[2024-01-24 14:14:36,181] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:36,189] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:36,190] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3f370a2-7547-4f7f-9bd2-c3252dfd6fc1/dqc_reference
[2024-01-24 14:14:38,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,812] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg911d6c86-6858-41a1-a0f0-d060ed975e53/GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/cds.fna -a GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:58,402] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:58,403] [INFO] Task started: HMMsearch
[2024-01-24 14:14:58,404] [INFO] Running command: hmmsearch --tblout GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3f370a2-7547-4f7f-9bd2-c3252dfd6fc1/dqc_reference/reference_markers.hmm GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:58,721] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:58,722] [INFO] Found 6/6 markers.
[2024-01-24 14:14:58,763] [INFO] Query marker FASTA was written to GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:14:58,763] [INFO] Task started: Blastn
[2024-01-24 14:14:58,764] [INFO] Running command: blastn -query GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f370a2-7547-4f7f-9bd2-c3252dfd6fc1/dqc_reference/reference_markers.fasta -out GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:59,464] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:59,468] [INFO] Selected 21 target genomes.
[2024-01-24 14:14:59,469] [INFO] Target genome list was writen to GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:14:59,477] [INFO] Task started: fastANI
[2024-01-24 14:14:59,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg911d6c86-6858-41a1-a0f0-d060ed975e53/GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna.gz --refList GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:17,894] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:17,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3f370a2-7547-4f7f-9bd2-c3252dfd6fc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:17,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3f370a2-7547-4f7f-9bd2-c3252dfd6fc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:17,910] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:17,910] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:17,911] [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
Sphingobacterium wenxiniae	strain=DSM 22789	GCA_900116225.1	683125	683125	type	True	100.0	1268	1270	95	conclusive
Sphingobacterium thalpophilum	strain=NCTC11429	GCA_901482695.1	259	259	type	True	79.5844	161	1270	95	below_threshold
Sphingobacterium humi	strain=JCM 31225	GCA_009768885.1	1796905	1796905	type	True	79.4405	173	1270	95	below_threshold
Sphingobacterium phlebotomi	strain=SSI9	GCA_008180195.1	2605433	2605433	type	True	78.9529	256	1270	95	below_threshold
Sphingobacterium psychroaquaticum	strain=DSM 22418	GCA_900177625.1	561061	561061	type	True	78.8328	220	1270	95	below_threshold
Sphingobacterium corticibacterium	strain=30C10-4-7	GCA_004208525.1	2484746	2484746	type	True	78.6508	246	1270	95	below_threshold
Sphingobacterium chuzhouense	strain=KCTC 42746	GCA_014692525.1	1742264	1742264	type	True	78.638	246	1270	95	below_threshold
Sphingobacterium soli	strain=DSM 101679	GCA_014138555.1	1914757	1914757	type	True	78.5364	150	1270	95	below_threshold
Sphingobacterium soli	strain=CGMCC 1.15966	GCA_014644335.1	1914757	1914757	type	True	78.4593	143	1270	95	below_threshold
Sphingobacterium endophyticum	strain=NYYP31	GCA_009733535.1	2546448	2546448	type	True	78.3415	158	1270	95	below_threshold
Sphingobacterium puteale	strain=M05W1-28	GCA_003627955.1	2420510	2420510	type	True	78.1567	129	1270	95	below_threshold
Sphingobacterium mizutaii	strain=NCTC12149	GCA_900187125.1	1010	1010	type	True	77.9997	146	1270	95	below_threshold
Sphingobacterium mizutaii	strain=NBRC 14946	GCA_007990895.1	1010	1010	type	True	77.9887	146	1270	95	below_threshold
Sphingobacterium mizutaii	strain=DSM 11724	GCA_900102835.1	1010	1010	type	True	77.8362	140	1270	95	below_threshold
Sphingobacterium gobiense	strain=ACCC 05757	GCA_002980575.1	1382456	1382456	type	True	77.8314	219	1270	95	below_threshold
Sphingobacterium haloxyli	strain=5JN-11	GCA_002980525.1	2100533	2100533	type	True	77.7928	211	1270	95	below_threshold
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	77.7521	180	1270	95	below_threshold
Sphingobacterium lumbrici	strain=1.3611	GCA_006476045.1	2559600	2559600	type	True	77.7451	148	1270	95	below_threshold
