bases2fastq

How to run bases2fastq in the computational infrastructure of INAB

Steps to run bases2fastq analysis:

Log in to the appropriate server:

o 160.40.71.4
Identify where your NGS results (.bcl files and SampleSheet) are located:

o e.g., /mnt/new_home/element/AV240301/20250131_AV240301_SARSDIAGNOSIS

Activate conda environment with dependencies for bases2fastq:

source activate /apps/miniconda3/envs/bases2fastq_dependencies

Create your RunManifest.csv:

o Information for preparing the RunManifest file can be found here.

o You can add a column named Project containing the name of the respective project for each sample.

o In the Data Section you can add a column named Project containing the name of the respective project for each sample.

Project can only contain alphanumeric characters, dashes, and underscores.
Move to your working folder:

o In case there are only samples from your lab run:
```
cd /mnt/new_home/stamatopoulos_research/
```
o In case there are samples from multiple labs run:
```
cd /mnt/new_home/illumina_common_fastq
```
Upload your RunManifest.csv to your working folder.

o Any SFTP program (e.g., Bitvise SSH Client) can be used to transfer RunManifest.csv. Just drag & drop the file from the left to the right window.
Define a distinctive name for the folder that will contain the bases2fastq results (e.g., 2025_05_21_ERIC_study) and use it as input (check the command below)

Now you can execute bases2fastq (version 2.1.0.1522407762), based on the following command:

nohup /apps/element/bases2fastq \
--num-threads 16 \
--group-fastq \
--legacy-fastq \
--run-manifest RunManifest.csv \
/mnt/new_home/element/AV240301/20250131_AV240301_SARSDIAGNOSIS/ \
2025_05_21_ERIC_study/ > ./2025_05_21_ERIC_study.log 2>&1 &

After the command for bases2fastq has run successfully, move your RunManifest.csv to the output folder:
```
mv RunManifest.csv 2025_05_21_ERIC_study
```
Files older than 2 weeks will be automatically deleted from shared folders!

For this reason, if we have run the analysis in a shared folder such as /mnt/new_home/element_common_fastq, we should transfer the final files to our own subfolder, which will be located under our research group’s folder.
```
rsync -r \
2025_05_21_ERIC_study \
/mnt/new_home/stamatopoulos_research
```