NGS data analysis pipeline

Question

[kesmond.osato]

Hello everyone,

Could you please assist me in resolving the error message that appears during my 3 steps of NGS data analysis? Your help would be greatly appreciated. I used the cmd in python src/assembly_and_polish.py

Constructing minimap index.
[E::fai_build3_core] Failed to open the file /home/mdehspk5/HCMV_glycoproteins_pipeline/tmp/denovo_assembly/Merged_fastq_BC18/UL_assm/reads_final.fa
[faidx] Could not build fai index /home/mdehspk5/HCMV_glycoproteins_pipeline/tmp/denovo_assembly/Merged_fastq_BC18/UL_assm/reads_final.fa.fai
Failed to run alignment of reads to draft.
Traceback (most recent call last):
  File "src/assembly_and_polish.py", line 70, in <module>
    seq = Fasta('%s_consensus/consensus.fasta' % prefix)
  File "/home/mdehspk5/anaconda3/envs/HCMV_glycoproteins_pipeline/lib/python3.6/site-packages/pyfasta/fasta.py", line 67, in __init__
    raise FastaNotFound('"' + fasta_name + '"')
pyfasta.fasta.FastaNotFound: "tmp/denovo_assembly/Merged_fastq_BC18/UL_consensus/consensus.fasta"

Thank you.

[Mensur Dlakic]

What is unclear in these messages? It doesn't seem the file is there.

Failed to open the file /home/mdehspk5/HCMV_glycoproteins_pipeline/tmp/denovo_assembly/Merged_fastq_BC18/UL_assm/reads_final.fa

FastaNotFound: tmp/denovo_assembly/Merged_fastq_BC18/UL_consensus/consensus.fasta"

What is the screen output of this command:

ls -al /home/mdehspk5/HCMV_glycoproteins_pipeline/tmp/denovo_assembly/Merged_fastq_BC18/UL_assm/reads_final.fa