bases2fastq

How to run bases2fastq in the computational infrastructure of INAB

1. Log in to the appropriate server:

Note

160.40.71.4 160.40.71.6 …

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

Note

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

3. Activate conda environment with dependencies for bases2fastq:

conda activate bases2fastq_dependencies

4. Create your RunManifest.csv:

Information for preparing the RunManifest file can be found here.

Note

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.

5. Move to your working folder:

In case there are only samples from your lab run:

cd /mnt/new_home/stamatopoulos_research/

In case there are samples from multiple labs run:

cd /mnt/new_home/illumina_common_fastq

6. Upload your RunManifest.csv to your working folder.

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.

7. Define a distinctive name for the folder that will contain the bases2fastq results and use it as input (see Step 8.)

Note

e.g., 2025_05_21_ERIC_study

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

nohup 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 &

9. After the command for bases2fastq has run successfully, move your RunManifest.csv to the output folder:

mv RunManifest.csv 2025_05_21_ERIC_study

10. 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