[2023-03-14 12:38:54,409] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:38:54,409] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:38:54,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg91a684b6-27db-41bc-b185-b77deb4a1f67/dqc_reference
[2023-03-14 12:38:57,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:38:57,146] [INFO] Task started: Prodigal
[2023-03-14 12:38:57,147] [INFO] Running command: cat /var/lib/cwl/stg715315d4-15a6-4d28-88f4-91e694e7372e/OceanDNA-b32011.fa | prodigal -d OceanDNA-b32011/cds.fna -a OceanDNA-b32011/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:39:23,618] [INFO] Task succeeded: Prodigal
[2023-03-14 12:39:23,618] [INFO] Task started: HMMsearch
[2023-03-14 12:39:23,618] [INFO] Running command: hmmsearch --tblout OceanDNA-b32011/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91a684b6-27db-41bc-b185-b77deb4a1f67/dqc_reference/reference_markers.hmm OceanDNA-b32011/protein.faa > /dev/null
[2023-03-14 12:39:23,824] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:39:23,824] [INFO] Found 6/6 markers.
[2023-03-14 12:39:23,848] [INFO] Query marker FASTA was written to OceanDNA-b32011/markers.fasta
[2023-03-14 12:39:23,849] [INFO] Task started: Blastn
[2023-03-14 12:39:23,849] [INFO] Running command: blastn -query OceanDNA-b32011/markers.fasta -db /var/lib/cwl/stg91a684b6-27db-41bc-b185-b77deb4a1f67/dqc_reference/reference_markers.fasta -out OceanDNA-b32011/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:39:24,496] [INFO] Task succeeded: Blastn
[2023-03-14 12:39:24,498] [INFO] Selected 27 target genomes.
[2023-03-14 12:39:24,498] [INFO] Target genome list was writen to OceanDNA-b32011/target_genomes.txt
[2023-03-14 12:39:24,518] [INFO] Task started: fastANI
[2023-03-14 12:39:24,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg715315d4-15a6-4d28-88f4-91e694e7372e/OceanDNA-b32011.fa --refList OceanDNA-b32011/target_genomes.txt --output OceanDNA-b32011/fastani_result.tsv --threads 1
[2023-03-14 12:39:43,635] [INFO] Task succeeded: fastANI
[2023-03-14 12:39:43,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91a684b6-27db-41bc-b185-b77deb4a1f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:39:43,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91a684b6-27db-41bc-b185-b77deb4a1f67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:39:43,655] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:39:43,655] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:39:43,655] [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
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	80.3646	282	1020	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	80.3422	276	1020	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.1291	237	1020	95	below_threshold
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	78.5993	220	1020	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.0254	182	1020	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.8985	161	1020	95	below_threshold
Caenibius tardaugens	strain=NBRC 16725	GCA_000466945.1	169176	169176	type	True	77.784	246	1020	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.7708	141	1020	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.7577	177	1020	95	below_threshold
Caenibius tardaugens	strain=NBRC 16725	GCA_003860345.1	169176	169176	type	True	77.7356	250	1020	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	77.7053	200	1020	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	77.5899	185	1020	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	77.569	185	1020	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	77.5606	195	1020	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	77.4119	160	1020	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	77.3966	167	1020	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	77.3699	197	1020	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	77.2816	209	1020	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	77.2477	174	1020	95	below_threshold
Novosphingobium pokkalii	strain=KCTC 42224	GCA_014652855.1	1770194	1770194	type	True	77.23	210	1020	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	77.2263	231	1020	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	77.1927	149	1020	95	below_threshold
Novosphingobium taihuense	strain=DSM 17507	GCA_014199635.1	260085	260085	type	True	77.1446	183	1020	95	below_threshold
Novosphingobium capsulatum	strain=NBRC 12533	GCA_001598375.1	13688	13688	type	True	77.1332	224	1020	95	below_threshold
Novosphingobium taihuense	strain=CGMCC 1.3432	GCA_007830315.1	260085	260085	type	True	77.1072	184	1020	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.0171	171	1020	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	76.8999	137	1020	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:39:43,660] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32011/tc_result.tsv
[2023-03-14 12:39:43,660] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:39:43,660] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:39:43,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91a684b6-27db-41bc-b185-b77deb4a1f67/dqc_reference/checkm_data
[2023-03-14 12:39:43,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:39:43,692] [INFO] Task started: CheckM
[2023-03-14 12:39:43,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32011/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32011/checkm_input OceanDNA-b32011/checkm_result
[2023-03-14 12:40:41,396] [INFO] Task succeeded: CheckM
[2023-03-14 12:40:41,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:40:41,399] [INFO] ===== Completeness check finished =====
[2023-03-14 12:40:41,399] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:40:41,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32011/markers.fasta)
[2023-03-14 12:40:41,400] [INFO] Task started: Blastn
[2023-03-14 12:40:41,401] [INFO] Running command: blastn -query OceanDNA-b32011/markers.fasta -db /var/lib/cwl/stg91a684b6-27db-41bc-b185-b77deb4a1f67/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32011/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:40:42,578] [INFO] Task succeeded: Blastn
[2023-03-14 12:40:42,579] [INFO] Selected 27 target genomes.
