How to run BCL Convert in the computational infrastructure of INAB

Steps to run the analysis:

1. Log in to the appropriate server:

o 160.40.71.4

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

o e.g., /mnt/new_home/illumina/nextseq2000/240412_VH00795_60_AAFLFTVM5

3. Create your SampleSheet.csv:

o Generally, a SampleSheet must include two sections: (1) the Settings Section and (2) the Data Section

o In the Data Section you can add a column named Sample_Project containing the name of the respective project for each sample. Sample_Project Optional can only contain alphanumeric characters, dashes, and underscores. Duplicate data strings with different cases (e.g., sampleProject and SampleProject) are not allowed. If these are used, analysis fails.

4. 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

5. Upload your SampleSheet.csv to your working folder:

o Any SFTP program (e.g., Bitvise SSH Client) can be used to transfer SampleSheet.csv. Just drag & drop the file from the left to the right window.

6. Define a distinctive name for your folder.

o The folder will contain the bcl-convert results (e.g., 2025_05_20_ERIC_study).

o Use it as input after the –output-directory argument (check the command below)

7. Run the analysis:

nohup bcl-convert \
--bcl-input-directory /mnt/new_home/illumina/nextseq2000/240412_VH00795_60_AAFLFTVM5 \
--output-directory 2025_05_20_ERIC_study \
--sample-sheet SampleSheet.csv \
--no-lane-splitting true \
--bcl-sampleproject-subdirectories \
-–force > ./2025_05_20_ERIC_study.log 2>&1 &

8. After the analysis is completed:

Move your SampleSheet.csv to the output folder:

mv SampleSheet.csv 2025_05_20_ERIC_study

9. 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/illumina_common_fastq, we should transfer the final files to our own subfolder, which will be located under our research group’s folder.

rsync -r \
/mnt/new_home/illumina_common_fastq/2025_05_20_ERIC_study \
/mnt/new_home/stamatopoulos_research