## How to extract fastq files from SRA
1. Install geofetch
```bash
pip install geofetch
```
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: geofetch in /home/bnt4me/.local/lib/python3.10/site-packages (0.12.7)
Requirement already satisfied: colorama>=0.3.9 in /usr/lib/python3/dist-packages (from geofetch) (0.4.4)
Requirement already satisfied: coloredlogs>=15.0.1 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (15.0.1)
Requirement already satisfied: logmuse>=0.2.6 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (0.2.7)
Requirement already satisfied: pandas>=1.5.3 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (2.2.2)
Requirement already satisfied: peppy>=0.40.6 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (0.40.7)
Requirement already satisfied: piper>=0.14.4 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (0.14.4)
Requirement already satisfied: requests>=2.28.1 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (2.31.0)
Requirement already satisfied: rich>=12.5.1 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (13.7.1)
Requirement already satisfied: ubiquerg>=0.6.2 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (0.8.1)
Requirement already satisfied: xmltodict>=0.13.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from geofetch) (0.13.0)
Requirement already satisfied: humanfriendly>=9.1 in /home/bnt4me/.local/lib/python3.10/site-packages (from coloredlogs>=15.0.1->geofetch) (10.0)
Requirement already satisfied: numpy>=1.22.4 in /home/bnt4me/.local/lib/python3.10/site-packages (from pandas>=1.5.3->geofetch) (1.25.2)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/bnt4me/.local/lib/python3.10/site-packages (from pandas>=1.5.3->geofetch) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /usr/lib/python3/dist-packages (from pandas>=1.5.3->geofetch) (2022.1)
Requirement already satisfied: tzdata>=2022.7 in /home/bnt4me/.local/lib/python3.10/site-packages (from pandas>=1.5.3->geofetch) (2023.3)
Requirement already satisfied: pyyaml in /usr/lib/python3/dist-packages (from peppy>=0.40.6->geofetch) (5.4.1)
Requirement already satisfied: pephubclient>=0.4.2 in /home/bnt4me/.local/lib/python3.10/site-packages (from peppy>=0.40.6->geofetch) (0.4.2)
Requirement already satisfied: psutil in /home/bnt4me/.local/lib/python3.10/site-packages (from piper>=0.14.4->geofetch) (5.9.4)
Requirement already satisfied: yacman>=0.9.3 in /home/bnt4me/.local/lib/python3.10/site-packages (from piper>=0.14.4->geofetch) (0.9.3)
Requirement already satisfied: pipestat>=0.11.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from piper>=0.14.4->geofetch) (0.12.1)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/bnt4me/.local/lib/python3.10/site-packages (from requests>=2.28.1->geofetch) (3.0.1)
Requirement already satisfied: idna<4,>=2.5 in /usr/lib/python3/dist-packages (from requests>=2.28.1->geofetch) (3.3)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/bnt4me/.local/lib/python3.10/site-packages (from requests>=2.28.1->geofetch) (1.26.18)
Requirement already satisfied: certifi>=2017.4.17 in /usr/lib/python3/dist-packages (from requests>=2.28.1->geofetch) (2020.6.20)
Requirement already satisfied: markdown-it-py>=2.2.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from rich>=12.5.1->geofetch) (3.0.0)
Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from rich>=12.5.1->geofetch) (2.17.2)
Requirement already satisfied: mdurl~=0.1 in /home/bnt4me/.local/lib/python3.10/site-packages (from markdown-it-py>=2.2.0->rich>=12.5.1->geofetch) (0.1.2)
Requirement already satisfied: typer>=0.7.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from pephubclient>=0.4.2->peppy>=0.40.6->geofetch) (0.9.4)
Requirement already satisfied: pydantic>2.5.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from pephubclient>=0.4.2->peppy>=0.40.6->geofetch) (2.7.3)
Requirement already satisfied: jsonschema in /home/bnt4me/.local/lib/python3.10/site-packages (from pipestat>=0.11.0->piper>=0.14.4->geofetch) (4.23.0)
