[2024-01-24 11:58:20,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,617] [INFO] DQC Reference Directory: /var/lib/cwl/stg06f7076b-a38d-4367-bae5-a586fbfe4188/dqc_reference
[2024-01-24 11:58:21,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,817] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg07c46216-cf35-4979-87e7-a784b7c1739d/GCF_003634665.1_ASM363466v1_genomic.fna.gz | prodigal -d GCF_003634665.1_ASM363466v1_genomic.fna/cds.fna -a GCF_003634665.1_ASM363466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:25,665] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:25,666] [INFO] Task started: HMMsearch
[2024-01-24 11:58:25,666] [INFO] Running command: hmmsearch --tblout GCF_003634665.1_ASM363466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06f7076b-a38d-4367-bae5-a586fbfe4188/dqc_reference/reference_markers.hmm GCF_003634665.1_ASM363466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:25,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:25,886] [INFO] Found 6/6 markers.
[2024-01-24 11:58:25,907] [INFO] Query marker FASTA was written to GCF_003634665.1_ASM363466v1_genomic.fna/markers.fasta
[2024-01-24 11:58:25,908] [INFO] Task started: Blastn
[2024-01-24 11:58:25,908] [INFO] Running command: blastn -query GCF_003634665.1_ASM363466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06f7076b-a38d-4367-bae5-a586fbfe4188/dqc_reference/reference_markers.fasta -out GCF_003634665.1_ASM363466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:26,595] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:26,599] [INFO] Selected 22 target genomes.
[2024-01-24 11:58:26,599] [INFO] Target genome list was writen to GCF_003634665.1_ASM363466v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:26,675] [INFO] Task started: fastANI
[2024-01-24 11:58:26,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg07c46216-cf35-4979-87e7-a784b7c1739d/GCF_003634665.1_ASM363466v1_genomic.fna.gz --refList GCF_003634665.1_ASM363466v1_genomic.fna/target_genomes.txt --output GCF_003634665.1_ASM363466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:35,607] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:35,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06f7076b-a38d-4367-bae5-a586fbfe4188/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:35,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06f7076b-a38d-4367-bae5-a586fbfe4188/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:35,621] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:58:35,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:58:35,621] [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
Otariodibacter oris	strain=DSM 23800	GCA_003634665.1	1032623	1032623	type	True	100.0	660	661	95	conclusive
Otariodibacter oris	strain=Baika1	GCA_009684715.1	1032623	1032623	type	True	99.9947	655	661	95	conclusive
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	79.126	261	661	95	below_threshold
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	79.0227	259	661	95	below_threshold
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	78.4835	200	661	95	below_threshold
Glaesserella parasuis	strain=NCTC4557	GCA_900450925.1	738	738	type	True	78.4769	201	661	95	below_threshold
Bisgaardia hudsonensis	strain=DSM 28231	GCA_004345785.1	109472	109472	type	True	78.326	155	661	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	78.1892	125	661	95	below_threshold
Actinobacillus capsulatus	strain=DSM 19761	GCA_000374285.1	717	717	type	True	78.1642	160	661	95	below_threshold
Nicoletella semolina	strain=DSM 16380	GCA_004345745.1	271160	271160	type	True	78.1622	141	661	95	below_threshold
Haemophilus sputorum	strain=CCUG 13788	GCA_000238795.2	1078480	1078480	type	True	78.1305	153	661	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.1244	131	661	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	78.0908	127	661	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	78.0817	210	661	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	78.0491	216	661	95	below_threshold
Mannheimia bovis	strain=ZY190616	GCA_014541205.1	2770636	2770636	type	True	77.9009	146	661	95	below_threshold
Pasteurella multocida subsp. gallicida	strain=NCTC10204	GCA_900636625.1	123812	747	type	True	77.8867	133	661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:35,624] [INFO] DFAST Taxonomy check result was written to GCF_003634665.1_ASM363466v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:35,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:35,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:35,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06f7076b-a38d-4367-bae5-a586fbfe4188/dqc_reference/checkm_data
[2024-01-24 11:58:35,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:35,653] [INFO] Task started: CheckM
[2024-01-24 11:58:35,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634665.1_ASM363466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634665.1_ASM363466v1_genomic.fna/checkm_input GCF_003634665.1_ASM363466v1_genomic.fna/checkm_result
[2024-01-24 11:58:54,471] [INFO] Task succeeded: CheckM
[2024-01-24 11:58:54,473] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:58:54,489] [INFO] ===== Completeness check finished =====
[2024-01-24 11:58:54,490] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:58:54,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634665.1_ASM363466v1_genomic.fna/markers.fasta)
[2024-01-24 11:58:54,491] [INFO] Task started: Blastn
[2024-01-24 11:58:54,491] [INFO] Running command: blastn -query GCF_003634665.1_ASM363466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06f7076b-a38d-4367-bae5-a586fbfe4188/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634665.1_ASM363466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:55,571] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:55,575] [INFO] Selected 23 target genomes.
