[2024-01-24 11:19:49,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:49,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:49,013] [INFO] DQC Reference Directory: /var/lib/cwl/stgc01ff14a-7cbf-4ba8-8bd1-223a179a6173/dqc_reference
[2024-01-24 11:19:50,229] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:50,230] [INFO] Task started: Prodigal
[2024-01-24 11:19:50,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg4400aacd-7977-4448-a152-3c7b7ef2ac36/GCF_019188485.1_ASM1918848v1_genomic.fna.gz | prodigal -d GCF_019188485.1_ASM1918848v1_genomic.fna/cds.fna -a GCF_019188485.1_ASM1918848v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:19:54,264] [INFO] Task succeeded: Prodigal
[2024-01-24 11:19:54,265] [INFO] Task started: HMMsearch
[2024-01-24 11:19:54,265] [INFO] Running command: hmmsearch --tblout GCF_019188485.1_ASM1918848v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc01ff14a-7cbf-4ba8-8bd1-223a179a6173/dqc_reference/reference_markers.hmm GCF_019188485.1_ASM1918848v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:19:54,576] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:19:54,578] [INFO] Found 6/6 markers.
[2024-01-24 11:19:54,608] [INFO] Query marker FASTA was written to GCF_019188485.1_ASM1918848v1_genomic.fna/markers.fasta
[2024-01-24 11:19:54,609] [INFO] Task started: Blastn
[2024-01-24 11:19:54,609] [INFO] Running command: blastn -query GCF_019188485.1_ASM1918848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc01ff14a-7cbf-4ba8-8bd1-223a179a6173/dqc_reference/reference_markers.fasta -out GCF_019188485.1_ASM1918848v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:19:55,228] [INFO] Task succeeded: Blastn
[2024-01-24 11:19:55,234] [INFO] Selected 25 target genomes.
[2024-01-24 11:19:55,234] [INFO] Target genome list was writen to GCF_019188485.1_ASM1918848v1_genomic.fna/target_genomes.txt
[2024-01-24 11:19:55,304] [INFO] Task started: fastANI
[2024-01-24 11:19:55,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg4400aacd-7977-4448-a152-3c7b7ef2ac36/GCF_019188485.1_ASM1918848v1_genomic.fna.gz --refList GCF_019188485.1_ASM1918848v1_genomic.fna/target_genomes.txt --output GCF_019188485.1_ASM1918848v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:05,962] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:05,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc01ff14a-7cbf-4ba8-8bd1-223a179a6173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:05,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc01ff14a-7cbf-4ba8-8bd1-223a179a6173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:05,977] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:20:05,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:05,978] [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
Ursidibacter maritimus	strain=Pb43106	GCA_019188485.1	1331689	1331689	type	True	100.0	649	649	95	conclusive
Ursidibacter maritimus	strain=Pb43106	GCA_009761395.1	1331689	1331689	type	True	99.9955	637	649	95	conclusive
Glaesserella parasuis	strain=CCUG 3712	GCA_002015085.1	738	738	type	True	79.3668	279	649	95	below_threshold
Glaesserella parasuis	strain=NCTC4557	GCA_900450925.1	738	738	type	True	79.2369	292	649	95	below_threshold
Otariodibacter oris	strain=DSM 23800	GCA_003634665.1	1032623	1032623	type	True	79.1206	262	649	95	below_threshold
Otariodibacter oris	strain=Baika1	GCA_009684715.1	1032623	1032623	type	True	79.0987	268	649	95	below_threshold
Frederiksenia canicola	strain=DSM 25797	GCA_003814575.1	123824	123824	type	True	79.0512	266	649	95	below_threshold
Vespertiliibacter pulmonis	strain=DSM 27238	GCA_003843855.1	1443036	1443036	type	True	78.872	273	649	95	below_threshold
Vespertiliibacter pulmonis	strain=CCUG 64585	GCA_013377275.1	1443036	1443036	type	True	78.8675	275	649	95	below_threshold
Mannheimia varigena	strain=177	GCA_013377235.1	85404	85404	type	True	78.663	193	649	95	below_threshold
Bibersteinia trehalosi	strain=DSM 23101	GCA_004346205.1	47735	47735	type	True	78.4624	213	649	95	below_threshold
Haemophilus sputorum	strain=CCUG 13788	GCA_000238795.2	1078480	1078480	type	True	78.363	196	649	95	below_threshold
Actinobacillus minor	strain=NM305	GCA_000175195.1	51047	51047	type	True	78.2968	226	649	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	78.2248	146	649	95	below_threshold
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	78.2121	144	649	95	below_threshold
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	78.1552	142	649	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	78.1021	148	649	95	below_threshold
Actinobacillus pleuropneumoniae	strain=4074	GCA_000178495.2	715	715	type	True	77.9376	188	649	95	below_threshold
Actinobacillus pleuropneumoniae	strain=S4074	GCA_003290385.1	715	715	type	True	77.9331	188	649	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:05,980] [INFO] DFAST Taxonomy check result was written to GCF_019188485.1_ASM1918848v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:05,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:05,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:05,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc01ff14a-7cbf-4ba8-8bd1-223a179a6173/dqc_reference/checkm_data