Requirement already satisfied: eido in /home/bnt4me/.local/lib/python3.10/site-packages (from pipestat>=0.11.0->piper>=0.14.4->geofetch) (0.2.4)
Requirement already satisfied: jinja2 in /usr/lib/python3/dist-packages (from pipestat>=0.11.0->piper>=0.14.4->geofetch) (3.0.3)
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.8.2->pandas>=1.5.3->geofetch) (1.16.0)
Requirement already satisfied: attmap>=0.13.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from yacman>=0.9.3->piper>=0.14.4->geofetch) (0.13.2)
Requirement already satisfied: oyaml in /home/bnt4me/.local/lib/python3.10/site-packages (from yacman>=0.9.3->piper>=0.14.4->geofetch) (1.0)
Requirement already satisfied: attrs>=22.2.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from jsonschema->pipestat>=0.11.0->piper>=0.14.4->geofetch) (25.3.0)
Requirement already satisfied: jsonschema-specifications>=2023.03.6 in /home/bnt4me/.local/lib/python3.10/site-packages (from jsonschema->pipestat>=0.11.0->piper>=0.14.4->geofetch) (2025.4.1)
Requirement already satisfied: referencing>=0.28.4 in /home/bnt4me/.local/lib/python3.10/site-packages (from jsonschema->pipestat>=0.11.0->piper>=0.14.4->geofetch) (0.36.2)
Requirement already satisfied: rpds-py>=0.7.1 in /home/bnt4me/.local/lib/python3.10/site-packages (from jsonschema->pipestat>=0.11.0->piper>=0.14.4->geofetch) (0.24.0)
Requirement already satisfied: annotated-types>=0.4.0 in /home/bnt4me/.local/lib/python3.10/site-packages (from pydantic>2.5.0->pephubclient>=0.4.2->peppy>=0.40.6->geofetch) (0.6.0)
Requirement already satisfied: pydantic-core==2.18.4 in /home/bnt4me/.local/lib/python3.10/site-packages (from pydantic>2.5.0->pephubclient>=0.4.2->peppy>=0.40.6->geofetch) (2.18.4)
Requirement already satisfied: typing-extensions>=4.6.1 in /home/bnt4me/.local/lib/python3.10/site-packages (from pydantic>2.5.0->pephubclient>=0.4.2->peppy>=0.40.6->geofetch) (4.8.0)
Requirement already satisfied: click<9.0.0,>=7.1.1 in /usr/lib/python3/dist-packages (from typer>=0.7.0->pephubclient>=0.4.2->peppy>=0.40.6->geofetch) (8.0.3)
[notice] A new release of pip is available: 23.2.1 -> 25.1.1
[notice] To update, run: python3 -m pip install --upgrade pip
```bash
geofetch --version
```
geofetch 0.12.8
1) Download SRA files and PEP using GEOfetch
Add flags:
1) `--add-convert-modifier` (To add looper configurations for conversion)
2) `--discard-soft` (To delete soft files. We don't need them :D)
```bash
geofetch -i GSE67303 -n red_algae -m `pwd` --add-convert-modifier --discard-soft
```
[INFO] [00:54:23] Metadata folder: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae
[INFO] [00:54:24] Trying GSE67303 (not a file) as accession...
[INFO] [00:54:24] Skipped 0 accessions. Starting now.
[INFO] [00:54:24] Processing accession 1 of 1: 'GSE67303'
[INFO] [00:54:24] Processed 4 samples.
[INFO] [00:54:24] Expanding metadata list...
[INFO] [00:54:24] Found SRA Project accession: SRP056574
[INFO] [00:54:24] Downloading SRP056574 sra metadata
[INFO] [00:54:25] Parsing SRA file to download SRR records
[INFO] [00:54:25] Getting SRR: SRR1930183 in (GSE67303)
2025-07-10T04:54:26 prefetch.2.11.3: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2025-07-10T04:54:26 prefetch.2.11.3: 1) Downloading 'SRR1930183'...
2025-07-10T04:54:26 prefetch.2.11.3: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2025-07-10T04:54:26 prefetch.2.11.3: Downloading via HTTPS...
2025-07-10T04:54:31 prefetch.2.11.3: HTTPS download succeed
2025-07-10T04:54:31 prefetch.2.11.3: 'SRR1930183' is valid
2025-07-10T04:54:31 prefetch.2.11.3: 1) 'SRR1930183' was downloaded successfully
2025-07-10T04:54:31 prefetch.2.11.3: 'SRR1930183' has 0 unresolved dependencies
[INFO] [00:54:31] Getting SRR: SRR1930184 in (GSE67303)
2025-07-10T04:54:32 prefetch.2.11.3: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2025-07-10T04:54:32 prefetch.2.11.3: 1) Downloading 'SRR1930184'...
