageThreshold 6 --summaryCoverageThreshold 7 --summaryCoverageThreshold 8 --summaryCoverageThreshold 9 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 25 --ignoreDeletionSites 2>logs/gatk/A_GATK_DepthofCoverage.log", "incomplete": false, "starttime": 1627497854.584032, "endtime": 1627497932.327078, "job_hash": 2952270596644, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== b/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== deleted file mode 100644 index fbd1546..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0FfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_MarkDuplicates", "input": ["results/mapped/A_aln_sort.bam"], "log": ["logs/gatk/A_GATK_MarkDuplicates.log"], "params": [], "shellcmd": "picard MarkDuplicates REMOVE_DUPLICATES=true I=results/mapped/A_aln_sort.bam O=results/DedupReads/A_aln_marked.bam M=results/DedupReads/A_marked_dup_metrics.txt 2>logs/gatk/A_GATK_MarkDuplicates.log", "incomplete": false, "starttime": 1627497376.159097, "endtime": 1627497433.419368, "job_hash": 2940385042020, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0= b/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0= deleted file mode 100644 index 8efa310..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "gASVzQEAAAAAAAAoQxJ0AGQBfA58EWQCjQMBAGQAUwCUKIwFaW5wdXSUjAZvdXRwdXSUjAZwYXJhbXOUjAl3aWxkY2FyZHOUjAd0aHJlYWRzlIwJcmVzb3VyY2VzlIwDbG9nlIwHdmVyc2lvbpSMBHJ1bGWUjAljb25kYV9lbnaUjA1jb250YWluZXJfaW1nlIwQc2luZ3VsYXJpdHlfYXJnc5SMD3VzZV9zaW5ndWxhcml0eZSMC2Vudl9tb2R1bGVzlIwMYmVuY2hfcmVjb3JklIwFam9iaWSUjAhpc19zaGVsbJSMD2JlbmNoX2l0ZXJhdGlvbpSMD2NsZWFudXBfc2NyaXB0c5SMCnNoYWRvd19kaXKUjA1lZGl0X25vdGVib29rlIwPY29uZGFfYmFzZV9wYXRolIwHYmFzZWRpcpR0lF2UKE6MeHBpY2FyZCBNYXJrRHVwbGljYXRlcyBSRU1PVkVfRFVQTElDQVRFUz10cnVlIEk9e2lucHV0LmJhbXNvcnRvdXR9IE89e291dHB1dC5iYW1kZWR1cH0gTT17b3V0cHV0LmJhbWRlZHVwbWV0cmljc30gMj57bG9nfZRoD2gShpRljAVzaGVsbJSFlHSULg==", "rule": "GATK_MarkDuplicates", "input": ["results/mapped/B_aln_sort.bam"], "log": ["logs/gatk/B_GATK_MarkDuplicates.log"], "params": [], "shellcmd": "picard MarkDuplicates REMOVE_DUPLICATES=true I=results/mapped/B_aln_sort.bam O=results/DedupReads/B_aln_marked.bam M=results/DedupReads/B_marked_dup_metrics.txt 2>logs/gatk/B_GATK_MarkDuplicates.log", "incomplete": false, "starttime": 1627497376.177127, "endtime": 1627497433.44736, "job_hash": 2940385042100, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0uYmFp b/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0uYmFp deleted file mode 100644 index 062dc52..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfYWxuX21hcmtlZC5iYW0uYmFp +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "samtools_index", "input": ["results/DedupReads/B_aln_marked.bam"], "log": ["logs/samtools/B_samtools.log"], "params": [], "shellcmd": "samtools index results/DedupReads/B_aln_marked.bam", "incomplete": false, "starttime": 1627497433.51336, "endtime": 1627497437.362066, "job_hash": 2940385042084, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfZGVwdGhfb2ZfY292ZXJhZ2U= b/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfZGVwdGhfb2ZfY292ZXJhZ2U= deleted file mode 100644 index 274e247..