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adamhockenberry / bacphlip

A python library for predicting phage lifestyle based on genome sequence
MIT License
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Error when analyzing a sequence #13

Open h170607 opened 2 days ago

h170607 commented 2 days ago

Analysis of a sequence always makes an error. But swapping the sequence (excluding the sequence name) to another works fine, I want to know what's special about this sequence.

The sequence is:

k141_4828_flag=0_multi=1.0000_len=327 ATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATTATTAAACTTGGTCTGACAGATACCAAGTTAACTCATATTTACTTTAGATTGTTTTAAAAATTAAGATTTAAATCAACCTAAAGTATATATTAGTAAACTAGGTCTGACAGTTACCAGGTTTACTCATATATACTTTAGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGTTCCTTTTTGATAATCTCATGACCAAAATCCCTTAAAGTGAGTTTTCGTTCAACTGAGCGTCAGACCCCG

The command is: bacphlip -i bacphlip_votu/k141_4828b.fa --local_hmmsearch home/share/Soft/hmmer-3.4/src/hmmsearch -f

The error message is:

Beginning BACPHLIP pipeline Finished six frame translation of genome (nucleotide) with output stored in bacphlip_votu/k141_4828b.fa.6frame

Error: Sequence file bacphlip_votu/k141_4828b.fa.6frame is empty or misformatted

Traceback (most recent call last): File "/home/tj2024/.conda/envs/bacphlip/lib/python3.8/site-packages/bacphlip/bacphlip.py", line 217, in hmmsearch_py subprocess.run(args=[hmmsearch_call, HMMER_DB, aa_fasta_file], check=True, stdout=outfile) File "/home/tj2024/.conda/envs/bacphlip/lib/python3.8/subprocess.py", line 516, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/groups/g900020/home/share/Soft/hmmer-3.4/src/hmmsearch', '/home/tj2024/.conda/envs/bacphlip/lib/python3.8/site-packages/bacphlip/data/prot_models.hmm', 'bacphlip_votu/k141_4828b.fa.6frame']' returned non-zero exit status 1.