2025-07-10T04:54:32 prefetch.2.11.3: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2025-07-10T04:54:32 prefetch.2.11.3: Downloading via HTTPS...
2025-07-10T04:54:36 prefetch.2.11.3: HTTPS download succeed
2025-07-10T04:54:36 prefetch.2.11.3: 'SRR1930184' is valid
2025-07-10T04:54:36 prefetch.2.11.3: 1) 'SRR1930184' was downloaded successfully
2025-07-10T04:54:36 prefetch.2.11.3: 'SRR1930184' has 0 unresolved dependencies
[INFO] [00:54:36] Getting SRR: SRR1930185 in (GSE67303)
2025-07-10T04:54:37 prefetch.2.11.3: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2025-07-10T04:54:37 prefetch.2.11.3: 1) Downloading 'SRR1930185'...
2025-07-10T04:54:37 prefetch.2.11.3: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2025-07-10T04:54:37 prefetch.2.11.3: Downloading via HTTPS...
2025-07-10T04:54:45 prefetch.2.11.3: HTTPS download succeed
2025-07-10T04:54:45 prefetch.2.11.3: 'SRR1930185' is valid
2025-07-10T04:54:45 prefetch.2.11.3: 1) 'SRR1930185' was downloaded successfully
2025-07-10T04:54:45 prefetch.2.11.3: 'SRR1930185' has 0 unresolved dependencies
[INFO] [00:54:45] Getting SRR: SRR1930186 in (GSE67303)
2025-07-10T04:54:46 prefetch.2.11.3: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2025-07-10T04:54:46 prefetch.2.11.3: 1) Downloading 'SRR1930186'...
2025-07-10T04:54:46 prefetch.2.11.3: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2025-07-10T04:54:46 prefetch.2.11.3: Downloading via HTTPS...
2025-07-10T04:54:52 prefetch.2.11.3: HTTPS download succeed
2025-07-10T04:54:52 prefetch.2.11.3: 'SRR1930186' is valid
2025-07-10T04:54:52 prefetch.2.11.3: 1) 'SRR1930186' was downloaded successfully
2025-07-10T04:54:52 prefetch.2.11.3: 'SRR1930186' has 0 unresolved dependencies
[INFO] [00:54:52] Finished processing 1 accession(s)
[INFO] [00:54:52] Cleaning soft files ...
[INFO] [00:54:52] Creating complete project annotation sheets and config file...
[INFO] [00:54:52] Sample annotation sheet: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/GSE67303_PEP/GSE67303_PEP_raw.csv . Saved!
[INFO] [00:54:52] File has been saved successfully
[INFO] [00:54:52] Config file: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/GSE67303_PEP/GSE67303_PEP.yaml
[INFO] [00:54:52] Looper config file: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/looper_config.yaml
Let's see if files were downloaded:
```bash
ls
```
fq_folder raw-data-downloading.ipynb SRR1930185
howto-sra-to-fastq.ipynb red_algae SRR1930186
processed-data-downloading.ipynb SRR1930183
python-usage.ipynb SRR1930184
now let's check how does our config file looks like:
```bash
cat ./red_algae/GSE67303_PEP/GSE67303_PEP.yaml
```
# Autogenerated by geofetch
name: GSE67303
pep_version: 2.1.0
sample_table: GSE67303_PEP_raw.csv
"experiment_metadata":
"series_contact_address": "930 N University Ave"
"series_contact_city": "Ann Arbor"
"series_contact_country": "USA"
"series_contact_department": "Chemistry"
"series_contact_email": "mtardu@umich.edu"
"series_contact_institute": "University of Michigan"
"series_contact_laboratory": "Koutmou Lab"
"series_contact_name": "mehmet,,tardu"
"series_contact_state": "MI"
"series_contact_zip_postal_code": "48109"
"series_contributor": "Mehmet,,Tardu + Ugur,M,Dikbas + Ibrahim,,Baris + Ibrahim,H,Kavakli"
"series_geo_accession": "GSE67303"
"series_last_update_date": "May 15 2019"
"series_overall_design": "Identification of blue light and red light regulated genes\
\ by deep sequencing in biological duplicates. qRT-PCR was performed to verify\
\ the RNA-seq results."