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfZGVwdGhfb2ZfY292ZXJhZ2U= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_DepthofCoverage", "input": ["resources/Aus0004.dict", "resources/Aus0004.fasta", "results/DedupReads/B_aln_marked.bam"], "log": ["logs/gatk/B_GATK_DepthofCoverage.log"], "params": [], "shellcmd": "java -Xmx5G -jar ./bin/GenomeAnalysisTK.jar -T DepthOfCoverage -R resources/Aus0004.fasta -o results/DedupReads/B_depth_of_coverage -I results/DedupReads/B_aln_marked.bam --summaryCoverageThreshold 1 --summaryCoverageThreshold 2 --summaryCoverageThreshold 3 --summaryCoverageThreshold 4 --summaryCoverageThreshold 5 --summaryCoverageThreshold 6 --summaryCoverageThreshold 7 --summaryCoverageThreshold 8 --summaryCoverageThreshold 9 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 25 --ignoreDeletionSites 2>logs/gatk/B_GATK_DepthofCoverage.log", "incomplete": false, "starttime": 1627497854.599033, "endtime": 1627497934.015033, "job_hash": 2952270596676, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== b/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== deleted file mode 100644 index 58c57fe..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9EZWR1cFJlYWRzL0JfbWFya2VkX2R1cF9tZXRyaWNzLnR4dA== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "GATK_MarkDuplicates", "input": ["results/mapped/B_aln_sort.bam"], "log": ["logs/gatk/B_GATK_MarkDuplicates.log"], "params": [], "shellcmd": "picard MarkDuplicates REMOVE_DUPLICATES=true I=results/mapped/B_aln_sort.bam O=results/DedupReads/B_aln_marked.bam M=results/DedupReads/B_marked_dup_metrics.txt 2>logs/gatk/B_GATK_MarkDuplicates.log", "incomplete": false, "starttime": 1627497376.184124, "endtime": 1627497433.447402, "job_hash": 2940385042100, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQV9yYXcudmNm b/.snakemake/metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQV9yYXcudmNm deleted file mode 100644 index 20fff0e..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQV9yYXcudmNm +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "freebayes", "input": ["resources/Aus0004.fasta", "resources/Aus0004.fasta.fai", "results/DedupReads/A_aln_marked.bam", "results/DedupReads/A_aln_marked.bam.bai"], "log": ["logs/freebayes/A_freebayes.log"], "params": [], "shellcmd": "freebayes-parallel <(fasta_generate_regions.py resources/Aus0004.fasta.fai 100000) 4 -f resources/Aus0004.fasta --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic results/DedupReads/A_aln_marked.bam > results/freebayes/A_raw.vcf", "incomplete": false, "starttime": 1627497437.543068, "endtime": 1627497593.338048, "job_hash": 2940385116932, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQl9yYXcudmNm b/.snakemake/metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQl9yYXcudmNm deleted file mode 100644 index 80a4141..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9mcmVlYmF5ZXMvQl9yYXcudmNm +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "freebayes", "input": ["resources/Aus0004.fasta", "resources/Aus0004.fasta.fai", "results/DedupReads/B_aln_marked.bam", "results/DedupReads/B_aln_marked.bam.bai"], "log": ["logs/freebayes/B_freebayes.log"], "params": [], "shellcmd": "freebayes-parallel <(fasta_generate_regions.py resources/Aus0004.fasta.fai 100000) 4 -f resources/Aus0004.fasta --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic results/DedupReads/B_aln_marked.bam > results/freebayes/B_raw.vcf", "incomplete": false, "starttime": 1627497437.448065, "endtime": 1627497566.791143, "job_hash": 2940385116948, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uYmFt b/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uYmFt deleted file mode 100644 index 56f60b1..