[2024-01-24 11:58:55,575] [INFO] Target genome list was writen to GCF_003634665.1_ASM363466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:58:55,596] [INFO] Task started: fastANI
[2024-01-24 11:58:55,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg07c46216-cf35-4979-87e7-a784b7c1739d/GCF_003634665.1_ASM363466v1_genomic.fna.gz --refList GCF_003634665.1_ASM363466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634665.1_ASM363466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:03,894] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:03,916] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:03,917] [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_009684715.1	s__Otariodibacter oris	99.9947	655	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Otariodibacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_009761395.1	s__Ursidibacter maritimus	78.9948	260	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	-
GCF_009761375.1	s__Ursidibacter arcticus	78.7445	254	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901764975.1	s__Glaesserella indolica	78.5403	219	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002015085.1	s__Glaesserella parasuis	78.523	198	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	97.47	96.13	0.90	0.84	115	-
GCA_002002485.1	s__GCF-002002485 sp002002485	78.4726	231	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__GCF-002002485	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038205.1	s__Muribacter muris	78.447	107	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Muribacter	95.0	96.52	96.51	0.85	0.84	5	-
GCF_013377195.1	s__Bisgaardia hudsonensis	78.4077	154	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Bisgaardia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011455495.1	s__Frederiksenia canicola	78.3838	189	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003252795.1	s__Haemophilus_D parainfluenzae_K	78.3056	123	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
GCA_011455275.1	s__Frederiksenia sp011455275	78.2454	179	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000191405.1	s__Haemophilus_D parainfluenzae	78.1808	125	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	78.1777	173	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	97.10	97.10	0.92	0.92	2	-
GCF_004345745.1	s__Nicoletella semolina	78.1622	141	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Nicoletella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374285.1	s__Actinobacillus capsulatus	78.1337	162	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377275.1	s__Vespertiliibacter pulmonis	78.0988	209	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Vespertiliibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000238795.1	s__Haemophilus_A sputorum	78.0602	156	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.57	96.93	0.93	0.88	6	-
GCF_018343795.1	s__Phocoenobacter atlantica	77.9775	159	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014931275.1	s__Haemophilus_D sp900755445	77.9533	132	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCF_014541205.1	s__Mannheimia bovis	77.9242	145	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011455695.1	s__Mannheimia granulomatis_A	77.8896	153	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521605.1	s__Mannheimia sp000521605	77.8579	152	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214375.1	s__Haemophilus_D sp905214375	77.3249	103	661	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:03,919] [INFO] GTDB search result was written to GCF_003634665.1_ASM363466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:03,919] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:03,923] [INFO] DFAST_QC result json was written to GCF_003634665.1_ASM363466v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:03,923] [INFO] DFAST_QC completed!
[2024-01-24 11:59:03,923] [INFO] Total running time: 0h0m43s