[2024-01-24 13:51:12,452] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:51:12,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:51:12,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg80fa01ce-c02a-489e-87a6-d04f8746ca5c/dqc_reference
[2024-01-24 13:51:13,750] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:51:13,751] [INFO] Task started: Prodigal
[2024-01-24 13:51:13,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg31173ff8-0ca0-44ee-850a-dc4daf060255/GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/cds.fna -a GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:51:21,691] [INFO] Task succeeded: Prodigal
[2024-01-24 13:51:21,692] [INFO] Task started: HMMsearch
[2024-01-24 13:51:21,692] [INFO] Running command: hmmsearch --tblout GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80fa01ce-c02a-489e-87a6-d04f8746ca5c/dqc_reference/reference_markers.hmm GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:51:21,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:51:21,983] [INFO] Found 6/6 markers.
[2024-01-24 13:51:22,020] [INFO] Query marker FASTA was written to GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:51:22,021] [INFO] Task started: Blastn
[2024-01-24 13:51:22,021] [INFO] Running command: blastn -query GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg80fa01ce-c02a-489e-87a6-d04f8746ca5c/dqc_reference/reference_markers.fasta -out GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:22,638] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:22,642] [INFO] Selected 23 target genomes.
[2024-01-24 13:51:22,642] [INFO] Target genome list was writen to GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:51:22,655] [INFO] Task started: fastANI
[2024-01-24 13:51:22,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg31173ff8-0ca0-44ee-850a-dc4daf060255/GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna.gz --refList GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:41,577] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:41,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80fa01ce-c02a-489e-87a6-d04f8746ca5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:41,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80fa01ce-c02a-489e-87a6-d04f8746ca5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:41,596] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:51:41,596] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:41,596] [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
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	100.0	1255	1257	95	conclusive
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	92.8912	1044	1257	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	77.4617	81	1257	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.2503	238	1257	95	below_threshold
Virgibacillus phasianinus	strain=LM2416	GCA_002216775.1	2017483	2017483	type	True	77.2212	163	1257	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	77.1554	172	1257	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.1502	204	1257	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	76.9	123	1257	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	76.8923	183	1257	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	76.7597	142	1257	95	below_threshold
Aquibacillus albus	strain=DSM 23711	GCA_016908325.1	1168171	1168171	type	True	76.742	83	1257	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.6947	102	1257	95	below_threshold
Lentibacillus kapialis	strain=JCM 12580	GCA_014646635.1	340214	340214	type	True	76.524	134	1257	95	below_threshold
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	76.5146	96	1257	95	below_threshold
Gracilibacillus suaedae	strain=LD4P30	GCA_017599345.1	2820273	2820273	type	True	76.4449	66	1257	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	76.3822	122	1257	95	below_threshold
Paraliobacillus salinarum	strain=G6-18	GCA_014083865.1	1158996	1158996	type	True	76.1731	64	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:41,604] [INFO] DFAST Taxonomy check result was written to GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:51:41,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:41,605] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:41,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80fa01ce-c02a-489e-87a6-d04f8746ca5c/dqc_reference/checkm_data
[2024-01-24 13:51:41,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:41,704] [INFO] Task started: CheckM
[2024-01-24 13:51:41,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/checkm_input GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:52:11,359] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:11,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:11,385] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:11,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:11,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:52:11,386] [INFO] Task started: Blastn
[2024-01-24 13:52:11,386] [INFO] Running command: blastn -query GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg80fa01ce-c02a-489e-87a6-d04f8746ca5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:12,745] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:12,750] [INFO] Selected 19 target genomes.
[2024-01-24 13:52:12,750] [INFO] Target genome list was writen to GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:12,766] [INFO] Task started: fastANI
[2024-01-24 13:52:12,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg31173ff8-0ca0-44ee-850a-dc4daf060255/GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna.gz --refList GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:26,548] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:26,569] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:26,570] [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_900110695.1	s__Lentibacillus subterraneus	100.0	1255	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	conclusive
GCF_017873675.1	s__Lentibacillus litoralis	92.8975	1043	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806455.1	s__Lentibacillus doumboii	78.1273	405	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650095.1	s__Gracilibacillus sp002797295	77.4996	80	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	77.2791	230	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638995.1	s__Virgibacillus_E oceani	77.2724	239	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187325.1	s__Virgibacillus_E ndiopensis	77.2463	262	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919725.1	s__Virgibacillus sp016919725	77.2391	136	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_002266285.1	s__Virgibacillus_G indicus	77.1388	205	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014642895.1	s__Virgibacillus_E populi	77.102	172	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	98.98	98.88	0.86	0.85	5	-
GCF_900112045.1	s__Lentibacillus halodurans	76.9054	182	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310895.1	s__Virgibacillus halodenitrificans	76.7446	143	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	98.29	98.21	0.89	0.88	7	-
GCF_016908325.1	s__Aquibacillus albus	76.7161	84	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004565465.1	s__Lentibacillus salicampi	76.678	165	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166595.1	s__Virgibacillus dokdonensis	76.5179	96	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.95	98.88	0.93	0.90	3	-
GCF_003369565.1	s__Oceanobacillus chungangensis	76.4056	122	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	76.4046	79	1257	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:26,572] [INFO] GTDB search result was written to GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:26,572] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:26,576] [INFO] DFAST_QC result json was written to GCF_900110695.1_IMG-taxon_2671180086_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:52:26,576] [INFO] DFAST_QC completed!
[2024-01-24 13:52:26,576] [INFO] Total running time: 0h1m14s