Phaster.py script error

Question

[The Terminator]

Hi all,

After cloning from GitHub, I tried to run Phaster.py (the Python script of PHASTER tool), I tried to run the script by using this command:

./phaster.py --contigs --fasta path/to/genome.fasta

The error was

2019-07-11 14:32:02,389 INFO: Submission of TH19.fna appears successful

2019-07-11 14:32:02,390 INFO: job_id: ZZ_0f276b0c53

2019-07-11 14:32:02,390 INFO: error: The sequence header is not on the first line. Please check!

Traceback (most recent call last):

File "/home/fox/phaster_scripts/phaster.py", line 162, in <module>

job_id, status, date = submit_job(fasta, options.url, {"contigs": int(options.contigs)})

File "/home/fox/phaster_scripts/phaster.py", line 99, in submit_job

return r_dict["job_id"], r_dict["status"], datetime.datetime.now()

KeyError: 'status'

I then looked again at the FASTA file but the header was always on the first line. Does anybody know how to solve this?

[Joe]

Can you show us the output of head genome.fasta and grep -c ">" genome.fasta

[The Terminator]

$ head Th19.fna
> gnl|MG|TH19_1
ATTTTGTACATGCTTAAACAAGCGAAAATGTACATGTTTATCTTGACATTTACAGAGTTA
CTCATTTTTCTATCACTCCTTTCATTTCGTCCTAATTACTATAACCATTTAGGAGGATAA
TCATGAGTTAGAAGTTAGGCACTTAATTTTCTTCGATAATGTAAGTAAAATATTCCATAC
ATAACAAATAGCATGAGTAAAACTTGTAACTCTACATTTTCCTTTAAAATAGCTGCGATA
GGGTCTGGTAAGTACGGTGATTTATCGTTTGTGTTTAAACCTAACCATTTATTTAAGAGG
CTAATGGTACAAAACATAAAAACACCGGACCAGCTTGCCGTAATTGCTTTTTGTTTAATT
TTTGTTTCACGTTCATCATCTGTAATCCAAGGATTAGCAGTTTTATCCCGCATTAACGGG
CAGTAAGACCCCCACCTCAAAATTCAGCGGAGGCAAAGAAGTTAGGTGGGGATCAACTGT
CCGTAAAAGCCCGATTGGTTCAACTAATAATCCGTGGGGGATGAACAAAACCCCCACGGA

$ grep -c ">" TH19.fna
201

[Joe]

Do you have any lines where there is a newline missing after the sequence or is the file in any way malformed? e.g.

>Seq1
ATATGACTAGCTACGTCGGACGT
ACGTACGATCGATCGGCATCGAT
ATCGACTAGCTAGCTACGTCGAT
ACGATCGC>Seq2
AATCGATCGATCGATCGAGCGAC
...

Is 201 the number of sequences you expect?