Error in processing files

[Krunal Rambhad]

Hello PICRUSt2 Team,

I am running PICRUSt2 on a human gut microbiome 16S rRNA dataset from a tuberculosis cohort.

System:

• Windows 11

• WSL2 Ubuntu

• 32 GB RAM

• WSL configuration:

  • memory=24GB

  • processors=12

  • swap=8GB

Workflow:

1. Raw paired-end FASTQ files were processed in QIIME2 (2024.10).

2. DADA2 denoising completed successfully.

3. Representative sequences and feature table were exported:

   • dna-sequences.fasta

   • feature-table.biom

I activated the PICRUSt2 conda environment and ran:

picrust2_pipeline.py
-s repseq_export/dna-sequences.fasta
-i table_export/feature-table.biom
-o picrust2_test
-p 12

The command exited immediately with exit code 1.

I also attempted to redirect output to a log file:

picrust2_pipeline.py
-s repseq_export/dna-sequences.fasta
-i table_export/feature-table.biom
-o picrust2_test
-p 2 \

picrust2_full.log 2>&1

However, the log file remained empty.

Additional observations:

• DADA2 completed successfully.

• WSL2 remained stable after DADA2 completion.

• No obvious error message was displayed before the command exited.

• The command appears to terminate before any processing begins.

Could you advise how to diagnose the cause of the immediate exit? Are there specific checks I should perform on the BIOM file, FASTA file, PICRUSt2 installation, or conda environment?

Thank you.