thierryjanssens

This enhancement would be instrumental as well to analyse scaffolds from a fragmented metagenome and parse the resulting annotations. I understand that prokka is not designed for annotating genetic material...

I am also running into this same issue. Upon importing tabular blast hits, some queries get an LCA of other Root, while the taxIDs of the blastn hits of these...

$ conda list # packages in environment at /mnt/scratch_dir/user/conda/envs/gff3tool_env: # # Name Version Build Channel _libgcc_mutex 0.1 main bzip2 1.0.8 h516909a_0 conda-forge ca-certificates 2019.6.16 hecc5488_0 conda-forge certifi 2019.6.16 py27_1 conda-forge...

Hi Robert, thank you. This creates a non-empty output: >0fe3e058-af74-41a3-a6ff-3dafc6d73f8c LN:i:775 RC:i:1 XC:f:0.000000 CGATGCTGCTTCGTTCAGTTATAAACTGGATCGAGGGCTGCGTCTTTTGACTAGGATGCTGGCGTAATGATCTAATGCCGCCCGTCTTGAAACACGGACCAAGGAGTCTAACGTCTATGCTGGTGTTTGGGGTGTAAAACCCGTACGCACGCGTAAATGAACGTAGGTTGGGGCCTTCGGGTGCACAATCGACCGACTAACGATGTTTTCGGATAGGTTTGAGTAGAGCATAGCTGTTGGGACCCGAAGATGGTGAACTATGCCTGAATAGGGTGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGGTTCTGACGTGCCGTCGATCGTCGAATTTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCTGCCGAAGTTTCCCTCAGGATAGCAGAAACTCGTATCAGTTTATGAGGTAAAGCGAATGATTAGCGGTACCGGGGATGAAATGTCGCGCTGACCGATTTACAAAACTTTAAATGTATGAAAGTCCTTGTTGGCAATTGAACGTGGACATATGGATGAAGGGTTTCTAGTGGGCCATTTTGGTAAGCAGAACTGGCGATGCGGGACGAACCGAACGTGGAGTTAAGGTGCCGGAATGTGTACTACGCTCATCAGACACCACAAAAGGTGTTAGTTGTCTAGACAGCCGGACGGTGGCCATGGAAGTCGGAATCCGCTAAGGAATGTGTAACAACTCACCTGCCGAGAAGATAGAGCGACAGGCAAGTCCTGGTAACTGGGACACAAGACTCG This is the content of the associated sam file: @SQ SN:0fe3e058-af74-41a3-a6ff-3dafc6d73f8c LN:775 @PG ID:minimap2 PN:minimap2 VN:2.17-r941...

Hello Matt, thanks for reaching out. I am sorry, I thought it was in my post. This is the code I used. The primers are from literature and producing good...

The same error is returned when using the following primers: 'AGAGTTTGATCMTGGC', 'TACCTTGTTACGACTT'

That is strange. In the reference organism the dsrA primer sets has binding sites on two positions in the genome: 

Dear Simon, I experience the same problem, i.e. an empty final csv file, despite the prediction o significant prophages by other packages. mga_linux_ia64 has been installed in the env bin...

Hello Simon, have you received the log files in the email of 2 days ago? Regards, Thierry