ERROR_ non-ACGTN characters in genome

Question

[Neel]

Hi, I am trying to run quast and i encountered this error, please help me.

**quast /home/bvs/neelam/complete_genome/complete.fna -o ./outdir1

Version: 5.0.2

System information: OS: Linux-5.8.0-59-generic-x86_64-with-debian-bullseye-sid (linux_64) Python version: 3.7.12 CPUs number: 96

Started: 2022-05-02 12:30:13

Logging to /home/bvs/neelam/complete_genome/outdir1/quast.log NOTICE: Maximum number of threads is set to 24 (use --threads option to set it manually)

CWD: /home/bvs/neelam/complete_genome Main parameters: MODE: default, threads: 24, minimum contig length: 500, minimum alignment length: 65, \ ambiguity: one, threshold for extensive misassembly size: 1000

Contigs: Pre-processing...

**ERROR! Skipping /home/bvs/neelam/complete_genome/complete.fna because it contains non-ACGTN characters.**

Thank you!

[Neel]

My genome.fna file look like this

CP040127.1 GCTTGCCGAACTGCTGGTGCAGCTCCGGATTTTCCAGTTCGCCCAGGCCTTTGCGCGCGA TCACCACGATATCCCAGCCAGCCAGGGTTTCCTGGTTATGGCGGAACGATTCGCGGATCA GGCGTTTGAGGCGATTGCGCTGGACGGCGAGCTTGACGTTCTTCTTGCCGATCACCAGGC CCAGGCGGGGGTGATCGAGACCGTTCTCGCGCGCCAGCAGCAGGACGTGCTTGCCGGGGA CCTTGCCGGTCGGAGAGTCGAAGACTGCGCTGAATTGCCGGGCTGTCAGTAGACGCTTGT CCCGGTCGAAGTCCCGACTCACCACCCGTACCGGATAAATCAGACGGTCAGACGCTTACG GCCTTTGGCGCGACGACGCGACAGAACCTGACGGCCGTTCTTGGTGGCCATACGGGCGCG GAAACCGTGGACGCGAGCGCGCTTGAGGGTGCTGGGTTGGAAAGTACGTTTCATGATTCG GTACCTGGGTTGACGACTTGAGGTCGCAGTGACCCCGTTTAAAGAGACCGGCGATTCTAG TGAAATCGAACGGGCAGGTCAATTTCCAACCAGCGATGACGTAATAGATAGATACAAGGA AGTCATTTTTCTTTTAAAGGATAGAAACGGTTAATGCTCTTGGGACGGCGCTTTTCTGTG CATAACTCGATGAAGCCCAGCAATTGCGTGTTTCTCCGGCAGGCAAAAGGTTGTCGAGAA CCGGTGTCGAGGCTGTTTCCTTCCTGAGCGAAGCCTGGGGATGAACGAGATGGTTATCCA CAGCGGTTTTTTCCACACGGCTGTGCGCAGGGATGTACCCCCTTCAAAGCAAGGGTTATC CACAAAGTCCAGGACGACCGTCCGTCGGCCTGCCTGCTTTTATTAAGGTCTTGATTTGCT TGGGGCCTCAGCGCATCGGCATGTGGATAAGTCCGGCCCGTCCGGCTACAATAGGCGCTT ATTTCGTTGTGCCGCCTTTCCAATCTTTGGGGGATATCCGTGTCCGTGGAACTTTGGCAG CAGTGCGTGGATCTTCTCCGCGATGAGCTGCCGTCCCAACAATTCAACACCTGGATCCGT CCCTTGCAGGTCGAAGCCGAAGGCGACGAATTGCGTGTGTATGCACCCAACCGTTTCGTC CTCGATTGGGTGAACGAGAAATACCTCGGTCGGCTTCTGGAACTGCTCGGTGAACGCGGC GAGGGTCAGTTGCCCGCGCTTTCCTTATTAATAGGCAGCAAGCGTAGCCGTACGCCGCGC GCCGCCATTGTCCCATCGCAGACCCACGTGGCTCCCCCGCCTCCGGTTGCTCCGCCGCCG GCGCCAGTGCAGCCGGTATCGGCCGCGCCCGTGGTAGTGCCACGTGAAGAGCTGCCGCCA GTGACGACGGCTCCCAGCGTTTCGAGCGATCCCTACGAGCCGGAAGAACCCAGCATCGAT CCGCTGGCCGCCGCCATGCCGGCCGGAGCAGCGCCTGCGGTGCGCACCGAGCGCAACGTC CAGGTCGAAGGTGCGCTGAAGCACACCAGCTATCTCAACCGTACCTTCACCTTCGAGAAC TTCGTCGAGGGCAAGTCCAACCAGTTGGCCCGCGCCGCCGCCTGGCAGGTGGCGGACAAC CTCAAGCACGGCTACAACCCGCTGTTCCTCTACGGTGGCGTCGGCCTGGGCAAGACCCAC CTGATGCATGCGGTGGGCAACCACCTGCTGAAGAAGAACCCGAACGCCAAGGTGGTCTAC CTGCATTCGGAACGTTTCGTCGCGGACATGGTGAAGGCCTTGCAGCTCAACGCCATCAAC GAATTCAAGCGCTTCTACCGCTCGGTGGACGCACTGTTGATCGACGACATCCAGTTCTTC GCCCGTAAGGAGCGCTCCCAGGAGGAGTTCTTCCACACCTTCAATGCCCTTCTCGAAGGC GGCCAGCAGGTGATCCTCACCAGCGACCGCTATCCGAAGGAAATCGAAGGCCTGGAAGAG CGGCTGAAATCCCGCTTCGGCTGGGGCCTGACGGTGGCCGTCGAGCCGCCGGAACTGGAA ACCCGGGTGGCGATCCTGATGAAGAAGGCCGAGCAGGCGAAGATCGAGCTGCCGCACGAT GCGGCCTTCTTCATCGCCCAGCGCATCCGTTCCAACGTGCGTGAACTGGAAGGTGCGCTG AAGCGGGTGATCGCCCACTCGCACTTCATGGGCCGGCCGATCACCATCGAGCTGATTCGC GAGTCGCTGAAGGACCTGTTGGCCCTTCAGGACAAGCTGGTCAGCATCGACAACATCCAG CGCACCGTCGCCGAGTACTACAAGATCAAGATATCCGATCTGTTGTCCAAGCGGCGTTCG CGCTCGGTGGCGCGCCCGCGCCAGGTGGCCATGGCGCTCTCCAAGGAGCTGACCAACCAC AGCCTGCCGGAGATCGGCGTGGCCTTCGGCGGTCGGGATCACACCACGGTGTTGCACGCC TGTCGTAAGATCGCTCAACTTAGGGAATCCGACGCGGATATCCGCGAGGACTACAAGAAC CTGCTGCGTACCCTGACAACCTGACGCAGCCCACGAGGCAAGGGACTAGACCATGCATTT CACCATTCAACGCGAAGCCCTGTTGAAACCGCTGCAACTGGTCGCCGGCGTCGTGGAACG CCGCCAGACATTGCCGGTTCTCTCCAACGTCCTGCTGGTGGTCGAAGGCCAGCAACTGTC GCTGACCGGCACCGACCTCGAAGTCGAGCTGGTTGGTCGCGTGGTACTGGAAGATGTCGC CGAACCCGGCGAGATCACCGTACCGGCGCGCAAGCTGATGGACATCTGCAAGAGCCTGCC GAACGACGTGCTGATCGACATCCGTGTCGAAGAGCAGAAACTCCTGGTGAAGGCCGGGCG TAGCCGCTTCACCCTGTCCACCCTGCCGGCCAACGATTTCCCCACCGTGGAGGAAGGTCC CGGCTCGCTGAACTTCAGCATTGCCCAGAGCAAGCTGCGTCGCCTGATCGACCGCACCAG CTTCGCCATGGCCCAGCAGGACGTGCGTTACTACCTCAACGGCATGCTGCTGGAAGTGAA--

if anyone knowhow to remove -- from end of genome file please let me know.

[Matthias Zepper]

I am pretty sure your problem is just the malformed header. Change it to

>CP040127.1
GCTTGCCGAACTGCTGGTGCAGCTCCGGATTTTCCAGTTCGCCCAGGCCTTTGCGCGCGA 

and try again. In case there are really other issues with the file, you can use tr, sed or reformat.sh from the BBTools suite:

reformat.sh in=/home/bvs/neelam/complete_genome/complete.fna out=/home/bvs/neelam/complete_genome/complete_fixed.fna fixjunk=t iupacToN=t dotdashxton=t  fixheaders=t

[Pierre Lindenbaum]

what is the output of

grep -v '^>' /home/bvs/neelam/complete_genome/complete.fna | tr -d 'ATGCN\n'

and

file /home/bvs/neelam/complete_genome/complete.fna

?