[2023-03-19 00:33:19,040] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,040] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ce7e877-8b91-4244-a1c4-e342902dab4f/dqc_reference
[2023-03-19 00:33:20,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,227] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,227] [INFO] Running command: cat /var/lib/cwl/stge8504337-2789-4add-8508-481468b07c60/OceanDNA-b27586.fa | prodigal -d OceanDNA-b27586/cds.fna -a OceanDNA-b27586/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:39,512] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:39,512] [INFO] Task started: HMMsearch
[2023-03-19 00:33:39,513] [INFO] Running command: hmmsearch --tblout OceanDNA-b27586/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ce7e877-8b91-4244-a1c4-e342902dab4f/dqc_reference/reference_markers.hmm OceanDNA-b27586/protein.faa > /dev/null
[2023-03-19 00:33:39,759] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:39,759] [INFO] Found 6/6 markers.
[2023-03-19 00:33:39,782] [INFO] Query marker FASTA was written to OceanDNA-b27586/markers.fasta
[2023-03-19 00:33:39,783] [INFO] Task started: Blastn
[2023-03-19 00:33:39,784] [INFO] Running command: blastn -query OceanDNA-b27586/markers.fasta -db /var/lib/cwl/stg3ce7e877-8b91-4244-a1c4-e342902dab4f/dqc_reference/reference_markers.fasta -out OceanDNA-b27586/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:40,530] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:40,531] [INFO] Selected 30 target genomes.
[2023-03-19 00:33:40,532] [INFO] Target genome list was writen to OceanDNA-b27586/target_genomes.txt
[2023-03-19 00:33:40,557] [INFO] Task started: fastANI
[2023-03-19 00:33:40,557] [INFO] Running command: fastANI --query /var/lib/cwl/stge8504337-2789-4add-8508-481468b07c60/OceanDNA-b27586.fa --refList OceanDNA-b27586/target_genomes.txt --output OceanDNA-b27586/fastani_result.tsv --threads 1
[2023-03-19 00:34:00,007] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:00,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ce7e877-8b91-4244-a1c4-e342902dab4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:34:00,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ce7e877-8b91-4244-a1c4-e342902dab4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:34:00,033] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:34:00,033] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:34:00,034] [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	76.9015	245	919	95	below_threshold
Paracoccus thiocyanatus	strain=ATCC 700171	GCA_900156255.1	34006	34006	type	True	76.8568	182	919	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	76.7613	199	919	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	76.7157	196	919	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	76.694	197	919	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.6699	202	919	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.6258	214	919	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	76.6091	205	919	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	76.5853	188	919	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	76.5142	161	919	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	76.483	178	919	95	below_threshold
Paracoccus laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	76.4707	163	919	95	below_threshold
Qingshengfaniella alkalisoli	strain=LN3S51	GCA_007855645.1	2599296	2599296	type	True	76.4696	82	919	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.4595	195	919	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	76.4573	181	919	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	76.4376	213	919	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	76.4081	208	919	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.3928	151	919	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	76.3678	185	919	95	below_threshold
Rhodovulum bhavnagarense	strain=DSM 24766	GCA_004343505.1	992286	992286	type	True	76.3227	145	919	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	76.3222	126	919	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.2549	192	919	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	75.9961	138	919	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	75.993	138	919	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.9728	148	919	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	75.9559	140	919	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	75.9373	105	919	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.8612	123	919	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	75.7433	107	919	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	75.6936	71	919	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:34:00,034] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27586/tc_result.tsv
[2023-03-19 00:34:00,035] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:34:00,035] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:34:00,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ce7e877-8b91-4244-a1c4-e342902dab4f/dqc_reference/checkm_data
[2023-03-19 00:34:00,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:34:00,052] [INFO] Task started: CheckM
[2023-03-19 00:34:00,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27586/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27586/checkm_input OceanDNA-b27586/checkm_result
[2023-03-19 00:34:49,401] [INFO] Task succeeded: CheckM
[2023-03-19 00:34:49,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:34:49,409] [INFO] ===== Completeness check finished =====
[2023-03-19 00:34:49,409] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:34:49,409] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27586/markers.fasta)
[2023-03-19 00:34:49,410] [INFO] Task started: Blastn
[2023-03-19 00:34:49,410] [INFO] Running command: blastn -query OceanDNA-b27586/markers.fasta -db /var/lib/cwl/stg3ce7e877-8b91-4244-a1c4-e342902dab4f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27586/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:34:50,734] [INFO] Task succeeded: Blastn
[2023-03-19 00:34:50,737] [INFO] Selected 34 target genomes.