[2023-03-14 12:40:42,579] [INFO] Target genome list was writen to OceanDNA-b32011/target_genomes_gtdb.txt
[2023-03-14 12:40:42,605] [INFO] Task started: fastANI
[2023-03-14 12:40:42,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg715315d4-15a6-4d28-88f4-91e694e7372e/OceanDNA-b32011.fa --refList OceanDNA-b32011/target_genomes_gtdb.txt --output OceanDNA-b32011/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:41:01,450] [INFO] Task succeeded: fastANI
[2023-03-14 12:41:01,473] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:41:01,473] [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_001008165.2	s__Croceibacterium atlanticum	80.3299	284	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827515.1	s__Pelagerythrobacter marinus	79.1282	237	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005145025.1	s__Novosphingobium sp005145025	78.3085	233	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	78.1546	230	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305965.1	s__Caenibius sp001305965	77.7575	279	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898545.1	s__Caenibius sp001898545	77.7526	223	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003860345.1	s__Caenibius tardaugens	77.7356	250	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002870965.1	s__Tsuneonella flava	77.7217	199	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	99.01	98.03	0.92	0.87	3	-
GCF_007570835.1	s__Croceicoccus sediminis	77.6053	184	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828025.1	s__Qipengyuania algicida	77.5766	194	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017987575.1	s__Novosphingobium sp017987575	77.5736	146	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	99.30	99.30	0.83	0.83	2	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	77.5636	206	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	77.5195	235	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_001516125.1	s__Erythrobacter sp001516125	77.5039	159	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001296025.1	s__Erythrobacter sp001296025	77.4659	210	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308255.1	s__Croceibacterium sp001897135	77.4276	220	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001014975.1	s__Novosphingobium sp002336885	77.3918	215	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.66	97.51	0.82	0.80	4	-
GCA_018240895.1	s__Novosphingobium sp018240895	77.3808	184	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958635.1	s__Altericroceibacterium_A xinjiangense	77.3794	181	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altericroceibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002855555.1	s__Novosphingobium sp002855555	77.3154	216	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	77.2957	208	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	77.2928	178	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117425.1	s__Novosphingobium sp900117425	77.2868	182	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.26	96.76	0.88	0.87	3	-
GCF_001625325.1	s__Caenibius estronivorus	77.2474	210	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359685.1	s__Croceibacterium sp014359685	77.1894	126	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598375.1	s__Novosphingobium capsulatum	77.1219	224	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.40	97.25	0.88	0.83	50	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	77.0321	170	1020	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:41:01,474] [INFO] GTDB search result was written to OceanDNA-b32011/result_gtdb.tsv
[2023-03-14 12:41:01,474] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:41:01,481] [INFO] DFAST_QC result json was written to OceanDNA-b32011/dqc_result.json
[2023-03-14 12:41:01,481] [INFO] DFAST_QC completed!
[2023-03-14 12:41:01,482] [INFO] Total running time: 0h2m7s