Last active
April 2, 2024 19:08
-
-
Save fomightez/efef613f653c10b2baee9e4897a43c84 to your computer and use it in GitHub Desktop.
Snakemake run test for SO https://stackoverflow.com/q/78260730/8508004 WITH BETTER VESION MATCHING!!!
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
{ | |
"cells": [ | |
{ | |
"cell_type": "markdown", | |
"id": "9ca6ae4a-2fbc-449a-ba5e-e5193220baff", | |
"metadata": {}, | |
"source": [ | |
"## Snakemake run test for SO https://stackoverflow.com/q/78260730/8508004 WITH BETTER VESION MATCHING!!!\n", | |
"\n", | |
"Ran in session launched from [here](https://gist.github.com/jtpio/35a72862c8be13dee31b61ebac2d9786) via clicking 'launch binder' badge. (Or click badge below for a fresh session!)\n", | |
"\n", | |
"[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gist/jtpio/35a72862c8be13dee31b61ebac2d9786/master?urlpath=/tree)\n", | |
"\n", | |
"This run makes the versions more like the OP!!!" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 1, | |
"id": "78fd5e8f-682c-4ff6-a9a9-0c360b4db25b", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"7.32.4\n" | |
] | |
} | |
], | |
"source": [ | |
"!snakemake -v" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 2, | |
"id": "8084336a-c10d-4254-9fa1-4703bf2c60e5", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]\n" | |
] | |
} | |
], | |
"source": [ | |
"import sys\n", | |
"print (sys.version)" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 3, | |
"id": "bafc96b3-29d8-44fd-8a58-5866542a4ce0", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
" README.md\n", | |
" requirements.txt\n", | |
" runtime.txt\n", | |
" Snakefile\n", | |
"'Snakemake run test for SO question 78260730 with versions matching OP.ipynb'\n" | |
] | |
} | |
], | |
"source": [ | |
"ls" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 4, | |
"id": "c389f424-d490-4092-afed-2d36ec658e18", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"Writing 's' (str) to file 'Snakefile'.\n" | |
] | |
} | |
], | |
"source": [ | |
"s='''rule A:\n", | |
" input:\n", | |
" i = 'B1477.all_merged_3split_dedupped_sorted.bam'\n", | |
" output:\n", | |
" o = 'B1477.all_merged_3split_dedupped_sorted2.bam'\n", | |
" shell:\n", | |
" \"cat {input.i} > {output.o}\"\n", | |
"'''\n", | |
"%store s >Snakefile" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "3be94589-cefa-46b5-8902-8e4b4ddf7b79", | |
"metadata": {}, | |
"source": [ | |
"Started runnng with only a `Snakefile` that had the above content." | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 5, | |
"id": "411ce30a-4a16-4506-b579-fd845dedaa50", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"\u001b[33mBuilding DAG of jobs...\u001b[0m\n", | |
"\u001b[31mMissingInputException in rule A in file /home/jovyan/Snakefile, line 1:\n", | |
"Missing input files for rule A:\n", | |
" output: B1477.all_merged_3split_dedupped_sorted2.bam\n", | |
" affected files:\n", | |
" B1477.all_merged_3split_dedupped_sorted.bam\u001b[0m\n" | |
] | |
} | |
], | |
"source": [ | |
"!snakemake --cores 1" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 6, | |
"id": "68736e64-1d0e-43c0-926a-3680de406a9f", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
" README.md\n", | |
" requirements.txt\n", | |
" runtime.txt\n", | |
" Snakefile\n", | |
"'Snakemake run test for SO question 78260730 with versions matching OP.ipynb'\n" | |
] | |
} | |
], | |
"source": [ | |
"ls" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "edb2993f-2c95-4bcb-ad66-c737d6e6c54f", | |
"metadata": {}, | |
"source": [ | |
"Make the input file." | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 7, | |
"id": "1e551dfa-4008-4bd1-a010-c1a7f83b3d9f", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"!touch B1477.all_merged_3split_dedupped_sorted.bam" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "dc6f344b-4598-4c04-b27f-42f7e0850b03", | |
"metadata": {}, | |
"source": [ | |
"Now try again." | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 8, | |
"id": "a7cd6cb9-80d8-405f-b77b-d21f6928477c", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"\u001b[33mBuilding DAG of jobs...\u001b[0m\n", | |
"\u001b[33mUsing shell: /usr/bin/bash\u001b[0m\n", | |
"\u001b[33mProvided cores: 1 (use --cores to define parallelism)\u001b[0m\n", | |
"\u001b[33mRules claiming more threads will be scaled down.\u001b[0m\n", | |
"\u001b[33mJob stats:\n", | |
"job count\n", | |
"----- -------\n", | |
"A 1\n", | |
"total 1\n", | |
"\u001b[0m\n", | |
