[2024-01-24 13:50:26,393] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:26,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:26,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg25c87409-aa16-4619-b5fb-90e1309efb63/dqc_reference
[2024-01-24 13:50:28,446] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:28,448] [INFO] Task started: Prodigal
[2024-01-24 13:50:28,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg27275860-1f29-4d33-8d64-f7ee64ea957f/GCF_004005845.1_ASM400584v1_genomic.fna.gz | prodigal -d GCF_004005845.1_ASM400584v1_genomic.fna/cds.fna -a GCF_004005845.1_ASM400584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:45,001] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:45,001] [INFO] Task started: HMMsearch
[2024-01-24 13:50:45,001] [INFO] Running command: hmmsearch --tblout GCF_004005845.1_ASM400584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25c87409-aa16-4619-b5fb-90e1309efb63/dqc_reference/reference_markers.hmm GCF_004005845.1_ASM400584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:45,355] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:45,356] [INFO] Found 6/6 markers.
[2024-01-24 13:50:45,425] [INFO] Query marker FASTA was written to GCF_004005845.1_ASM400584v1_genomic.fna/markers.fasta
[2024-01-24 13:50:45,426] [INFO] Task started: Blastn
[2024-01-24 13:50:45,426] [INFO] Running command: blastn -query GCF_004005845.1_ASM400584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c87409-aa16-4619-b5fb-90e1309efb63/dqc_reference/reference_markers.fasta -out GCF_004005845.1_ASM400584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:46,369] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:46,373] [INFO] Selected 26 target genomes.
[2024-01-24 13:50:46,374] [INFO] Target genome list was writen to GCF_004005845.1_ASM400584v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:46,387] [INFO] Task started: fastANI
[2024-01-24 13:50:46,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg27275860-1f29-4d33-8d64-f7ee64ea957f/GCF_004005845.1_ASM400584v1_genomic.fna.gz --refList GCF_004005845.1_ASM400584v1_genomic.fna/target_genomes.txt --output GCF_004005845.1_ASM400584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:06,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:06,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25c87409-aa16-4619-b5fb-90e1309efb63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:06,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25c87409-aa16-4619-b5fb-90e1309efb63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:06,402] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:51:06,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:06,402] [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
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	100.0	1769	1769	95	conclusive
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	77.3897	219	1769	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	76.4613	186	1769	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3805	146	1769	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.3219	80	1769	95	below_threshold
Aestuariispira insulae	strain=CECT 8488	GCA_003385955.1	1461337	1461337	type	True	76.2267	111	1769	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	76.1839	111	1769	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	76.1412	114	1769	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.1294	135	1769	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.119	61	1769	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.0695	107	1769	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.0259	127	1769	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	75.9691	53	1769	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.947	88	1769	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.9082	120	1769	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.9069	120	1769	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.8582	106	1769	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.8145	94	1769	95	below_threshold
Niveispirillum cyanobacteriorum	strain=TH16	GCA_002868735.1	1612173	1612173	type	True	75.7806	97	1769	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.7457	101	1769	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.7257	129	1769	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	75.6917	95	1769	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	75.673	93	1769	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	75.6363	60	1769	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	75.5612	64	1769	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	75.5384	113	1769	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:06,404] [INFO] DFAST Taxonomy check result was written to GCF_004005845.1_ASM400584v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:06,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:06,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:06,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25c87409-aa16-4619-b5fb-90e1309efb63/dqc_reference/checkm_data
[2024-01-24 13:51:06,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:06,459] [INFO] Task started: CheckM
[2024-01-24 13:51:06,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005845.1_ASM400584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005845.1_ASM400584v1_genomic.fna/checkm_input GCF_004005845.1_ASM400584v1_genomic.fna/checkm_result
[2024-01-24 13:51:55,313] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:55,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:55,346] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:55,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:55,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005845.1_ASM400584v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:55,348] [INFO] Task started: Blastn
[2024-01-24 13:51:55,348] [INFO] Running command: blastn -query GCF_004005845.1_ASM400584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c87409-aa16-4619-b5fb-90e1309efb63/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005845.1_ASM400584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:57,028] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:57,037] [INFO] Selected 25 target genomes.
[2024-01-24 13:51:57,037] [INFO] Target genome list was writen to GCF_004005845.1_ASM400584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:57,057] [INFO] Task started: fastANI
[2024-01-24 13:51:57,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg27275860-1f29-4d33-8d64-f7ee64ea957f/GCF_004005845.1_ASM400584v1_genomic.fna.gz --refList GCF_004005845.1_ASM400584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005845.1_ASM400584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:19,058] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:19,086] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:19,087] [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_004005845.1	s__Hwanghaeella grinnelliae	100.0	1769	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Hwanghaeella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012926505.1	s__GCA-2696645 sp012926505	77.3897	219	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792345.1	s__GCA-2696645 sp017792345	77.2735	258	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	-
GCF_017963645.1	s__Marivibrio halodurans	76.4515	187	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Marivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224925.1	s__Magnetospirillum sp018224925	76.3912	66	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385955.1	s__Aestuariispira insulae	76.2267	111	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Aestuariispira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119115.1	s__Azospirillum sp003119115	76.1854	114	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_001315015.1	s__Azospirillum brasilense	76.1669	112	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_001639105.2	s__Azospirillum humicireducens	76.1412	114	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233655.1	s__Azospirillum ramasamyi	76.0385	126	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827795.1	s__Azospirillum brasilense_E	75.9694	119	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCA_009377445.1	s__WHUA01 sp009377445	75.9245	94	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	75.9204	111	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	75.9082	120	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014192915.1	s__Azospirillum sp014192915	75.8659	115	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923295.1	s__Azospirillum sp003115975	75.8458	142	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004923315.1	s__Azospirillum sp003116065	75.8308	142	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_008365375.1	s__Azospirillum sp008365375	75.799	110	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868735.1	s__Niveispirillum cyanobacteriorum	75.7806	97	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Niveispirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001427865.1	s__Croceibacterium sp001427865	75.6997	52	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899075.1	s__Devosia_A sp001899075	75.5617	63	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016791425.1	s__CADEEL01 sp016791425	75.4054	53	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__CADEEL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927615.1	s__BOG-933 sp903927615	75.2272	53	1769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__BOG-933	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:19,089] [INFO] GTDB search result was written to GCF_004005845.1_ASM400584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:19,090] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:19,095] [INFO] DFAST_QC result json was written to GCF_004005845.1_ASM400584v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:19,095] [INFO] DFAST_QC completed!
[2024-01-24 13:52:19,095] [INFO] Total running time: 0h1m53s