[2024-01-24 11:05:25,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg5afa7f9a-e597-4439-b7ba-f8789fa452cd/dqc_reference
[2024-01-24 11:05:26,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,883] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c17c178-ebe7-449b-a9ef-7af690be1999/GCF_016127355.1_ASM1612735v1_genomic.fna.gz | prodigal -d GCF_016127355.1_ASM1612735v1_genomic.fna/cds.fna -a GCF_016127355.1_ASM1612735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:34,677] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:34,677] [INFO] Task started: HMMsearch
[2024-01-24 11:05:34,677] [INFO] Running command: hmmsearch --tblout GCF_016127355.1_ASM1612735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5afa7f9a-e597-4439-b7ba-f8789fa452cd/dqc_reference/reference_markers.hmm GCF_016127355.1_ASM1612735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:34,908] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:34,909] [INFO] Found 6/6 markers.
[2024-01-24 11:05:34,930] [INFO] Query marker FASTA was written to GCF_016127355.1_ASM1612735v1_genomic.fna/markers.fasta
[2024-01-24 11:05:34,930] [INFO] Task started: Blastn
[2024-01-24 11:05:34,930] [INFO] Running command: blastn -query GCF_016127355.1_ASM1612735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5afa7f9a-e597-4439-b7ba-f8789fa452cd/dqc_reference/reference_markers.fasta -out GCF_016127355.1_ASM1612735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:35,667] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:35,672] [INFO] Selected 18 target genomes.
[2024-01-24 11:05:35,673] [INFO] Target genome list was writen to GCF_016127355.1_ASM1612735v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:35,681] [INFO] Task started: fastANI
[2024-01-24 11:05:35,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c17c178-ebe7-449b-a9ef-7af690be1999/GCF_016127355.1_ASM1612735v1_genomic.fna.gz --refList GCF_016127355.1_ASM1612735v1_genomic.fna/target_genomes.txt --output GCF_016127355.1_ASM1612735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:48,850] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:48,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5afa7f9a-e597-4439-b7ba-f8789fa452cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:48,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5afa7f9a-e597-4439-b7ba-f8789fa452cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:48,870] [INFO] Found 18 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:05:48,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:48,871] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Kingella denitrificans	strain=FDAARGOS_1060	GCA_016127355.1	502	502	type	True	100.0	739	740	95	conclusive
Kingella denitrificans	strain=NCTC10995	GCA_900451365.1	502	502	type	True	99.9986	739	740	95	conclusive
Kingella denitrificans	strain=ATCC 33394	GCA_000190695.1	502	502	type	True	99.9152	725	740	95	conclusive
Eikenella halliae	strain=NML130454	GCA_001648475.1	1795832	1795832	type	True	81.9964	291	740	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	81.2683	282	740	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=ATCC 29315	GCA_000818035.1	88719	495	type	True	81.2142	278	740	95	below_threshold
Eikenella exigua	strain=PXX	GCA_008805035.1	2528037	2528037	type	True	80.9634	225	740	95	below_threshold
Kingella bonacorsii	strain=Marseille-Q4569	GCA_016623605.1	2796361	2796361	type	True	79.7795	333	740	95	below_threshold
Kingella oralis	strain=DSM 18271	GCA_014054985.1	505	505	type	True	79.6219	307	740	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	79.1962	236	740	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	79.1283	242	740	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	78.6913	237	740	95	below_threshold
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	78.5781	266	740	95	below_threshold
Kingella kingae	strain=NCTC10529	GCA_900475905.1	504	504	type	True	78.5595	270	740	95	below_threshold
Conchiformibius steedae	strain=DSM 2580	GCA_014054725.1	153493	153493	type	True	78.4099	208	740	95	below_threshold
Kingella kingae	strain=ATCC 23330	GCA_000213535.1	504	504	type	True	78.271	260	740	95	below_threshold
Conchiformibius steedae	strain=DSM 2580	GCA_000620925.1	153493	153493	type	True	78.0336	204	740	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	77.8748	241	740	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:48,872] [INFO] DFAST Taxonomy check result was written to GCF_016127355.1_ASM1612735v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:48,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:48,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:48,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5afa7f9a-e597-4439-b7ba-f8789fa452cd/dqc_reference/checkm_data
[2024-01-24 11:05:48,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:48,904] [INFO] Task started: CheckM
[2024-01-24 11:05:48,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016127355.1_ASM1612735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016127355.1_ASM1612735v1_genomic.fna/checkm_input GCF_016127355.1_ASM1612735v1_genomic.fna/checkm_result
[2024-01-24 11:06:16,318] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:16,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:16,340] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:16,340] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:16,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016127355.1_ASM1612735v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:16,341] [INFO] Task started: Blastn
[2024-01-24 11:06:16,341] [INFO] Running command: blastn -query GCF_016127355.1_ASM1612735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5afa7f9a-e597-4439-b7ba-f8789fa452cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_016127355.1_ASM1612735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:17,605] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:17,610] [INFO] Selected 20 target genomes.