"series_platform_id": "GPL19949"
"series_platform_organism": "Cyanidioschyzon merolae strain 10D"
"series_platform_taxid": "280699"
"series_pubmed_id": "27614431"
"series_relation": "BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA279462\
\ + SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP056574"
"series_sample_id": "GSM1644066 + GSM1644067 + GSM1644068 + GSM1644069"
"series_sample_organism": "Cyanidioschyzon merolae strain 10D"
"series_sample_taxid": "280699"
"series_status": "Public on Sep 01 2016"
"series_submission_date": "Mar 26 2015"
"series_summary": "Light is one of the main environmental cues that affects the\
\ physiology and behavior of many organisms. The effect of light on genome-wide\
\ transcriptional regulation has been well-studied in green algae and plants,\
\ but not in red algae. Cyanidioschyzon merolae is used as a model red algae,\
\ and is suitable for studies on transcriptomics because of its compact genome\
\ with a relatively small number of genes. In addition, complete genome sequences\
\ of the nucleus, mitochondrion, and chloroplast of this organism have been determined.\
\ Together, these attributes make C. merolae an ideal model organism to study\
\ the response to light stimuli at the transcriptional and the systems biology\
\ levels. Previous studies have shown that light significantly affects cell signaling\
\ in this organism, but there are no reports on its blue light- and red light-mediated\
\ transcriptional responses. We investigated the direct effects of blue and red\
\ light at the transcriptional level using RNA-seq. Blue and red light were found\
\ to regulate 35% of the total genes in C. merolae. Blue light affected the transcription\
\ of genes involved protein synthesis while red light specifically regulated the\
\ transcription of genes involved in photosynthesis and DNA repair. Blue or red\
\ light regulated genes involved in carbon metabolism and pigment biosynthesis.\
\ Overall, our data showed that red and blue light regulate the majority of the\
\ cellular, cell division, and repair processes in C. merolae."
"series_supplementary_file": "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67303/suppl/GSE67303_DEG_cuffdiff.xlsx"
"series_title": "RNA-seq analysis of the transcriptional response to blue and red\
\ light in the extremophilic red alga, Cyanidioschyzon merolae"
"series_type": "Expression profiling by high throughput sequencing"
sample_modifiers:
append:
# Project metadata:
sample_treatment_protocol_ch1: "Cells were exposed to blue-light (15 µmole m-2s-1) for 30 minutes"
sample_growth_protocol_ch1: "Cyanidioschyzon merolae cells were grown in 2xMA media"
sample_extract_protocol_ch1: "Dark kept and blue-light exposed C.merolae cells were removed and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries., RNA libraries were prepared for sequencing using standard Illumina protocols"
sample_data_processing: "The purified cDNA library was sequenced on Illumina''s MiSeq sequencing platform following vendor''s instruction for running the instrument., Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cyanidioschyzon merolae 10D reference genome (assembly ID:ASM9120v1) using TopHat (v2.0.5)., Differential expression analysis was conducted by using cuffdiff tool in cufflink suite (v2.2)"
supplementary_files_format_and_content: "Excel spreadsheet includes FPKM values for Darkness and Blue-Light exposed samples with p and q values of cuffdiff output."
# End of project metadata
# Adding sra convert looper pipeline
SRR_files: SRA
derive:
attributes: [read1, read2, SRR_files]
sources:
SRA: "${SRARAW}/{srr}/{srr}.sra"
FQ: "${SRAFQ}/{srr}.fastq.gz"
FQ1: "${SRAFQ}/{srr}_1.fastq.gz"
FQ2: "${SRAFQ}/{srr}_2.fastq.gz"
imply:
- if:
organism: "Mus musculus"
then:
genome: mm10
- if:
organism: "Homo sapiens"
then:
genome: hg38
- if:
read_type: "PAIRED"
then:
read1: FQ1
read2: FQ2
- if:
read_type: "SINGLE"
then:
read1: FQ1
To run pipeline, you should set up few enviromental variables:
1) SRARAW - folder where SRA files were downloaded
2) SRAFQ -folder where fastq should be produced
3) CODE - (first you should clone geofetch), and $CODE is where geofetch folder is located
```bash
# Set SRARAW env
export SRARAW=`pwd`
```
```bash
# Create folder where you want to store fq
mkdir fq_folder
```
```bash
# Set SRAFQ env
export SRAFQ=`pwd`/fq_folder
```
### Now install looper if you don't have it
```bash
# pip install looper
```
```bash
looper --version
```
2.0.1
Let's check where is looper config file and whats inside:
```bash
ls red_algae
```
GSE67303_PEP looper_config.yaml output_dir
```bash
cat red_algae/looper_config.yaml
```
pep_config: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/GSE67303_PEP/GSE67303_PEP.yaml
output_dir: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir
pipeline_interfaces:
- /home/bnt4me/.local/lib/python3.10/site-packages/geofetch/templates/pipeline_interface_convert.yaml
Geofetch automatically generated paths to pep_config and pipeline interfaces that are embedded into geofetch
```bash
looper run --config ./red_algae/looper_config.yaml -p local --output-dir .