"\u001b[33mSelect jobs to execute...\u001b[0m\n", | |
"\u001b[32m\u001b[0m\n", | |
"\u001b[32m[Tue Apr 2 18:24:48 2024]\u001b[0m\n", | |
"\u001b[32mrule A:\n", | |
" input: B1477.all_merged_3split_dedupped_sorted.bam\n", | |
" output: B1477.all_merged_3split_dedupped_sorted2.bam\n", | |
" jobid: 0\n", | |
" reason: Missing output files: B1477.all_merged_3split_dedupped_sorted2.bam\n", | |
" resources: tmpdir=/tmp\u001b[0m\n", | |
"\u001b[32m\u001b[0m\n", | |
"\u001b[32m[Tue Apr 2 18:24:48 2024]\u001b[0m\n", | |
"\u001b[32mFinished job 0.\u001b[0m\n", | |
"\u001b[32m1 of 1 steps (100%) done\u001b[0m\n", | |
"\u001b[33mComplete log: .snakemake/log/2024-04-02T182447.945729.snakemake.log\u001b[0m\n" | |
] | |
} | |
], | |
"source": [ | |
"!snakemake --cores 1" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 9, | |
"id": "92f2c41e-0634-4dc0-834d-0dd9774c47b1", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
" B1477.all_merged_3split_dedupped_sorted2.bam\n", | |
" B1477.all_merged_3split_dedupped_sorted.bam\n", | |
" README.md\n", | |
" requirements.txt\n", | |
" runtime.txt\n", | |
" Snakefile\n", | |
"'Snakemake run test for SO question 78260730 with versions matching OP.ipynb'\n" | |
] | |
} | |
], | |
"source": [ | |
"ls" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "1c98de98-a163-4982-a413-6e74c70b742a", | |
"metadata": {}, | |
"source": [ | |
"Worked, and says reason for run: **`reason: Missing output files: B1477.all_merged_3split_dedupped_sorted2.bam`**.\n", | |
"\n", | |
"I didn't see that with version 7.3.8. Nice feature added since then it seems." | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "6bb0d2c8-9729-4da2-a54f-1e3004702f6b", | |
"metadata": {}, | |
"source": [ | |
"#### What if remove the output and do dry run?" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 10, | |
"id": "10be6a4d-c233-46c7-8ab2-2dff15534071", | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"!rm -rf B1477.all_merged_3split_dedupped_sorted2.bam" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 11, | |
"id": "73d5dbb3-f4f4-4901-82b5-ed505f89b7a0", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
" B1477.all_merged_3split_dedupped_sorted.bam\n", | |
" README.md\n", | |
" requirements.txt\n", | |
" runtime.txt\n", | |
" Snakefile\n", | |
"'Snakemake run test for SO question 78260730 with versions matching OP.ipynb'\n" | |
] | |
} | |
], | |
"source": [ | |
"ls" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 12, | |
"id": "80c41494-f8b7-425d-ada4-a3ea539e1c04", | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"\u001b[33mBuilding DAG of jobs...\u001b[0m\n", | |
"\u001b[33mJob stats:\n", | |
"job count\n", | |
"----- -------\n", | |
"A 1\n", | |
"total 1\n", | |
"\u001b[0m\n", | |
"\u001b[32m\u001b[0m\n", | |
"\u001b[32m[Tue Apr 2 18:24:53 2024]\u001b[0m\n", | |
"\u001b[32mrule A:\n", | |
" input: B1477.all_merged_3split_dedupped_sorted.bam\n", | |
" output: B1477.all_merged_3split_dedupped_sorted2.bam\n", | |
" jobid: 0\n", | |
" reason: Missing output files: B1477.all_merged_3split_dedupped_sorted2.bam\n", | |
" resources: tmpdir=/tmp\u001b[0m\n", | |
"\u001b[32m\u001b[0m\n", | |
"\u001b[33mJob stats:\n", | |
"job count\n", | |
"----- -------\n", | |
"A 1\n", | |
"total 1\n", | |
"\u001b[0m\n", | |
"\u001b[33mReasons:\n", | |
" (check individual jobs above for details)\n", | |
" missing output files:\n", | |
" A\u001b[0m\n", | |
"\u001b[33m\u001b[0m\n", | |
"\u001b[33mThis was a dry-run (flag -n). The order of jobs does not reflect the order of execution.\u001b[0m\n" | |
] | |
} | |
], | |
"source": [ | |
"!snakemake -n" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"id": "6d6c7086-ccfa-49ad-8713-4fcc8074d7e2", | |
"metadata": {}, | |
"source": [ | |
"Indicates why it would run the rule: \n", | |
"\n", | |
"\n", | |
"```text\n", | |
"reason: Missing output files: B1477.all_merged_3split_dedupped_sorted2.bam\n", | |
"```" | |
] | |
} | |
], | |
"metadata": { | |
"kernelspec": { | |
"display_name": "Python 3 (ipykernel)", | |
"language": "python", | |
"name": "python3" | |
}, | |
"language_info": { | |
"codemirror_mode": { | |
"name": "ipython", | |
"version": 3 | |
}, | |
"file_extension": ".py", | |
"mimetype": "text/x-python", | |
"name": "python", | |
"nbconvert_exporter": "python", | |
"pygments_lexer": "ipython3", | |
"version": "3.10.12" | |
} | |
}, | |
"nbformat": 4, | |
"nbformat_minor": 5 | |
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment