Closed bheimbu closed 11 months ago
Hi @tseemann,
I'm a bit confused here. fna and .faa files should have the same headers, right? But my files look like this:
*.fna
>BEC2_contig1 GCAGGTGTGTGTAGCATGGTGTGTGGTGAGAGGGGTCAGTACGTCCGTTGTCAGGCAGGG AAGGTTTTATGGGTGTTTGGTTCTTAGTAGGGTGTCAAAGATAGCAAAGATAACCTTAAG ATTGATTATGGGAAATTTTAATGACGGCGGTTGAGCATTTGCAGTTTTCTTGTTGATCGG TTTAAACTGCAATTGTACCTGCGGGCTGCTGCATGCGTTTCGGCGTGAATCTTGAGCGGC ATTCGCGAAATATTTATCAGAATATAAAAGTCGCGGACAGCAGTTGTTGGGAATTAATAA ACGCACTTTATGTTCAAGTCCTTTTGTTACAGTTATGTTTATGTGTGAGGGAGTTTCAGG ACAAACTGCAATATAGCGTAGTTGGAGGTAAGGAAAAGAAAATTACAGGAAACAGAGACT ATTAAATAGTTAGGTGCTTCGTAATTTGTGTTTTTCTCTAAATAATTTTTTTTGGCGCTA CAGCCACCCCCCCCCCCAGTGGGCCAGGGCCTCATTATCGTGGCTTCACAATCACACTCA GACACACTACACTCGGTAGAACTCCTCCGTACGAGTGATCAGCCGAACGCAGAGACCTCT ACCTGTCAACACGCAACACTCACAAGAGACAAAGGTCCGCGCCCTCCGGCGGGATTCGAA CCCGCAATCCCAGGAAGCGAGCGGCCGCAGAACGACGCCTTAGACCGCGCGGCCACCGGG ATCGGCCAGAAACATCAGAATGATTAATAGAGCAACGGTGACGACGACACTTACTGCCGG GAAACAAAAACACGCAACAGCCTGCTGATGCAGTTAATTGTAATTACACAAATATTTACT TACTTACTTACTCCATGGCGCAGAGTCCTTCTTGAGAAGCTGACTGGTTCTGCAGCTGGT CATATTCCCCACATTTTATCGAACCCGGAAGTTCATTTCCGCACTCACAAGTGCCCGCCA CCTGTCCCTATCCTGAGCCAACTCCATCCAGTCCCCACAAACCCCTCCCACTTCCTGCAG GTCCATCTTAATATTATCCTCCCATCTACGTCTGGGTCTCCCCAATGGTCTCTTTCCCTC AGGTTTCCTCACCAGAAGCCTGTGCACACCTCTCGCCTCCCCATACGCGCCACATGCCCC GACCATCTCATTCTTCTCGATTTTATCACC >BEC2_contig2 TTGACAGTATACCAAAAAGGTGTTTATTACTCAGGAATTAAGATCTACAATTATCTACCA ACAGTCATTAAAGAATTATCTGGTGATAAGAATAAATTCAAACTAGCTCTAAAAAGATAC CTCTTACATAATTCCCTTTACAGTCTGGAGGAATATTTTAATCCATAATTAACTATGATA TTAACATTATTCTTATTATTACTTATACTTACTTTAATTAAGTACCTTTAATTGTTAATG TAGCTATCCTATGACACTACAGTAAGGCACAACTTGTGCTGAAAGTACACTGGCTTTATT TATTATGCTAAATGTATACATGACCAGTTCCACATCTGTATAAGATCAATGGAATGTGAA
*.faa
>PJHIIHGH_00001 hypothetical protein MVGACGAYGEARGVHRLLVRKPEGKRPLGRPRRRWEDNIKMDLQEVGGVCGDWMELAQDR DRWRALVSAEMNFRVR >PJHIIHGH_00002 hypothetical protein MEDKCADREDLSNMHSLLQNIKANSEVAPETPALKAYKLPSLIVRYFQDPSAQHWAFMTS NVTRAVDVTRVNQTRTDILQMSSYSRSTELHVLHPTSRLKIMEDNAGTRNNKKSHLYRPA KCSALC
It's possible to recapitulate, on which contig e.g. PJHIIHGH_00001 sits, using a *.gtf file (https://github.com/EnvGen/metagenomics-workshop/blob/master/in-house/prokkagff2gtf.sh), however this is rather tedious.
My prokka command looks like this: prokka --force --cpus 10 --metagenome --prefix $sample --outdir prokka/$sample $sample.fna
prokka --force --cpus 10 --metagenome --prefix $sample --outdir prokka/$sample $sample.fna
Any help is highly appreciated,
Bastian
Hi @tseemann,
I'm a bit confused here. fna and .faa files should have the same headers, right? But my files look like this:
*.fna
*.faa
It's possible to recapitulate, on which contig e.g. PJHIIHGH_00001 sits, using a *.gtf file (https://github.com/EnvGen/metagenomics-workshop/blob/master/in-house/prokkagff2gtf.sh), however this is rather tedious.
My prokka command looks like this:
prokka --force --cpus 10 --metagenome --prefix $sample --outdir prokka/$sample $sample.fnaAny help is highly appreciated,
Bastian