```
Looper version: 2.0.1
Command: run
Using default divvy config. You may specify in env var: ['DIVCFG']
Activating compute package 'local'
## [1 of 4] sample: cm_bluelight_rep1; pipeline: sra_convert
Writing script to /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/submission/sra_convert_cm_bluelight_rep1.sub
Job script (n=1; 0.00Gb): /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/submission/sra_convert_cm_bluelight_rep1.sub
Compute node: alex-laptop
Start time: 2025-07-10 00:59:02
Using outfolder: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930183
No pipestat output schema was supplied to PipestatManager.
Initializing results file '/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930183/stats.yaml'
### Pipeline run code and environment:
* Command: `/home/bnt4me/.local/bin/sraconvert --srr /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930183/SRR1930183.sra -O /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline`
* Compute host: `alex-laptop`
* Working dir: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks`
* Outfolder: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930183/`
* Log file: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930183/sra_convert_log.md`
* Start time: (07-10 00:59:03) elapsed: 0.0 _TIME_
### Version log:
* Python version: `3.10.12`
* Pypiper dir: `/home/bnt4me/.local/lib/python3.10/site-packages/pypiper`
* Pypiper version: `0.14.4`
* Pipeline dir: `/home/bnt4me/.local/bin`
* Pipeline version:
### Arguments passed to pipeline:
* `bamfolder`: ``
* `config_file`: `sraconvert.yaml`
* `format`: `fastq`
* `fqfolder`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder`
* `keep_sra`: `False`
* `logdev`: `False`
* `mode`: `convert`
* `output_parent`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline`
* `recover`: `False`
* `sample_name`: `None`
* `silent`: `False`
* `srafolder`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks`
* `srr`: `['/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930183/SRR1930183.sra']`
* `verbosity`: `None`
### Initialized Pipestat Object:
* PipestatManager (sra_convert)
* Backend: File
* - results: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930183/stats.yaml
* - status: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930183
* Multiple Pipelines Allowed: False
* Pipeline name: sra_convert
* Pipeline type: sample
* Status Schema key: None
* Results formatter: default_formatter
* Results schema source: None
* Status schema source: None
* Records count: 2
* Sample name: DEFAULT_SAMPLE_NAME
----------------------------------------
Processing 1 of 1 files: SRR1930183
Target to produce: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder/SRR1930183_1.fastq.gz`
> `fasterq-dump /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930183/SRR1930183.sra -O /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder` (871210)
spots read : 1,068,319
reads read : 2,136,638
reads written : 2,136,638
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.069GB.
PID: 871210; Command: fasterq-dump; Return code: 0; Memory used: 0.069GB
Already completed files: []
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:02
* Total elapsed time (all runs): 0:00:02
* Peak memory (this run): 0.0685 GB
* Pipeline completed time: 2025-07-10 00:59:05
Using default schema: /home/bnt4me/.local/bin/pipestat_output_schema.yaml
## [2 of 4] sample: cm_bluelight_rep2; pipeline: sra_convert
Writing script to /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/submission/sra_convert_cm_bluelight_rep2.sub
Job script (n=1; 0.00Gb): /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/submission/sra_convert_cm_bluelight_rep2.sub
Compute node: alex-laptop
Start time: 2025-07-10 00:59:06
Using outfolder: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930184
No pipestat output schema was supplied to PipestatManager.