[2024-01-24 11:06:17,611] [INFO] Target genome list was writen to GCF_016127355.1_ASM1612735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:17,627] [INFO] Task started: fastANI
[2024-01-24 11:06:17,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c17c178-ebe7-449b-a9ef-7af690be1999/GCF_016127355.1_ASM1612735v1_genomic.fna.gz --refList GCF_016127355.1_ASM1612735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016127355.1_ASM1612735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:30,932] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:30,948] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:30,948] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000190695.1	s__Kingella_A denitrificans	99.9152	725	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A	95.0	98.63	96.04	0.97	0.93	4	conclusive
GCF_001648475.1	s__Eikenella halliae	82.0662	290	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990355.1	s__Eikenella corrodens_B	81.9861	292	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187105.1	s__Eikenella corrodens	81.5887	278	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.96	95.30	0.90	0.87	23	-
GCF_900113545.1	s__Neisseria elongata	81.3454	291	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	-
GCA_000220865.1	s__Neisseria macacae	80.9702	264	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.509	99.99	99.99	0.98	0.98	2	-
GCF_008805035.1	s__Eikenella exigua	80.8129	221	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.49	95.37	0.95	0.91	11	-
GCA_001067655.1	s__Neisseria lactamica_B	80.6758	227	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_005886145.1	s__Neisseria sp000090875	80.1838	252	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_003044565.1	s__Neisseria sicca_A	79.9564	246	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.01	95.27	0.94	0.92	3	-
GCF_016025525.2	s__Eikenella sp016025525	79.6043	250	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014054985.1	s__Kingella_B oralis	79.6006	310	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	98.22	96.45	0.95	0.91	3	-
GCF_014055005.1	s__Neisseria dentiae	79.2569	281	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCA_905373195.1	s__Kingella_B oralis_A	79.1469	175	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226875.1	s__Eikenella shayeganii	78.575	228	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.47	96.47	0.85	0.85	2	-
GCF_014054525.1	s__Alysiella filiformis	78.5261	231	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014054725.1	s__Conchiformibius steedae	78.4219	203	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius	95.0	98.09	96.18	0.94	0.87	3	-
GCF_900111845.1	s__Kingella kingae	77.9996	273	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	98.43	98.16	0.96	0.94	37	-
GCF_000745955.1	s__Alysiella crassa	77.7883	200	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_000751855.1	s__Kingella negevensis	77.6706	176	740	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	99.09	98.48	0.96	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:30,950] [INFO] GTDB search result was written to GCF_016127355.1_ASM1612735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:30,951] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:30,958] [INFO] DFAST_QC result json was written to GCF_016127355.1_ASM1612735v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:30,959] [INFO] DFAST_QC completed!
[2024-01-24 11:06:30,959] [INFO] Total running time: 0h1m5s