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fixed cloning geofetch repository
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@khoroshevskyi
khoroshevskyi committed Aug 1, 2023
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Showing 1 changed file with 19 additions and 19 deletions.
38 changes: 19 additions & 19 deletions docs_jupyter/how_to_convert_fastq_from_sra.ipynb
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"Metadata folder: /home/bnt4me/virginia/repos/geofetch/docs_jupyter/red_algae\n",
"Trying GSE67303 (not a file) as accession...\n",
"Skipped 0 accessions. Starting now.\n",
"\u001b[38;5;200mProcessing accession 1 of 1: 'GSE67303'\u001b[0m\n",
"\u001B[38;5;200mProcessing accession 1 of 1: 'GSE67303'\u001B[0m\n",
"Processed 4 samples.\n",
"Expanding metadata list...\n",
"Found SRA Project accession: SRP056574\n",
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"Finished processing 1 accession(s)\n",
"Cleaning soft files ...\n",
"Creating complete project annotation sheets and config file...\n",
"\u001b[92mSample annotation sheet: /home/bnt4me/virginia/repos/geofetch/docs_jupyter/red_algae/GSE67303_PEP/GSE67303_PEP_raw.csv . Saved!\u001b[0m\n",
"\u001b[92mFile has been saved successfully\u001b[0m\n",
"\u001B[92mSample annotation sheet: /home/bnt4me/virginia/repos/geofetch/docs_jupyter/red_algae/GSE67303_PEP/GSE67303_PEP_raw.csv . Saved!\u001B[0m\n",
"\u001B[92mFile has been saved successfully\u001B[0m\n",
" Config file: /home/bnt4me/virginia/repos/geofetch/docs_jupyter/red_algae/GSE67303_PEP/GSE67303_PEP.yaml\n"
]
}
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0m\u001b[01;34mbuild\u001b[0m python-usage.ipynb \u001b[01;34mSRR1930184\u001b[0m\n",
"\u001b[01;34mcode\u001b[0m raw-data-downloading.ipynb \u001b[01;34mSRR1930185\u001b[0m\n",
"how_to_fastq_from_sra.ipynb \u001b[01;34mred_algae\u001b[0m \u001b[01;34mSRR1930186\u001b[0m\n",
"processed-data-downloading.ipynb \u001b[01;34mSRR1930183\u001b[0m\n"
"\u001B[0m\u001B[01;34mbuild\u001B[0m python-usage.ipynb \u001B[01;34mSRR1930184\u001B[0m\n",
"\u001B[01;34mcode\u001B[0m raw-data-downloading.ipynb \u001B[01;34mSRR1930185\u001B[0m\n",
"how_to_fastq_from_sra.ipynb \u001B[01;34mred_algae\u001B[0m \u001B[01;34mSRR1930186\u001B[0m\n",
"processed-data-downloading.ipynb \u001B[01;34mSRR1930183\u001B[0m\n"
]
}
],
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"outputs": [],
"source": [
"# Unfortunately you have to pull gefetch folder from github, and set CODE variable:\n",
"mkdir code && cd code && git pull https://github.com/pepkit/geofetch.git && export CODE=`pwd` && cd .."
"mkdir code && cd code && git clone https://github.com/pepkit/geofetch.git && export CODE=`pwd` && cd .."
]
},
{
Expand All @@ -349,10 +349,10 @@
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0m\u001b[01;34mbuild\u001b[0m processed-data-downloading.ipynb \u001b[01;34mSRR1930183\u001b[0m\n",
"\u001b[01;34mcode\u001b[0m python-usage.ipynb \u001b[01;34mSRR1930184\u001b[0m\n",
"\u001b[01;34mfq_folder\u001b[0m raw-data-downloading.ipynb \u001b[01;34mSRR1930185\u001b[0m\n",
"how_to_fastq_from_sra.ipynb \u001b[01;34mred_algae\u001b[0m \u001b[01;34mSRR1930186\u001b[0m\n"
"\u001B[0m\u001B[01;34mbuild\u001B[0m processed-data-downloading.ipynb \u001B[01;34mSRR1930183\u001B[0m\n",
"\u001B[01;34mcode\u001B[0m python-usage.ipynb \u001B[01;34mSRR1930184\u001B[0m\n",
"\u001B[01;34mfq_folder\u001B[0m raw-data-downloading.ipynb \u001B[01;34mSRR1930185\u001B[0m\n",
"how_to_fastq_from_sra.ipynb \u001B[01;34mred_algae\u001B[0m \u001B[01;34mSRR1930186\u001B[0m\n"
]
}
],
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"output_type": "stream",
"text": [
"looper 1.4.3\n",
"\u001b[0m\n"
"\u001B[0m\n"
]
}
],
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[0m\u001b[01;34mGSE67303_PEP\u001b[0m\n"
"\u001B[0m\u001B[01;34mGSE67303_PEP\u001B[0m\n"
]
}
],
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"Using amendments: sra_convert\n",
"Activating compute package 'local'\n",
"Pipestat compatible: False\n",
"\u001b[36m## [1 of 4] sample: cm_bluelight_rep1; pipeline: sra_convert\u001b[0m\n",
"\u001B[36m## [1 of 4] sample: cm_bluelight_rep1; pipeline: sra_convert\u001B[0m\n",
"Writing script to /home/bnt4me/virginia/repos/geofetch/docs_jupyter/submission/sra_convert_cm_bluelight_rep1.sub\n",
"Job script (n=1; 0.06Gb): ./submission/sra_convert_cm_bluelight_rep1.sub\n",
"Compute node: bnt4me-Precision-5560\n",
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"* Total elapsed time (all runs): 0:00:02\n",
"* Peak memory (this run): 0.0803 GB\n",
"* Pipeline completed time: 2023-08-01 13:06:44\n",
"\u001b[36m## [2 of 4] sample: cm_bluelight_rep2; pipeline: sra_convert\u001b[0m\n",
"\u001B[36m## [2 of 4] sample: cm_bluelight_rep2; pipeline: sra_convert\u001B[0m\n",
"Writing script to /home/bnt4me/virginia/repos/geofetch/docs_jupyter/submission/sra_convert_cm_bluelight_rep2.sub\n",
"Job script (n=1; 0.04Gb): ./submission/sra_convert_cm_bluelight_rep2.sub\n",
"Compute node: bnt4me-Precision-5560\n",
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"* Total elapsed time (all runs): 0:00:02\n",
"* Peak memory (this run): 0.0118 GB\n",
"* Pipeline completed time: 2023-08-01 13:06:47\n",
"\u001b[36m## [3 of 4] sample: cm_darkness_rep1; pipeline: sra_convert\u001b[0m\n",
"\u001B[36m## [3 of 4] sample: cm_darkness_rep1; pipeline: sra_convert\u001B[0m\n",
"Writing script to /home/bnt4me/virginia/repos/geofetch/docs_jupyter/submission/sra_convert_cm_darkness_rep1.sub\n",
"Job script (n=1; 0.09Gb): ./submission/sra_convert_cm_darkness_rep1.sub\n",
"Compute node: bnt4me-Precision-5560\n",
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"* Total elapsed time (all runs): 0:00:03\n",
"* Peak memory (this run): 0.0793 GB\n",
"* Pipeline completed time: 2023-08-01 13:06:50\n",
"\u001b[36m## [4 of 4] sample: cm_darkness_rep2; pipeline: sra_convert\u001b[0m\n"
"\u001B[36m## [4 of 4] sample: cm_darkness_rep2; pipeline: sra_convert\u001B[0m\n"
]
},
{
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"Samples valid for job generation: 4 of 4\n",
"Commands submitted: 4 of 4\n",
"Jobs submitted: 4\n",
"\u001b[0m\n"
"\u001B[0m\n"
]
}
],
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