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uYmFt +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "gASVNAMAAAAAAAAoQxJ0AGQBfA58EWQCjQMBAGQAUwCUKIwFaW5wdXSUjAZvdXRwdXSUjAZwYXJhbXOUjAl3aWxkY2FyZHOUjAd0aHJlYWRzlIwJcmVzb3VyY2VzlIwDbG9nlIwHdmVyc2lvbpSMBHJ1bGWUjAljb25kYV9lbnaUjA1jb250YWluZXJfaW1nlIwQc2luZ3VsYXJpdHlfYXJnc5SMD3VzZV9zaW5ndWxhcml0eZSMC2Vudl9tb2R1bGVzlIwMYmVuY2hfcmVjb3JklIwFam9iaWSUjAhpc19zaGVsbJSMD2JlbmNoX2l0ZXJhdGlvbpSMD2NsZWFudXBfc2NyaXB0c5SMCnNoYWRvd19kaXKUjA1lZGl0X25vdGVib29rlIwPY29uZGFfYmFzZV9wYXRolIwHYmFzZWRpcpR0lF2UKE5Y3AEAAHJnaWQ9YGVjaG8ge2lucHV0LnIxfSB8IGN1dCAtZCcvJyAtZjMgfCBzZWQgJ3MvX1IxXzAwMS5mYXN0cS5nei8vZydgICYmIHJnc209YGVjaG8ge2lucHV0LnIxfSB8IGN1dCAtZCcvJyAtZjMgfCBzZWQgJ3MvX1IxXzAwMS5mYXN0cS5nei8vZydgICYmIGJvd3RpZTIgLXgge3BhcmFtcy5pbmRleH0gLTEge2lucHV0LnIxfSAtMiB7aW5wdXQucjJ9IC1VIHtpbnB1dC5yMV91bnBhaXJlZH0gLVUge2lucHV0LnIyX3VucGFpcmVkfSAtUyB7b3V0cHV0LnNhbW91dH0gLXQgLXAgOCAtLW5vbi1kZXRlcm1pbmlzdGljIC0tZW5kLXRvLWVuZCAtLXJnLWlkICRyZ2lkIC0tcmcgU006JHJnc20gLS1yZyBMQjoxIC0tcmcgUEw6SWxsdW1pbmEgJiYgc2FtdG9vbHMgdmlldyAtU2Ige291dHB1dC5zYW1vdXR9ID4ge291dHB1dC5iYW1vdXR9ICYmIHNhbXRvb2xzIHNvcnQgLU8gQkFNIC1vIHtvdXRwdXQuYmFtc29ydG91dH0ge291dHB1dC5iYW1vdXR9lGgPaBKGlGWMBXNoZWxslIWUdJQu", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "results/trimmed/A_R1_001.fastq.gz", "results/trimmed/A_R1_unpaired.fastq.gz", "results/trimmed/A_R2_001.fastq.gz", "results/trimmed/A_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/A.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "rgid=`echo results/trimmed/A_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && rgsm=`echo results/trimmed/A_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && bowtie2 -x resources/Aus0004.fasta -1 results/trimmed/A_R1_001.fastq.gz -2 results/trimmed/A_R2_001.fastq.gz -U results/trimmed/A_R1_unpaired.fastq.gz -U results/trimmed/A_R2_unpaired.fastq.gz -S results/mapped/A_aln.sam -t -p 8 --non-deterministic --end-to-end --rg-id $rgid --rg SM:$rgsm --rg LB:1 --rg PL:Illumina && samtools view -Sb results/mapped/A_aln.sam > results/mapped/A_aln.bam && samtools sort -O BAM -o results/mapped/A_aln_sort.bam results/mapped/A_aln.bam", "incomplete": false, "starttime": 1627497256.730092, "endtime": 1627497375.647091, "job_hash": 2940385042036, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uc2Ft b/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uc2Ft deleted file mode 100644 index 1871f27..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG4uc2Ft +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "results/trimmed/A_R1_001.fastq.gz", "results/trimmed/A_R1_unpaired.fastq.gz", "results/trimmed/A_R2_001.fastq.gz", "results/trimmed/A_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/A.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "rgid=`echo results/trimmed/A_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && rgsm=`echo results/trimmed/A_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && bowtie2 -x resources/Aus0004.fasta -1 results/trimmed/A_R1_001.fastq.gz -2 results/trimmed/A_R2_001.fastq.gz -U results/trimmed/A_R1_unpaired.fastq.gz -U results/trimmed/A_R2_unpaired.fastq.gz -S results/mapped/A_aln.sam -t -p 8 --non-deterministic --end-to-end --rg-id $rgid --rg SM:$rgsm --rg LB:1 --rg PL:Illumina && samtools view -Sb results/mapped/A_aln.sam > results/mapped/A_aln.bam && samtools sort -O BAM -o results/mapped/A_aln_sort.bam results/mapped/A_aln.bam", "incomplete": false, "starttime": 1627497256.725099, "endtime": 1627497375.646095, "job_hash": 2940385042036, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG5fc29ydC5iYW0= b/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG5fc29ydC5iYW0= deleted file mode 100644 index 0f10fd3..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQV9hbG5fc29ydC5iYW0= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "results/trimmed/A_R1_001.fastq.gz", "results/trimmed/A_R1_unpaired.fastq.gz", "results/trimmed/A_R2_001.fastq.gz", "results/trimmed/A_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/A.