[2023-03-15 22:15:27,637] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:15:27,638] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:15:27,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg62e137cb-3e18-474c-81f5-eb0442cce913/dqc_reference
[2023-03-15 22:15:29,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:15:29,361] [INFO] Task started: Prodigal
[2023-03-15 22:15:29,361] [INFO] Running command: cat /var/lib/cwl/stg82dfb180-a6c9-4763-8395-65bef5b354df/OceanDNA-b31957.fa | prodigal -d OceanDNA-b31957/cds.fna -a OceanDNA-b31957/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:15:45,326] [INFO] Task succeeded: Prodigal
[2023-03-15 22:15:45,326] [INFO] Task started: HMMsearch
[2023-03-15 22:15:45,326] [INFO] Running command: hmmsearch --tblout OceanDNA-b31957/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62e137cb-3e18-474c-81f5-eb0442cce913/dqc_reference/reference_markers.hmm OceanDNA-b31957/protein.faa > /dev/null
[2023-03-15 22:15:45,502] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:15:45,502] [INFO] Found 6/6 markers.
[2023-03-15 22:15:45,540] [INFO] Query marker FASTA was written to OceanDNA-b31957/markers.fasta
[2023-03-15 22:15:45,540] [INFO] Task started: Blastn
[2023-03-15 22:15:45,540] [INFO] Running command: blastn -query OceanDNA-b31957/markers.fasta -db /var/lib/cwl/stg62e137cb-3e18-474c-81f5-eb0442cce913/dqc_reference/reference_markers.fasta -out OceanDNA-b31957/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:15:46,245] [INFO] Task succeeded: Blastn
[2023-03-15 22:15:46,249] [INFO] Selected 25 target genomes.
[2023-03-15 22:15:46,249] [INFO] Target genome list was writen to OceanDNA-b31957/target_genomes.txt
[2023-03-15 22:15:46,264] [INFO] Task started: fastANI
[2023-03-15 22:15:46,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg82dfb180-a6c9-4763-8395-65bef5b354df/OceanDNA-b31957.fa --refList OceanDNA-b31957/target_genomes.txt --output OceanDNA-b31957/fastani_result.tsv --threads 1
[2023-03-15 22:16:00,995] [INFO] Task succeeded: fastANI
[2023-03-15 22:16:00,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62e137cb-3e18-474c-81f5-eb0442cce913/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:16:00,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62e137cb-3e18-474c-81f5-eb0442cce913/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:16:01,010] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:16:01,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:16:01,011] [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
Aurantiacibacter xanthus	strain=CCTCC AB 2015396	GCA_003584015.1	1784712	1784712	type	True	79.134	380	826	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	79.0964	270	826	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.8452	287	826	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.7693	330	826	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.7127	351	826	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.6891	287	826	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.6681	356	826	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.5487	319	826	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.5428	309	826	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.5385	303	826	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.5291	315	826	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	78.5276	343	826	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	78.4469	301	826	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.3352	227	826	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.3107	276	826	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	78.2886	360	826	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.2745	262	826	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.2521	308	826	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.2507	285	826	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.2117	298	826	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.1806	286	826	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.1361	281	826	95	below_threshold
Aurantiacibacter rhizosphaerae	strain=GH3-10	GCA_009807005.1	2691582	2691582	type	True	78.0883	331	826	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	78.0234	303	826	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	77.7466	200	826	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:16:01,013] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31957/tc_result.tsv
[2023-03-15 22:16:01,018] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:16:01,018] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:16:01,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62e137cb-3e18-474c-81f5-eb0442cce913/dqc_reference/checkm_data
[2023-03-15 22:16:01,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:16:01,025] [INFO] Task started: CheckM
[2023-03-15 22:16:01,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31957/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31957/checkm_input OceanDNA-b31957/checkm_result
[2023-03-15 22:16:42,676] [INFO] Task succeeded: CheckM
[2023-03-15 22:16:42,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:16:42,746] [INFO] ===== Completeness check finished =====
[2023-03-15 22:16:42,746] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:16:42,746] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31957/markers.fasta)
[2023-03-15 22:16:42,747] [INFO] Task started: Blastn
[2023-03-15 22:16:42,747] [INFO] Running command: blastn -query OceanDNA-b31957/markers.fasta -db /var/lib/cwl/stg62e137cb-3e18-474c-81f5-eb0442cce913/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31957/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:16:43,912] [INFO] Task succeeded: Blastn
[2023-03-15 22:16:43,918] [INFO] Selected 26 target genomes.
[2023-03-15 22:16:43,918] [INFO] Target genome list was writen to OceanDNA-b31957/target_genomes_gtdb.txt
[2023-03-15 22:16:44,008] [INFO] Task started: fastANI
[2023-03-15 22:16:44,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg82dfb180-a6c9-4763-8395-65bef5b354df/OceanDNA-b31957.fa --refList OceanDNA-b31957/target_genomes_gtdb.txt --output OceanDNA-b31957/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:16:58,809] [INFO] Task succeeded: fastANI
[2023-03-15 22:16:58,824] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:16:58,824] [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
GCA_002341345.1	s__Alteraurantiacibacter sp002341345	82.4389	480	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	79.4368	445	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584015.1	s__Alteraurantiacibacter xanthus	79.134	380	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827405.1	s__Alteraurantiacibacter aestuarii	79.0964	270	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359685.1	s__Croceibacterium sp014359685	79.0124	251	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.7969	329	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	78.748	364	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605195.1	s__Alteraurantiacibacter odishensis	78.7287	349	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	78.6893	351	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434915.1	s__Alteraurantiacibacter suaedae	78.6681	356	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	78.6255	341	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	78.583	313	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.5634	326	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	78.533	321	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.4949	305	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605475.1	s__Alteraurantiacibacter aquimixticola_A	78.4563	325	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105095.1	s__Erythrobacter sp900105095	78.4539	326	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011320115.1	s__Croceibacterium segetis	78.422	287	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828065.1	s__Croceibacterium soli	78.3937	310	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683845.1	s__Croceibacterium sp001683845	78.2629	303	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.2404	295	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028625.1	s__Pelagerythrobacter marensis	78.2379	286	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009807005.1	s__Alteraurantiacibacter rhizosphaerae	78.1054	330	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	78.0091	302	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819685.1	s__Qipengyuania sp018819685	77.7031	209	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	99.48	99.48	0.85	0.85	2	-
GCA_018240895.1	s__Novosphingobium sp018240895	77.2482	185	826	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:16:58,827] [INFO] GTDB search result was written to OceanDNA-b31957/result_gtdb.tsv
[2023-03-15 22:16:58,831] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:16:58,837] [INFO] DFAST_QC result json was written to OceanDNA-b31957/dqc_result.json
[2023-03-15 22:16:58,837] [INFO] DFAST_QC completed!
[2023-03-15 22:16:58,837] [INFO] Total running time: 0h1m31s