I've broken the ONT branch

[iqbal-lab]

I have no idea how on earth I've managed it, but since pulling from master, it no longer loads data into the de Bruijn graph. I thought for a minute it was due to the ONT input data, but same problem with Illumina data

[iqbal-lab]

This bug at this commit 9b9a878d3bf3ea62425d8f13a634e8f3af3bf6f2

[Phelimb]

This looks fine to me. bp_loaded is uint_64_t so printing with %f wasn't working.

Was there a sample you were getting an error from that made you add the debug statements in the first place ?

[iqbal-lab]

yes, the new ont data, it failed on

[iqbal-lab]

Ran valgrind. First error:

=922== Invalid read of size 4 ==922== at 0x41B8B4: update_phylo_group_presence_and_coverage_from_species (species.c:445) ==922== by 0x41BB4F: get_species_info (species.c:494) ==922== by 0x403B99: main (main.c:273)

[iqbal-lab]

Fixed that last error here, along with many memory leaks 50ef031ea0c4470da10c27fbdfd0435f924e5af9

[iqbal-lab]

OK, this breaks Staph - I'm guessing latest panel changes for species.

./Mykrobe.predictor.staph --file /data2/users/phelim/data/staph/nanopore/20150120_MN02148_FAA12662_BOWDEN03_MdC_JR_Brut_v4/reads/downloads/all/2d.fq --install_dir ~/dev/git/myKrobe-predictor bp loaded 97616869 { "expected_depth": "2", "mean_read_length": "494", "phylogenetics": { "phylo_group": { "Staphylococcus aureus": "2", "Coagulase-Negative Staphylococcus": "0" }, "species": { "Unidentified Staphylococcus": "0" }, "lineage": { "N/A": "-1" } }, "susceptibility" :{ }, "called_variants" :{ } }

[Phelimb]

Fixed in cce69f0621eaf912cf1092ab8b22f7a205379ff6

./Mykrobe.predictor.staph --install_dir ~/git/myKrobe-predictor/ --file /data2/users/phelim/data/staph/nanopore/20150120_MN02148_FAA12662_BOWDEN03_MdC_JR_Brut_v4/reads/downloads/all/2d.fq

bp loaded 97616869 { "expected_depth": "2", "mean_read_length": "494", "phylogenetics": { "phylo_group": { "Staphylococcus aureus": "2" }, "species": { "S. aureus": "2" }, "lineage": { "N/A": "-1" } }, "susceptibility" :{ "Gentamicin": "R", "Penicillin": "R", "Methicillin": "R", "Trimethoprim": "R", "Erythromycin": "R", "FusidicAcid": "S", "Ciprofloxacin": "R", "Rifampicin": "S", "Tetracycline": "S", "Vancomycin": "S", "Mupirocin": "S", "Clindamycin": "R(inducible)" }, "called_variants" :{ "gyrA_S84L" :{ "R_per_cov": "100", "S_per_cov": "0", "R_median_cov": "5", "S_median_cov": "0", "conf": "27", "induced_resistance": "Ciprofloxacin" } }, "called_genes" :{ "aacAaphD" :{ "per_cov": "66", "median_cov": "1", "conf": "1218", "induced_resistance": "Gentamicin" }, "blaZ" :{ "per_cov": "57", "median_cov": "1", "conf": "504", "induced_resistance": "Penicillin" }, "dfrA" :{ "per_cov": "67", "median_cov": "1", "conf": "369", "induced_resistance": "Trimethoprim" }, "ermC" :{ "per_cov": "56", "median_cov": "1", "conf": "90", "induced_resistance": "Erythromycin" }, "mecA" :{ "per_cov": "82", "median_cov": "3", "conf": "5462", "induced_resistance": "Methicillin" } }, "virulence_toxins" :{ "PVL": "negative" } }

[iqbal-lab]

Great!