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "rgid=`echo results/trimmed/A_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && rgsm=`echo results/trimmed/A_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && bowtie2 -x resources/Aus0004.fasta -1 results/trimmed/A_R1_001.fastq.gz -2 results/trimmed/A_R2_001.fastq.gz -U results/trimmed/A_R1_unpaired.fastq.gz -U results/trimmed/A_R2_unpaired.fastq.gz -S results/mapped/A_aln.sam -t -p 8 --non-deterministic --end-to-end --rg-id $rgid --rg SM:$rgsm --rg LB:1 --rg PL:Illumina && samtools view -Sb results/mapped/A_aln.sam > results/mapped/A_aln.bam && samtools sort -O BAM -o results/mapped/A_aln_sort.bam results/mapped/A_aln.bam", "incomplete": false, "starttime": 1627497256.734097, "endtime": 1627497375.648088, "job_hash": 2940385042036, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uYmFt b/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uYmFt deleted file mode 100644 index ea9f4e6..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uYmFt +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "results/trimmed/B_R1_001.fastq.gz", "results/trimmed/B_R1_unpaired.fastq.gz", "results/trimmed/B_R2_001.fastq.gz", "results/trimmed/B_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/B.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "rgid=`echo results/trimmed/B_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && rgsm=`echo results/trimmed/B_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && bowtie2 -x resources/Aus0004.fasta -1 results/trimmed/B_R1_001.fastq.gz -2 results/trimmed/B_R2_001.fastq.gz -U results/trimmed/B_R1_unpaired.fastq.gz -U results/trimmed/B_R2_unpaired.fastq.gz -S results/mapped/B_aln.sam -t -p 8 --non-deterministic --end-to-end --rg-id $rgid --rg SM:$rgsm --rg LB:1 --rg PL:Illumina && samtools view -Sb results/mapped/B_aln.sam > results/mapped/B_aln.bam && samtools sort -O BAM -o results/mapped/B_aln_sort.bam results/mapped/B_aln.bam", "incomplete": false, "starttime": 1627497141.257108, "endtime": 1627497256.208076, "job_hash": 2940385042116, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uc2Ft b/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uc2Ft deleted file mode 100644 index cf3cadf..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG4uc2Ft +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "results/trimmed/B_R1_001.fastq.gz", "results/trimmed/B_R1_unpaired.fastq.gz", "results/trimmed/B_R2_001.fastq.gz", "results/trimmed/B_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/B.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "rgid=`echo results/trimmed/B_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && rgsm=`echo results/trimmed/B_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && bowtie2 -x resources/Aus0004.fasta -1 results/trimmed/B_R1_001.fastq.gz -2 results/trimmed/B_R2_001.fastq.gz -U results/trimmed/B_R1_unpaired.fastq.gz -U results/trimmed/B_R2_unpaired.fastq.gz -S results/mapped/B_aln.sam -t -p 8 --non-deterministic --end-to-end --rg-id $rgid --rg SM:$rgsm --rg LB:1 --rg PL:Illumina && samtools view -Sb results/mapped/B_aln.sam > results/mapped/B_aln.bam && samtools sort -O BAM -o results/mapped/B_aln_sort.bam results/mapped/B_aln.bam", "incomplete": false, "starttime": 1627497141.253099, "endtime": 1627497256.207084, "job_hash": 2940385042116, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG5fc29ydC5iYW0= b/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG5fc29ydC5iYW0= deleted file mode 100644 index cbdd5f8..0000000 --- a/.snakemake/metadata/cmVzdWx0cy9tYXBwZWQvQl9hbG5fc29ydC5iYW0= +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "bowtie2Align", "input": ["resources/Aus0004.fasta.1.bt2", "results/trimmed/B_R1_001.fastq.gz", "results/trimmed/B_R1_unpaired.fastq.gz", "results/trimmed/B_R2_001.fastq.gz", "results/trimmed/B_R2_unpaired.fastq.gz"], "log": ["logs/bowtie2/B.log"], "params": ["'resources/Aus0004.fasta'"], "shellcmd": "rgid=`echo results/trimmed/B_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && rgsm=`echo results/trimmed/B_R1_001.fastq.gz | cut -d'/' -f3 | sed 's/_R1_001.fastq.gz//g'` && bowtie2 -x resources/Aus0004.fasta -1 results/trimmed/B_R1_001.fastq.gz -2 results/trimmed/B_R2_001.fastq.gz -U results/trimmed/B_R1_unpaired.fastq.gz -U results/trimmed/B_R2_unpaired.fastq.gz -S results/mapped/B_aln.sam -t -p 8 --non-deterministic --end-to-end --rg-id $rgid --rg SM:$rgsm --rg LB:1 --rg PL:Illumina && samtools view -Sb results/mapped/B_aln.sam > results/mapped/B_aln.bam && samtools sort -O BAM -o results/mapped/B_aln_sort.bam results/mapped/B_aln.bam", "incomplete": false, "starttime": 1627497141.261093, "endtime": 1627497256.209072, "job_hash": 2940385042116, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/dHJpbW1lZC9BX1IxX3VucGFpcmVkLmZhc3RxLmd6 b/.snakemake/metadata/dHJpbW1lZC9BX1IxX3VucGFpcmVkLmZhc3RxLmd6 deleted file mode 100644 index a315c34..0000000 --- a/.snakemake/metadata/dHJpbW1lZC9BX1IxX3VucGFpcmVkLmZhc3RxLmd6 +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz"], "log": ["logs/trimmomatic/A.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz trimmed/A_R1_001.fastq.gz trimmed/A_R1_unpaired.fastq.gz trimmed/A_R2_001.fastq.gz trimmed/A_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/A.log", "incomplete": false, "starttime": 1627483382.630071, "endtime": 1627483651.924071, "job_hash": 2957219239556, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/dHJpbW1lZC9BX1IxXzAwMS5mYXN0cS5neg== b/.snakemake/metadata/dHJpbW1lZC9BX1IxXzAwMS5mYXN0cS5neg== deleted file mode 100644 index e0bc860..0000000 --- a/.snakemake/metadata/dHJpbW1lZC9BX1IxXzAwMS5mYXN0cS5neg== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz"], "log": ["logs/trimmomatic/A.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz trimmed/A_R1_001.fastq.gz trimmed/A_R1_unpaired.fastq.gz trimmed/A_R2_001.fastq.gz trimmed/A_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/A.log", "incomplete": false, "starttime": 1627483382.62203, "endtime": 1627483651.922187, "job_hash": 2957219239556, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/dHJpbW1lZC9BX1IyX3VucGFpcmVkLmZhc3RxLmd6 b/.snakemake/metadata/dHJpbW1lZC9BX1IyX3VucGFpcmVkLmZhc3RxLmd6 deleted file mode 100644 index 296d4de..0000000 --- a/.snakemake/metadata/dHJpbW1lZC9BX1IyX3VucGFpcmVkLmZhc3RxLmd6 +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz"], "log": ["logs/trimmomatic/A.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz trimmed/A_R1_001.fastq.gz trimmed/A_R1_unpaired.fastq.gz trimmed/A_R2_001.fastq.gz trimmed/A_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/A.log", "incomplete": false, "starttime": 1627483382.634064, "endtime": 1627483651.925014, "job_hash": 2957219239556, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/dHJpbW1lZC9BX1IyXzAwMS5mYXN0cS5neg== b/.snakemake/metadata/dHJpbW1lZC9BX1IyXzAwMS5mYXN0cS5neg== deleted file mode 100644 index 524cba1..0000000 --- a/.snakemake/metadata/dHJpbW1lZC9BX1IyXzAwMS5mYXN0cS5neg== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz"], "log": ["logs/trimmomatic/A.