Initializing results file '/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930184/stats.yaml'
### Pipeline run code and environment:
* Command: `/home/bnt4me/.local/bin/sraconvert --srr /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930184/SRR1930184.sra -O /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline`
* Compute host: `alex-laptop`
* Working dir: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks`
* Outfolder: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930184/`
* Log file: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930184/sra_convert_log.md`
* Start time: (07-10 00:59:06) elapsed: 0.0 _TIME_
### Version log:
* Python version: `3.10.12`
* Pypiper dir: `/home/bnt4me/.local/lib/python3.10/site-packages/pypiper`
* Pypiper version: `0.14.4`
* Pipeline dir: `/home/bnt4me/.local/bin`
* Pipeline version:
### Arguments passed to pipeline:
* `bamfolder`: ``
* `config_file`: `sraconvert.yaml`
* `format`: `fastq`
* `fqfolder`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder`
* `keep_sra`: `False`
* `logdev`: `False`
* `mode`: `convert`
* `output_parent`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline`
* `recover`: `False`
* `sample_name`: `None`
* `silent`: `False`
* `srafolder`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks`
* `srr`: `['/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930184/SRR1930184.sra']`
* `verbosity`: `None`
### Initialized Pipestat Object:
* PipestatManager (sra_convert)
* Backend: File
* - results: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930184/stats.yaml
* - status: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930184
* Multiple Pipelines Allowed: False
* Pipeline name: sra_convert
* Pipeline type: sample
* Status Schema key: None
* Results formatter: default_formatter
* Results schema source: None
* Status schema source: None
* Records count: 2
* Sample name: DEFAULT_SAMPLE_NAME
----------------------------------------
Processing 1 of 1 files: SRR1930184
Target to produce: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder/SRR1930184_1.fastq.gz`
> `fasterq-dump /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930184/SRR1930184.sra -O /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder` (871261)
spots read : 762,229
reads read : 1,524,458
reads written : 1,524,458
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.083GB.
PID: 871261; Command: fasterq-dump; Return code: 0; Memory used: 0.083GB
Already completed files: []
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:02
* Total elapsed time (all runs): 0:00:02
* Peak memory (this run): 0.0832 GB
* Pipeline completed time: 2025-07-10 00:59:08
Using default schema: /home/bnt4me/.local/bin/pipestat_output_schema.yaml
## [3 of 4] sample: cm_darkness_rep1; pipeline: sra_convert
Writing script to /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/submission/sra_convert_cm_darkness_rep1.sub
Job script (n=1; 0.00Gb): /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/submission/sra_convert_cm_darkness_rep1.sub
Compute node: alex-laptop
Start time: 2025-07-10 00:59:08
Using outfolder: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930185
No pipestat output schema was supplied to PipestatManager.
Initializing results file '/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930185/stats.yaml'
### Pipeline run code and environment:
* Command: `/home/bnt4me/.local/bin/sraconvert --srr /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930185/SRR1930185.sra -O /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline`
* Compute host: `alex-laptop`
* Working dir: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks`
* Outfolder: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930185/`
* Log file: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930185/sra_convert_log.md`
* Start time: (07-10 00:59:09) elapsed: 0.0 _TIME_
### Version log:
* Python version: `3.10.12`
* Pypiper dir: `/home/bnt4me/.local/lib/python3.10/site-packages/pypiper`
* Pypiper version: `0.14.4`
* Pipeline dir: `/home/bnt4me/.local/bin`
* Pipeline version:
### Arguments passed to pipeline:
* `bamfolder`: ``
* `config_file`: `sraconvert.yaml`
* `format`: `fastq`
* `fqfolder`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder`
* `keep_sra`: `False`
* `logdev`: `False`
* `mode`: `convert`
* `output_parent`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline`
* `recover`: `False`
* `sample_name`: `None`
* `silent`: `False`
* `srafolder`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks`
* `srr`: `['/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930185/SRR1930185.sra']`
* `verbosity`: `None`
### Initialized Pipestat Object:
* PipestatManager (sra_convert)
* Backend: File
* - results: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930185/stats.yaml
* - status: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930185
* Multiple Pipelines Allowed: False
* Pipeline name: sra_convert
* Pipeline type: sample
* Status Schema key: None
* Results formatter: default_formatter
* Results schema source: None
* Status schema source: None
* Records count: 2
* Sample name: DEFAULT_SAMPLE_NAME
----------------------------------------
Processing 1 of 1 files: SRR1930185
Target to produce: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder/SRR1930185_1.fastq.gz`
> `fasterq-dump /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930185/SRR1930185.sra -O /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder` (871306)
spots read : 1,707,508
reads read : 3,415,016
reads written : 3,415,016
Command completed. Elapsed time: 0:00:04. Running peak memory: 0.07GB.