[2023-03-19 00:34:50,737] [INFO] Target genome list was writen to OceanDNA-b27586/target_genomes_gtdb.txt
[2023-03-19 00:34:50,862] [INFO] Task started: fastANI
[2023-03-19 00:34:50,862] [INFO] Running command: fastANI --query /var/lib/cwl/stge8504337-2789-4add-8508-481468b07c60/OceanDNA-b27586.fa --refList OceanDNA-b27586/target_genomes_gtdb.txt --output OceanDNA-b27586/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:35:11,143] [INFO] Task succeeded: fastANI
[2023-03-19 00:35:11,161] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:35:11,162] [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_009380135.2	s__Fertoeibacter niger	76.9079	248	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	76.9006	236	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015485375.1	s__UBA3077 sp015485375	76.8879	137	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3077	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156255.1	s__Paracoccus thiocyanatus	76.8459	183	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
GCF_009833495.1	s__Oceanomicrobium pacificus	76.7613	199	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120685.1	s__Pararhodobacter sp007120685	76.7445	141	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.30	99.30	0.84	0.84	2	-
GCA_016936395.1	s__ETT8 sp016936395	76.7444	178	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748285.1	s__Profundibacter sp002748285	76.7045	153	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	76.6507	188	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	76.6481	178	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.5266	210	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762325.1	s__Roseovarius faecimaris	76.4978	178	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278325.1	s__JADQCB01 sp016278325	76.4822	173	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.4664	178	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCA_007118445.1	s__Roseinatronobacter sp007118445	76.457	149	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.03	98.90	0.77	0.72	3	-
GCF_014640115.1	s__Muriiphilus lacisalsi	76.4302	152	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142935.1	s__Rhodovulum sp900142935	76.4129	146	919	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	76.4091	162	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003265325.1	s__Halovulum sediminis	76.4084	182	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688285.1	s__Rhodophyticola porphyridii	76.4022	150	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	76.3947	159	919	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	76.3614	163	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	99.99	99.99	0.99	0.98	3	-
GCF_004343505.1	s__Rhodovulum bhavnagarense	76.3449	142	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032275.1	s__JAAURK01 sp012032275	76.3375	140	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAURK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487335.1	s__S012-89 sp015487335	76.3129	152	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__S012-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121115.1	s__PUOA01 sp007121115	76.3046	143	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	99.30	99.15	0.84	0.78	4	-
GCF_001720585.1	s__Cereibacter_A johrii	76.3041	121	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCA_015689745.1	s__Roseicyclus sp015689745	76.2038	154	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	76.194	185	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151335.1	s__UBA5972 sp013151335	76.1692	104	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007827395.1	s__Rhodophyticola sp007827395	76.1621	140	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	95.40	95.35	0.93	0.92	216	-
GCF_900177545.1	s__Muriiphilus sp900177545	76.162	158	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012905.2	s__Cereibacter_A sphaeroides	75.9926	138	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	-
GCF_014196795.1	s__Sagittula marina	75.7433	107	919	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:35:11,165] [INFO] GTDB search result was written to OceanDNA-b27586/result_gtdb.tsv
[2023-03-19 00:35:11,166] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:35:11,171] [INFO] DFAST_QC result json was written to OceanDNA-b27586/dqc_result.json
[2023-03-19 00:35:11,172] [INFO] DFAST_QC completed!
[2023-03-19 00:35:11,172] [INFO] Total running time: 0h1m52s