IndexError in "reference_assembly"

[kq1986]

Hello Tobias,

I followed your tutorial with the latest version (2.2.6) but it always gave this error when running the reference_assembly:

**secapr reference_assembly --reads pipeline_exercise/cleaned_trimmed_reads --reference_type alignment-consensus --reference pipeline_exercise/alignments/contig_alignments --output pipeline_exercise/mapped_reads --min_coverage 4

Creating consensus sequences from input alignments... Done.

################################################## Processing sample T_pella5 Traceback (most recent call last): File "/public/home/kq/miniconda3/envs/secapr/bin/secapr", line 8, in sys.exit(main()) File "/public/home/kq/miniconda3/envs/secapr/lib/python3.8/site-packages/secapr/main.py", line 55, in main args.func(args) File "/public/home/kq/miniconda3/envs/secapr/lib/python3.8/site-packages/secapr/reference_assembly.py", line 825, in main sorted_bam = mapping_bwa(subfolder_path,reference,sample_id,sample_output_folder,args) File "/public/home/kq/miniconda3/envs/secapr/lib/python3.8/site-packages/secapr/reference_assembly.py", line 271, in mapping_bwa final_sam_name = samfiles[0] IndexError: list index out of range**

Could you please help me identify the problem?

Thank you.

Qi

[tandermann]

Dear Qi,

The error should be fixed now in the newest version (v2.2.8). Let me know if you continue to run into problems!