[2024-01-25 18:11:20,715] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:20,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:20,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg9885e9ac-b1db-4289-8391-da864bd6d3c6/dqc_reference
[2024-01-25 18:11:21,870] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:21,871] [INFO] Task started: Prodigal
[2024-01-25 18:11:21,871] [INFO] Running command: gunzip -c /var/lib/cwl/stgfeade4e6-839f-4561-b25a-396c0c264c11/GCF_002015075.1_ASM201507v1_genomic.fna.gz | prodigal -d GCF_002015075.1_ASM201507v1_genomic.fna/cds.fna -a GCF_002015075.1_ASM201507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:25,819] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:25,819] [INFO] Task started: HMMsearch
[2024-01-25 18:11:25,819] [INFO] Running command: hmmsearch --tblout GCF_002015075.1_ASM201507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9885e9ac-b1db-4289-8391-da864bd6d3c6/dqc_reference/reference_markers.hmm GCF_002015075.1_ASM201507v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:26,020] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:26,021] [INFO] Found 6/6 markers.
[2024-01-25 18:11:26,043] [INFO] Query marker FASTA was written to GCF_002015075.1_ASM201507v1_genomic.fna/markers.fasta
[2024-01-25 18:11:26,043] [INFO] Task started: Blastn
[2024-01-25 18:11:26,043] [INFO] Running command: blastn -query GCF_002015075.1_ASM201507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9885e9ac-b1db-4289-8391-da864bd6d3c6/dqc_reference/reference_markers.fasta -out GCF_002015075.1_ASM201507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:26,624] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:26,627] [INFO] Selected 20 target genomes.
[2024-01-25 18:11:26,627] [INFO] Target genome list was writen to GCF_002015075.1_ASM201507v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:26,643] [INFO] Task started: fastANI
[2024-01-25 18:11:26,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeade4e6-839f-4561-b25a-396c0c264c11/GCF_002015075.1_ASM201507v1_genomic.fna.gz --refList GCF_002015075.1_ASM201507v1_genomic.fna/target_genomes.txt --output GCF_002015075.1_ASM201507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:35,835] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:35,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9885e9ac-b1db-4289-8391-da864bd6d3c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:35,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9885e9ac-b1db-4289-8391-da864bd6d3c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:35,846] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:11:35,846] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:35,846] [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
Canicola haemoglobinophilus	strain=CCUG 3714	GCA_002015075.1	733	733	type	True	100.0	723	727	95	conclusive
Canicola haemoglobinophilus	strain=NCTC1659	GCA_900450725.1	733	733	type	True	99.9975	727	727	95	conclusive
Avibacterium gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	78.6655	230	727	95	below_threshold
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	78.6578	230	727	95	below_threshold
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	78.6232	224	727	95	below_threshold
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	78.5857	228	727	95	below_threshold
Haemophilus influenzae	strain=NCTC8143	GCA_001457655.1	727	727	type	True	78.5726	198	727	95	below_threshold
Bisgaardia hudsonensis	strain=M327/99/2	GCA_013377195.1	109472	109472	type	True	78.5458	234	727	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	78.4929	200	727	95	below_threshold
Bisgaardia hudsonensis	strain=DSM 28231	GCA_004345785.1	109472	109472	type	True	78.4301	235	727	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	78.2517	205	727	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.0063	167	727	95	below_threshold
Lonepinella koalarum	strain=DSM 10053	GCA_004339625.1	53417	53417	type	True	77.8946	197	727	95	below_threshold
Conservatibacter flavescens	strain=7.4	GCA_002795425.1	28161	28161	type	True	77.802	175	727	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	77.7685	181	727	95	below_threshold
Rodentibacter pneumotropicus	strain=DSM 21403	GCA_000379905.1	758	758	type	True	77.6806	178	727	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:35,848] [INFO] DFAST Taxonomy check result was written to GCF_002015075.1_ASM201507v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:35,849] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:35,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:35,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9885e9ac-b1db-4289-8391-da864bd6d3c6/dqc_reference/checkm_data
[2024-01-25 18:11:35,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:35,880] [INFO] Task started: CheckM
[2024-01-25 18:11:35,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002015075.1_ASM201507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002015075.1_ASM201507v1_genomic.fna/checkm_input GCF_002015075.1_ASM201507v1_genomic.fna/checkm_result
[2024-01-25 18:11:53,431] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:53,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:53,448] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:53,449] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:53,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002015075.1_ASM201507v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:53,449] [INFO] Task started: Blastn
[2024-01-25 18:11:53,449] [INFO] Running command: blastn -query GCF_002015075.1_ASM201507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9885e9ac-b1db-4289-8391-da864bd6d3c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002015075.1_ASM201507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:54,298] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:54,301] [INFO] Selected 18 target genomes.
[2024-01-25 18:11:54,302] [INFO] Target genome list was writen to GCF_002015075.1_ASM201507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:54,357] [INFO] Task started: fastANI
[2024-01-25 18:11:54,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgfeade4e6-839f-4561-b25a-396c0c264c11/GCF_002015075.1_ASM201507v1_genomic.fna.gz --refList GCF_002015075.1_ASM201507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002015075.1_ASM201507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:02,493] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:02,504] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:02,504] [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_002015075.1	s__Canicola haemoglobinophilus	100.0	723	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Canicola	95.0	99.15	98.65	0.96	0.92	4	conclusive
GCF_014202395.1	s__Histophilus somni	81.9353	440	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Histophilus	95.0	99.10	98.34	0.94	0.85	61	-
GCF_900454865.1	s__Pasteurella canis	79.0504	236	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Pasteurella	95.0	98.76	98.68	0.94	0.91	4	-
GCF_002921145.1	s__Avibacterium endocarditidis	78.7706	198	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.5151	N/A	N/A	N/A	N/A	1	-
GCF_002795405.1	s__Caviibacterium pharyngocola	78.729	182	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Caviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002921135.1	s__Avibacterium gallinarum	78.6404	225	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	100.00	100.00	1.00	1.00	3	-
GCF_900454535.1	s__Avibacterium avium	78.624	223	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_900638385.1	s__Actinobacillus_C delphinicola	78.5955	120	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457655.1	s__Haemophilus influenzae	78.5852	198	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.9609	97.88	97.07	0.94	0.87	511	-
GCF_013377195.1	s__Bisgaardia hudsonensis	78.5634	233	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900635775.1	s__Avibacterium volantium	78.4573	249	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCA_900444965.1	s__Basfia_A rossii	78.3237	207	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900475755.1	s__Haemophilus influenzae_D	78.2798	213	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.4263	96.90	95.46	0.91	0.81	69	-
GCF_006384255.1	s__Haemophilus seminalis	78.2495	204	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	96.02	95.40	0.91	0.84	26	-
GCF_001998905.1	s__Rodentibacter_A heylii_A	78.0658	148	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000125.1	s__Rodentibacter heidelbergensis	78.0473	156	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004565475.1	s__Lonepinella koalarum	77.9282	195	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Lonepinella	95.0	99.41	98.83	0.96	0.92	3	-
GCF_000379905.1	s__Rodentibacter pneumotropicus	77.7217	175	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:02,506] [INFO] GTDB search result was written to GCF_002015075.1_ASM201507v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:02,506] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:02,509] [INFO] DFAST_QC result json was written to GCF_002015075.1_ASM201507v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:02,510] [INFO] DFAST_QC completed!
[2024-01-25 18:12:02,510] [INFO] Total running time: 0h0m42s