PID: 871306; Command: fasterq-dump; Return code: 0; Memory used: 0.07GB
Already completed files: []
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:04
* Total elapsed time (all runs): 0:00:04
* Peak memory (this run): 0.0701 GB
* Pipeline completed time: 2025-07-10 00:59:13
Using default schema: /home/bnt4me/.local/bin/pipestat_output_schema.yaml
## [4 of 4] sample: cm_darkness_rep2; pipeline: sra_convert
Writing script to /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/submission/sra_convert_cm_darkness_rep2.sub
Job script (n=1; 0.00Gb): /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/submission/sra_convert_cm_darkness_rep2.sub
Compute node: alex-laptop
Start time: 2025-07-10 00:59:13
Using outfolder: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930186
No pipestat output schema was supplied to PipestatManager.
Initializing results file '/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930186/stats.yaml'
### Pipeline run code and environment:
* Command: `/home/bnt4me/.local/bin/sraconvert --srr /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930186/SRR1930186.sra -O /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline`
* Compute host: `alex-laptop`
* Working dir: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks`
* Outfolder: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930186/`
* Log file: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930186/sra_convert_log.md`
* Start time: (07-10 00:59:14) elapsed: 0.0 _TIME_
### Version log:
* Python version: `3.10.12`
* Pypiper dir: `/home/bnt4me/.local/lib/python3.10/site-packages/pypiper`
* Pypiper version: `0.14.4`
* Pipeline dir: `/home/bnt4me/.local/bin`
* Pipeline version:
### Arguments passed to pipeline:
* `bamfolder`: ``
* `config_file`: `sraconvert.yaml`
* `format`: `fastq`
* `fqfolder`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder`
* `keep_sra`: `False`
* `logdev`: `False`
* `mode`: `convert`
* `output_parent`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline`
* `recover`: `False`
* `sample_name`: `None`
* `silent`: `False`
* `srafolder`: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks`
* `srr`: `['/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930186/SRR1930186.sra']`
* `verbosity`: `None`
### Initialized Pipestat Object:
* PipestatManager (sra_convert)
* Backend: File
* - results: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930186/stats.yaml
* - status: /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/red_algae/output_dir/results_pipeline/SRR1930186
* Multiple Pipelines Allowed: False
* Pipeline name: sra_convert
* Pipeline type: sample
* Status Schema key: None
* Results formatter: default_formatter
* Results schema source: None
* Status schema source: None
* Records count: 2
* Sample name: DEFAULT_SAMPLE_NAME
----------------------------------------
Processing 1 of 1 files: SRR1930186
Target to produce: `/home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder/SRR1930186_1.fastq.gz`
> `fasterq-dump /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/SRR1930186/SRR1930186.sra -O /home/bnt4me/virginia/repos/pepspec/docs/geofetch/notebooks/fq_folder` (871369)
spots read : 1,224,029
reads read : 2,448,058
reads written : 2,448,058
Command completed. Elapsed time: 0:00:02. Running peak memory: 0.083GB.
PID: 871369; Command: fasterq-dump; Return code: 0; Memory used: 0.083GB
Already completed files: []
### Pipeline completed. Epilogue
* Elapsed time (this run): 0:00:02
* Total elapsed time (all runs): 0:00:02
* Peak memory (this run): 0.0832 GB
* Pipeline completed time: 2025-07-10 00:59:16
Using default schema: /home/bnt4me/.local/bin/pipestat_output_schema.yaml
Looper finished
Samples valid for job generation: 4 of 4
### Check if everything worked:
```bash
cd fq_folder
```
```bash
ls
```
SRR1930183_1.fastq SRR1930184_1.fastq SRR1930185_1.fastq SRR1930186_1.fastq
SRR1930183_2.fastq SRR1930184_2.fastq SRR1930185_2.fastq SRR1930186_2.fastq
Everything was executed sucessfully and SRA files were converted into fastq files