[2024-01-24 15:09:55,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg43a9c35a-3967-42a3-a280-beb87614d687/dqc_reference
[2024-01-24 15:09:58,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,166] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,167] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4226066-f972-4ff1-909e-680326a6f5f4/GCF_020447305.1_ASM2044730v2_genomic.fna.gz | prodigal -d GCF_020447305.1_ASM2044730v2_genomic.fna/cds.fna -a GCF_020447305.1_ASM2044730v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:10,249] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:10,249] [INFO] Task started: HMMsearch
[2024-01-24 15:10:10,249] [INFO] Running command: hmmsearch --tblout GCF_020447305.1_ASM2044730v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43a9c35a-3967-42a3-a280-beb87614d687/dqc_reference/reference_markers.hmm GCF_020447305.1_ASM2044730v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:10,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:10,608] [INFO] Found 6/6 markers.
[2024-01-24 15:10:10,643] [INFO] Query marker FASTA was written to GCF_020447305.1_ASM2044730v2_genomic.fna/markers.fasta
[2024-01-24 15:10:10,643] [INFO] Task started: Blastn
[2024-01-24 15:10:10,643] [INFO] Running command: blastn -query GCF_020447305.1_ASM2044730v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg43a9c35a-3967-42a3-a280-beb87614d687/dqc_reference/reference_markers.fasta -out GCF_020447305.1_ASM2044730v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:11,520] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:11,635] [INFO] Selected 32 target genomes.
[2024-01-24 15:10:11,636] [INFO] Target genome list was writen to GCF_020447305.1_ASM2044730v2_genomic.fna/target_genomes.txt
[2024-01-24 15:10:11,656] [INFO] Task started: fastANI
[2024-01-24 15:10:11,657] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4226066-f972-4ff1-909e-680326a6f5f4/GCF_020447305.1_ASM2044730v2_genomic.fna.gz --refList GCF_020447305.1_ASM2044730v2_genomic.fna/target_genomes.txt --output GCF_020447305.1_ASM2044730v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:33,522] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:33,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43a9c35a-3967-42a3-a280-beb87614d687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:33,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43a9c35a-3967-42a3-a280-beb87614d687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:33,549] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:10:33,549] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:10:33,550] [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
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	77.8789	287	1069	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	77.834	256	1069	95	below_threshold
Rhodovulum bhavnagarense	strain=DSM 24766	GCA_004343505.1	992286	992286	type	True	77.5989	181	1069	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	77.4633	162	1069	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.355	142	1069	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	77.1844	165	1069	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.1056	210	1069	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.0487	153	1069	95	below_threshold
Qingshengfaniella alkalisoli	strain=LN3S51	GCA_007855645.1	2599296	2599296	type	True	77.0443	101	1069	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	77.0281	211	1069	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.0158	185	1069	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	77.012	243	1069	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.9839	221	1069	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	76.974	241	1069	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	76.9511	231	1069	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	76.9241	224	1069	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	76.8863	186	1069	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	76.8093	215	1069	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.7982	232	1069	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.7895	183	1069	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	76.7694	213	1069	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	76.72	192	1069	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.6752	224	1069	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	76.6601	158	1069	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.623	208	1069	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.5683	145	1069	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	76.403	155	1069	95	below_threshold
Gemmobacter tilapiae	strain=KCTC 23310	GCA_014652215.1	875041	875041	type	True	76.4008	157	1069	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	76.3599	194	1069	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	76.1712	99	1069	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	76.1309	118	1069	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.9735	160	1069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:33,551] [INFO] DFAST Taxonomy check result was written to GCF_020447305.1_ASM2044730v2_genomic.fna/tc_result.tsv
[2024-01-24 15:10:33,552] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:33,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:33,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43a9c35a-3967-42a3-a280-beb87614d687/dqc_reference/checkm_data
[2024-01-24 15:10:33,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:33,585] [INFO] Task started: CheckM
[2024-01-24 15:10:33,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020447305.1_ASM2044730v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020447305.1_ASM2044730v2_genomic.fna/checkm_input GCF_020447305.1_ASM2044730v2_genomic.fna/checkm_result
[2024-01-24 15:11:11,141] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:11,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:11,167] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:11,168] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:11,168] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020447305.1_ASM2044730v2_genomic.fna/markers.fasta)
[2024-01-24 15:11:11,169] [INFO] Task started: Blastn
[2024-01-24 15:11:11,169] [INFO] Running command: blastn -query GCF_020447305.1_ASM2044730v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg43a9c35a-3967-42a3-a280-beb87614d687/dqc_reference/reference_markers_gtdb.fasta -out GCF_020447305.1_ASM2044730v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:12,585] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:12,588] [INFO] Selected 35 target genomes.
