[2024-01-24 14:39:45,826] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,828] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,828] [INFO] DQC Reference Directory: /var/lib/cwl/stgf33e5e3f-0a94-4a6a-b208-3855c6b8cd8a/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,366] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,366] [INFO] Running command: gunzip -c /var/lib/cwl/stg28e73f00-1b0c-44c9-97f2-831ac62ade42/GCF_009806515.1_ASM980651v1_genomic.fna.gz | prodigal -d GCF_009806515.1_ASM980651v1_genomic.fna/cds.fna -a GCF_009806515.1_ASM980651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:02,422] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:02,422] [INFO] Task started: HMMsearch
[2024-01-24 14:40:02,422] [INFO] Running command: hmmsearch --tblout GCF_009806515.1_ASM980651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf33e5e3f-0a94-4a6a-b208-3855c6b8cd8a/dqc_reference/reference_markers.hmm GCF_009806515.1_ASM980651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:02,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:02,788] [INFO] Found 6/6 markers.
[2024-01-24 14:40:02,844] [INFO] Query marker FASTA was written to GCF_009806515.1_ASM980651v1_genomic.fna/markers.fasta
[2024-01-24 14:40:02,845] [INFO] Task started: Blastn
[2024-01-24 14:40:02,845] [INFO] Running command: blastn -query GCF_009806515.1_ASM980651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf33e5e3f-0a94-4a6a-b208-3855c6b8cd8a/dqc_reference/reference_markers.fasta -out GCF_009806515.1_ASM980651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:03,813] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:03,818] [INFO] Selected 29 target genomes.
[2024-01-24 14:40:03,819] [INFO] Target genome list was writen to GCF_009806515.1_ASM980651v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:03,837] [INFO] Task started: fastANI
[2024-01-24 14:40:03,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg28e73f00-1b0c-44c9-97f2-831ac62ade42/GCF_009806515.1_ASM980651v1_genomic.fna.gz --refList GCF_009806515.1_ASM980651v1_genomic.fna/target_genomes.txt --output GCF_009806515.1_ASM980651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:27,889] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:27,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf33e5e3f-0a94-4a6a-b208-3855c6b8cd8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:27,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf33e5e3f-0a94-4a6a-b208-3855c6b8cd8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:27,922] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:40:27,923] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:40:27,923] [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
Geminicoccus roseus	strain=DSM 18922	GCA_000427665.1	404900	404900	type	True	83.4667	998	1438	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.7232	203	1438	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.6656	202	1438	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.6133	210	1438	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.5992	321	1438	95	below_threshold
Arboricoccus pini	strain=B29T1	GCA_900187945.1	1963835	1963835	type	True	76.4751	141	1438	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.3891	317	1438	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.3761	159	1438	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.2932	203	1438	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.2551	173	1438	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_000515255.1	1087	1087	type	True	76.2447	161	1438	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.2304	211	1438	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.2065	198	1438	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.1862	191	1438	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.1677	269	1438	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	76.1602	210	1438	95	below_threshold
Rhodovibrio salinarum	strain=DSM 9154	GCA_016583505.1	1087	1087	type	True	76.1522	162	1438	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	76.1442	238	1438	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.1344	131	1438	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.1126	265	1438	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.0803	235	1438	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	76.0709	97	1438	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.9921	220	1438	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	75.8956	170	1438	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	75.8584	195	1438	95	below_threshold
Tistrella bauzanensis	strain=CGMCC 1.10188	GCA_014636235.1	657419	657419	type	True	75.8352	206	1438	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.8329	178	1438	95	below_threshold
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	75.7884	172	1438	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	75.2837	91	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:27,926] [INFO] DFAST Taxonomy check result was written to GCF_009806515.1_ASM980651v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:27,926] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:27,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:27,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf33e5e3f-0a94-4a6a-b208-3855c6b8cd8a/dqc_reference/checkm_data
[2024-01-24 14:40:27,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:27,993] [INFO] Task started: CheckM
[2024-01-24 14:40:27,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009806515.1_ASM980651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009806515.1_ASM980651v1_genomic.fna/checkm_input GCF_009806515.1_ASM980651v1_genomic.fna/checkm_result
[2024-01-24 14:41:11,841] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:11,842] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:11,864] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:11,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:11,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009806515.1_ASM980651v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:11,866] [INFO] Task started: Blastn
[2024-01-24 14:41:11,866] [INFO] Running command: blastn -query GCF_009806515.1_ASM980651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf33e5e3f-0a94-4a6a-b208-3855c6b8cd8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009806515.1_ASM980651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:13,741] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:13,748] [INFO] Selected 26 target genomes.
[2024-01-24 14:41:13,748] [INFO] Target genome list was writen to GCF_009806515.1_ASM980651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:13,772] [INFO] Task started: fastANI
[2024-01-24 14:41:13,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg28e73f00-1b0c-44c9-97f2-831ac62ade42/GCF_009806515.1_ASM980651v1_genomic.fna.gz --refList GCF_009806515.1_ASM980651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009806515.1_ASM980651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:35,331] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:35,353] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:41:35,354] [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_000427665.1	s__Geminicoccus roseus	83.4755	997	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Geminicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826935.1	s__CADEGR01 sp902826935	77.2423	346	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__CADEGR01	95.0	98.81	98.69	0.93	0.92	4	-
GCA_007131045.1	s__SLRI01 sp007131045	77.1459	215	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__SLRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908425.1	s__JAAAPF01 sp009908425	76.8088	205	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__JAAAPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966715.1	s__Blastochloris tepida	76.711	204	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	76.5927	212	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.5793	322	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	76.5668	253	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490605.1	s__HRBIN39 sp015490605	76.5455	120	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__HRBIN39	95.0	97.05	97.05	0.84	0.84	2	-
GCF_900177295.1	s__Tistlia consotensis	76.5275	349	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.5133	254	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.5123	233	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900187945.1	s__Arboricoccus pini	76.4889	140	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__Arboricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	76.3834	246	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	76.3674	211	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264455.2	s__Tistrella mobilis	76.3371	267	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Tistrellales;f__Tistrellaceae;g__Tistrella	95.0	96.38	95.97	0.88	0.84	5	-
GCF_016467395.1	s__Reyranella sp016467395	76.3278	261	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.2862	209	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	76.2824	249	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870055.1	s__Reyranella sp016870055	76.2132	172	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429045.1	s__Salinarimonas rosea	76.2048	213	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	76.1914	177	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992495.1	s__Reyranella soli	76.1754	268	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019235415.1	s__Reyranella sp019235415	76.0585	202	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.35	99.35	0.86	0.86	2	-
GCA_015232025.1	s__JADFZP01 sp015232025	75.9213	157	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641655.1	s__Alteriqipengyuania_A marina	75.8887	70	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania_A	95.0	98.02	98.02	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:35,356] [INFO] GTDB search result was written to GCF_009806515.1_ASM980651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:35,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:35,367] [INFO] DFAST_QC result json was written to GCF_009806515.1_ASM980651v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:35,367] [INFO] DFAST_QC completed!
[2024-01-24 14:41:35,368] [INFO] Total running time: 0h1m50s