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/A_R2_001.fastq.gz trimmed/A_R1_001.fastq.gz trimmed/A_R1_unpaired.fastq.gz trimmed/A_R2_001.fastq.gz trimmed/A_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/A.log", "incomplete": false, "starttime": 1627483382.626133, "endtime": 1627483651.923149, "job_hash": 2957219239556, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/dHJpbW1lZC9CX1IxX3VucGFpcmVkLmZhc3RxLmd6 b/.snakemake/metadata/dHJpbW1lZC9CX1IxX3VucGFpcmVkLmZhc3RxLmd6 deleted file mode 100644 index e10d65a..0000000 --- a/.snakemake/metadata/dHJpbW1lZC9CX1IxX3VucGFpcmVkLmZhc3RxLmd6 +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz"], "log": ["logs/trimmomatic/B.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz trimmed/B_R1_001.fastq.gz trimmed/B_R1_unpaired.fastq.gz trimmed/B_R2_001.fastq.gz trimmed/B_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/B.log", "incomplete": false, "starttime": 1627483382.601026, "endtime": 1627483648.043014, "job_hash": 2957219239636, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/dHJpbW1lZC9CX1IxXzAwMS5mYXN0cS5neg== b/.snakemake/metadata/dHJpbW1lZC9CX1IxXzAwMS5mYXN0cS5neg== deleted file mode 100644 index 7497938..0000000 --- a/.snakemake/metadata/dHJpbW1lZC9CX1IxXzAwMS5mYXN0cS5neg== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz"], "log": ["logs/trimmomatic/B.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz trimmed/B_R1_001.fastq.gz trimmed/B_R1_unpaired.fastq.gz trimmed/B_R2_001.fastq.gz trimmed/B_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/B.log", "incomplete": false, "starttime": 1627483382.593043, "endtime": 1627483648.041031, "job_hash": 2957219239636, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/dHJpbW1lZC9CX1IyX3VucGFpcmVkLmZhc3RxLmd6 b/.snakemake/metadata/dHJpbW1lZC9CX1IyX3VucGFpcmVkLmZhc3RxLmd6 deleted file mode 100644 index a2349ab..0000000 --- a/.snakemake/metadata/dHJpbW1lZC9CX1IyX3VucGFpcmVkLmZhc3RxLmd6 +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz"], "log": ["logs/trimmomatic/B.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz trimmed/B_R1_001.fastq.gz trimmed/B_R1_unpaired.fastq.gz trimmed/B_R2_001.fastq.gz trimmed/B_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/B.log", "incomplete": false, "starttime": 1627483382.604028, "endtime": 1627483648.044011, "job_hash": 2957219239636, "conda_env": null, "container_img_url": null} \ No newline at end of file diff --git a/.snakemake/metadata/dHJpbW1lZC9CX1IyXzAwMS5mYXN0cS5neg== b/.snakemake/metadata/dHJpbW1lZC9CX1IyXzAwMS5mYXN0cS5neg== deleted file mode 100644 index 27b0fad..0000000 --- a/.snakemake/metadata/dHJpbW1lZC9CX1IyXzAwMS5mYXN0cS5neg== +++ /dev/null @@ -1 +0,0 @@ -{"version": null, "code": "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", "rule": "trimmomatic_pe", "input": ["/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz", "/scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz"], "log": ["logs/trimmomatic/B.log"], "params": ["'/config/adapters/NexteraPE-PE.fa'", "0", "10", "2", "20", "30", "4", "40", "8", "True"], "shellcmd": "trimmomatic PE /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R1_001.fastq.gz /scratch/esnitkin_root/esnitkin/apirani/Project_VRE_metagenomics_analysis/2021_06_25_LDV_Simulation/Simulated_data/test_data/B_R2_001.fastq.gz trimmed/B_R1_001.fastq.gz trimmed/B_R1_unpaired.fastq.gz trimmed/B_R2_001.fastq.gz trimmed/B_R2_unpaired.fastq.gz ILLUMINACLIP:/config/adapters/NexteraPE-PE.fa:2:30:10:8:True SLIDINGWINDOW:4:20 MINLEN:40 HEADCROP:0 &>logs/trimmomatic/B.log", "incomplete": false, "starttime": 1627483382.597028, "endtime": 1627483648.042017, "job_hash": 2957219239636, "conda_env": null, "container_img_url": null} \ No newline at end of file