[2024-01-24 15:11:12,589] [INFO] Target genome list was writen to GCF_020447305.1_ASM2044730v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:12,612] [INFO] Task started: fastANI
[2024-01-24 15:11:12,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4226066-f972-4ff1-909e-680326a6f5f4/GCF_020447305.1_ASM2044730v2_genomic.fna.gz --refList GCF_020447305.1_ASM2044730v2_genomic.fna/target_genomes_gtdb.txt --output GCF_020447305.1_ASM2044730v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:35,514] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:35,546] [INFO] Found 35 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:11:35,546] [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_000429765.1	s__Wagnerdoeblera nectariphila	77.8337	256	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343505.1	s__Rhodovulum bhavnagarense	77.5492	184	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001720585.1	s__Cereibacter_A johrii	77.472	163	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.4211	240	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_009649175.1	s__Rhodovulum strictum	77.3755	236	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278325.1	s__JADQCB01 sp016278325	77.3663	219	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177545.1	s__Muriiphilus sp900177545	77.1696	175	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.157	267	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003688285.1	s__Rhodophyticola porphyridii	77.0487	153	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156255.1	s__Paracoccus thiocyanatus	77.02	211	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
GCF_003709565.1	s__Paracoccus siganidrum	77.0135	242	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900142935.1	s__Rhodovulum sp900142935	76.9984	178	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936395.1	s__ETT8 sp016936395	76.9958	199	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640115.1	s__Muriiphilus lacisalsi	76.9884	169	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485375.1	s__UBA3077 sp015485375	76.9396	148	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	76.9241	224	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762325.1	s__Roseovarius faecimaris	76.8995	185	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	76.8449	178	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644125.1	s__Rhodophyticola sp017644125	76.8413	174	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCF_002900965.1	s__ETT8 sp002900965	76.827	218	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.808	241	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007827395.1	s__Rhodophyticola sp007827395	76.6927	155	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	95.40	95.35	0.93	0.92	216	-
GCF_003265325.1	s__Halovulum sediminis	76.685	200	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748285.1	s__Profundibacter sp002748285	76.6808	173	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	76.6561	195	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.6353	181	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120685.1	s__Pararhodobacter sp007120685	76.6259	167	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.30	99.30	0.84	0.84	2	-
GCA_015689745.1	s__Roseicyclus sp015689745	76.6125	168	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	76.5855	158	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCA_015487335.1	s__S012-89 sp015487335	76.5835	159	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	76.5831	193	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118445.1	s__Roseinatronobacter sp007118445	76.5398	151	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.03	98.90	0.77	0.72	3	-
GCA_012032275.1	s__JAAURK01 sp012032275	76.4986	147	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAURK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121115.1	s__PUOA01 sp007121115	76.4485	157	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	99.30	99.15	0.84	0.78	4	-
GCA_013151335.1	s__UBA5972 sp013151335	76.1876	131	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:35,549] [INFO] GTDB search result was written to GCF_020447305.1_ASM2044730v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:35,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:35,556] [INFO] DFAST_QC result json was written to GCF_020447305.1_ASM2044730v2_genomic.fna/dqc_result.json
[2024-01-24 15:11:35,556] [INFO] DFAST_QC completed!
[2024-01-24 15:11:35,556] [INFO] Total running time: 0h1m40s