Open Sebastien-Raguideau opened 3 years ago
Hi Seb, it looks like a gene calling error from the pyrodigal https://github.com/althonos/pyrodigal. Can you send me the fasta-file and I'll have a look? Also, can you try without the -meta 1
flag? Additionally, PhageBoost currently uses single thread so -j
will do you no good :)
Hi Kimmo,
Thanks for the super fast answer.
Since then I tried to launch per sequence and it worked a lot better. No malloc issue.
BUT, I do get some cryptic error messages on some of the contigs. I looked into it and this seems to happens only when contigs length is quite small ~ 600 nuc. You may want to catch that.
processing: contig_12488
time after genecalls: 0.20870280265808105
Traceback (most recent call last):
File "/home/sebr/seb/Applications/miniconda3/envs/phageboost/bin/PhageBoost", line 8, in <module>
sys.exit(main())
File "/home/sebr/seb/Applications/miniconda3/envs/phageboost/lib/python3.7/site-packages/PhageBoost/main.py", line 205, in main
df = calculate_features(genecalls)
File "/home/sebr/seb/Applications/miniconda3/envs/phageboost/lib/python3.7/site-packages/PhageBoost/main.py", line 59, in calculate_features
df, _, _ = calc_features.df2AAandDNAfeatures(genecalls, name='header')
File "/home/sebr/seb/Applications/miniconda3/envs/phageboost/lib/python3.7/site-packages/PhageBoost/calc_features.py", line 215, in df2AAandDNAfeatures
DF, DF_AA, DF_DNA = RunAAandDNA(dna_entries, aa_entries, locations)
File "/home/sebr/seb/Applications/miniconda3/envs/phageboost/lib/python3.7/site-packages/PhageBoost/calc_features.py", line 201, in RunAAandDNA
DF_DNA = RunDNA(DNA_entries, locations, verbose = verbose)
File "/home/sebr/seb/Applications/miniconda3/envs/phageboost/lib/python3.7/site-packages/PhageBoost/calc_features.py", line 189, in RunDNA
df_CAI = calculate_CAI(entries)
File "/home/sebr/seb/Applications/miniconda3/envs/phageboost/lib/python3.7/site-packages/PhageBoost/calc_features.py", line 73, in calculate_CAI
CAI.generate_index(sequences)
File "/home/sebr/seb/Applications/miniconda3/envs/phageboost/lib/python3.7/site-packages/Bio/SeqUtils/CodonUsage.py", line 121, in generate_index
rcsu.append(self.codon_count[codon] / denominator)
ZeroDivisionError: float division by zero
Here is the corresponding file : contig_12488.fa
In the mean time if you want to have a look at that malloc issue, I'll send you a dl link to the assembly in a min. Thanks for help, and your soft :)
Hi Kimmo I'm Trying to launch PhageBoost command line on 1 of my dataset, and I get this super long error. It looks like a cython issue? Install wise I followed the Pypi instructions. Here is the command line I launched:
PhageBoost -j 50 -f contigs/contig.fa -meta 1 --mincontigsize 500 -o phageboost
Any idea ?