[2024-01-24 11:20:05,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:06,003] [INFO] Task started: CheckM
[2024-01-24 11:20:06,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019188485.1_ASM1918848v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019188485.1_ASM1918848v1_genomic.fna/checkm_input GCF_019188485.1_ASM1918848v1_genomic.fna/checkm_result
[2024-01-24 11:20:25,374] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:25,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:25,395] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:25,396] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:25,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019188485.1_ASM1918848v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:25,397] [INFO] Task started: Blastn
[2024-01-24 11:20:25,397] [INFO] Running command: blastn -query GCF_019188485.1_ASM1918848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc01ff14a-7cbf-4ba8-8bd1-223a179a6173/dqc_reference/reference_markers_gtdb.fasta -out GCF_019188485.1_ASM1918848v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:26,207] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:26,212] [INFO] Selected 22 target genomes.
[2024-01-24 11:20:26,212] [INFO] Target genome list was writen to GCF_019188485.1_ASM1918848v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:20:26,233] [INFO] Task started: fastANI
[2024-01-24 11:20:26,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg4400aacd-7977-4448-a152-3c7b7ef2ac36/GCF_019188485.1_ASM1918848v1_genomic.fna.gz --refList GCF_019188485.1_ASM1918848v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019188485.1_ASM1918848v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:20:35,461] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:35,481] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:20:35,481] [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_009761395.1	s__Ursidibacter maritimus	99.9955	637	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	99.92	99.03	0.98	0.97	15	conclusive
GCF_009761375.1	s__Ursidibacter arcticus	91.6929	486	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Ursidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002015085.1	s__Glaesserella parasuis	79.3407	280	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	97.47	96.13	0.90	0.84	115	-
GCF_901764975.1	s__Glaesserella indolica	79.207	312	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260095.1	s__Glaesserella australis	79.1724	298	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011455495.1	s__Frederiksenia canicola	79.1502	265	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009684715.1	s__Otariodibacter oris	79.0697	268	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Otariodibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003101015.1	s__Actinobacillus_A porcitonsillarum	78.9664	221	649	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_013377275.1	s__Vespertiliibacter pulmonis	78.843	276	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Vespertiliibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011455275.1	s__Frederiksenia sp011455275	78.8316	262	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Frederiksenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377235.1	s__Mannheimia varigena	78.6548	194	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	97.47	97.09	0.96	0.94	7	-
GCF_011455695.1	s__Mannheimia granulomatis_A	78.576	197	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mannheimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636745.1	s__Actinobacillus equuli	78.5674	203	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	98.82	97.64	0.96	0.93	3	-
GCF_901687125.1	s__Actinobacillus vicugnae	78.4102	232	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238795.1	s__Haemophilus_A sputorum	78.3632	196	649	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_004802395.1	s__Haemophilus influenzae_E	78.3114	132	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.8621	97.44	97.09	0.92	0.89	88	-
GCF_000175195.1	s__Actinobacillus_A minor	78.2947	225	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Actinobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215245.1	s__Haemophilus_D sp905215245	78.0381	114	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.18	95.12	0.97	0.97	5	-
GCA_018381425.1	s__Haemophilus_D parainfluenzae_O	77.9029	87	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.89	95.76	0.75	0.73	3	-
GCF_018343795.1	s__Phocoenobacter atlantica	77.8212	159	649	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Phocoenobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:20:35,483] [INFO] GTDB search result was written to GCF_019188485.1_ASM1918848v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:20:35,483] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:20:35,487] [INFO] DFAST_QC result json was written to GCF_019188485.1_ASM1918848v1_genomic.fna/dqc_result.json
[2024-01-24 11:20:35,488] [INFO] DFAST_QC completed!
[2024-01-24 11:20:35,488] [INFO] Total running time: 0h0m46s