Sphingobacterium olei	strain=HAL-9	GCA_005048855.1	2571155	2571155	type	True	77.6437	175	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:17,913] [INFO] DFAST Taxonomy check result was written to GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:15:17,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:17,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:17,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3f370a2-7547-4f7f-9bd2-c3252dfd6fc1/dqc_reference/checkm_data
[2024-01-24 14:15:17,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:17,958] [INFO] Task started: CheckM
[2024-01-24 14:15:17,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/checkm_input GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:16:13,197] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:13,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:13,222] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:13,223] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:13,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:16:13,224] [INFO] Task started: Blastn
[2024-01-24 14:16:13,225] [INFO] Running command: blastn -query GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3f370a2-7547-4f7f-9bd2-c3252dfd6fc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:15,490] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:15,494] [INFO] Selected 24 target genomes.
[2024-01-24 14:16:15,494] [INFO] Target genome list was writen to GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:15,515] [INFO] Task started: fastANI
[2024-01-24 14:16:15,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg911d6c86-6858-41a1-a0f0-d060ed975e53/GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna.gz --refList GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:36,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:37,078] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:37,078] [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_900116225.1	s__Sphingobacterium wenxiniae	100.0	1268	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008180195.1	s__Sphingobacterium phlebotomi	78.9686	254	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177625.1	s__Sphingobacterium psychroaquaticum	78.8119	221	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.08	99.08	0.93	0.93	2	-
GCF_004208525.1	s__Sphingobacterium sp004208525	78.6789	244	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692525.1	s__Sphingobacterium chuzhouense	78.6548	245	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933815.1	s__Sphingobacterium sp002933815	78.6204	145	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274825.1	s__Sphingobacterium hotanense	78.527	136	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.82	97.82	0.91	0.91	2	-
GCF_011043555.1	s__Sphingobacterium sp011043555	78.5023	206	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557615.1	s__Sphingobacterium sp009557615	78.4602	132	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014692515.1	s__Sphingobacterium sp014692515	78.3884	216	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733535.1	s__Sphingobacterium endophyticum	78.3236	158	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014219015.1	s__Sphingobacterium sp002476975	78.3215	159	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.27	97.88	0.91	0.89	5	-
GCF_008124885.1	s__Sphingobacterium composti_A	78.2842	174	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627955.1	s__Sphingobacterium puteale	78.1567	129	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187125.1	s__Sphingobacterium mizutaii	77.9811	146	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	99.36	98.08	0.96	0.87	4	-
GCA_002420705.1	s__Sphingobacterium sp002420705	77.9586	129	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980575.1	s__Sphingobacterium gobiense	77.8427	219	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006476045.1	s__Sphingobacterium lumbrici	77.7892	144	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002980525.1	s__Sphingobacterium haloxyli	77.7767	212	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829075.1	s__Sphingobacterium composti	77.7483	179	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048855.1	s__Sphingobacterium olei	77.6249	174	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015210005.1	s__Sphingobacterium sp015210005	77.4803	126	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012030425.1	s__Sphingobacterium kitahiroshimense	77.2669	128	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	97.48	96.84	0.85	0.82	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:37,082] [INFO] GTDB search result was written to GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:37,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:37,089] [INFO] DFAST_QC result json was written to GCF_900116225.1_IMG-taxon_2634166295_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:16:37,090] [INFO] DFAST_QC completed!
[2024-01-24 14:16:37,090] [INFO] Total running time: 0h2m1s