[2023-03-15 05:43:38,816] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:43:38,817] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:43:38,817] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4f3ab19-705b-4982-a861-7998c73cd261/dqc_reference
[2023-03-15 05:43:39,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:43:39,916] [INFO] Task started: Prodigal
[2023-03-15 05:43:39,916] [INFO] Running command: cat /var/lib/cwl/stg3f674a1c-b592-4b53-bda6-b07ea2c2cfeb/OceanDNA-b30165.fa | prodigal -d OceanDNA-b30165/cds.fna -a OceanDNA-b30165/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:43:56,030] [INFO] Task succeeded: Prodigal
[2023-03-15 05:43:56,030] [INFO] Task started: HMMsearch
[2023-03-15 05:43:56,030] [INFO] Running command: hmmsearch --tblout OceanDNA-b30165/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4f3ab19-705b-4982-a861-7998c73cd261/dqc_reference/reference_markers.hmm OceanDNA-b30165/protein.faa > /dev/null
[2023-03-15 05:43:56,214] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:43:56,215] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3f674a1c-b592-4b53-bda6-b07ea2c2cfeb/OceanDNA-b30165.fa]
[2023-03-15 05:43:56,298] [INFO] Query marker FASTA was written to OceanDNA-b30165/markers.fasta
[2023-03-15 05:43:56,299] [INFO] Task started: Blastn
[2023-03-15 05:43:56,299] [INFO] Running command: blastn -query OceanDNA-b30165/markers.fasta -db /var/lib/cwl/stgd4f3ab19-705b-4982-a861-7998c73cd261/dqc_reference/reference_markers.fasta -out OceanDNA-b30165/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:43:56,855] [INFO] Task succeeded: Blastn
[2023-03-15 05:43:56,876] [INFO] Selected 29 target genomes.
[2023-03-15 05:43:56,876] [INFO] Target genome list was writen to OceanDNA-b30165/target_genomes.txt
[2023-03-15 05:43:56,891] [INFO] Task started: fastANI
[2023-03-15 05:43:56,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f674a1c-b592-4b53-bda6-b07ea2c2cfeb/OceanDNA-b30165.fa --refList OceanDNA-b30165/target_genomes.txt --output OceanDNA-b30165/fastani_result.tsv --threads 1
[2023-03-15 05:44:14,054] [INFO] Task succeeded: fastANI
[2023-03-15 05:44:14,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4f3ab19-705b-4982-a861-7998c73cd261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:44:14,055] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4f3ab19-705b-4982-a861-7998c73cd261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:44:14,070] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:44:14,070] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:44:14,071] [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
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.1743	185	861	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	77.1551	189	861	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	76.7701	182	861	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.7405	106	861	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.6983	117	861	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	76.6837	116	861	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	76.6609	116	861	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.6411	129	861	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.526	97	861	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.4615	119	861	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	76.3506	115	861	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.2863	144	861	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.1562	74	861	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.1198	93	861	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.0843	112	861	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.0742	111	861	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	76.0721	95	861	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.0308	86	861	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	75.9952	83	861	95	below_threshold
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	75.9943	71	861	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	75.9933	87	861	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	75.9857	117	861	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	75.9794	93	861	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	75.9594	76	861	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	75.9594	76	861	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	75.9471	89	861	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	75.914	92	861	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	75.8138	83	861	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	75.7848	74	861	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:44:14,071] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30165/tc_result.tsv
[2023-03-15 05:44:14,081] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:44:14,081] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:44:14,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4f3ab19-705b-4982-a861-7998c73cd261/dqc_reference/checkm_data
[2023-03-15 05:44:14,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:44:14,089] [INFO] Task started: CheckM
[2023-03-15 05:44:14,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30165/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30165/checkm_input OceanDNA-b30165/checkm_result
[2023-03-15 05:44:56,680] [INFO] Task succeeded: CheckM
[2023-03-15 05:44:56,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:44:56,700] [INFO] ===== Completeness check finished =====
[2023-03-15 05:44:56,700] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:44:56,700] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30165/markers.fasta)
[2023-03-15 05:44:56,701] [INFO] Task started: Blastn
[2023-03-15 05:44:56,701] [INFO] Running command: blastn -query OceanDNA-b30165/markers.fasta -db /var/lib/cwl/stgd4f3ab19-705b-4982-a861-7998c73cd261/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30165/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:44:57,481] [INFO] Task succeeded: Blastn
[2023-03-15 05:44:57,482] [INFO] Selected 27 target genomes.
[2023-03-15 05:44:57,482] [INFO] Target genome list was writen to OceanDNA-b30165/target_genomes_gtdb.txt
[2023-03-15 05:44:57,512] [INFO] Task started: fastANI
[2023-03-15 05:44:57,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f674a1c-b592-4b53-bda6-b07ea2c2cfeb/OceanDNA-b30165.fa --refList OceanDNA-b30165/target_genomes_gtdb.txt --output OceanDNA-b30165/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:45:14,105] [INFO] Task succeeded: fastANI
[2023-03-15 05:45:14,120] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:45:14,120] [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_013002465.1	s__JABDJO01 sp013002465	77.5657	260	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	76.8636	146	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	76.7701	182	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	76.7634	125	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	76.6609	116	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	76.6414	130	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013042605.1	s__IMCC34051 sp013042605	76.544	131	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
GCF_002300555.1	s__Salipiger sp002300555	76.4764	85	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	76.4506	110	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	76.3775	125	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003075.1	s__IMCC34051 sp013003075	76.3364	98	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260265.1	s__Roseovarius sp003260265	76.3115	105	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014075275.1	s__Boseongicola sp014075275	76.2633	91	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.87	99.87	0.99	0.99	2	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	76.2477	88	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017743995.1	s__Ruegeria sp017743995	76.2428	98	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003245.1	s__JABDJX01 sp013003245	76.2392	136	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643905.1	s__Marivita sp017643905	76.1965	102	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	76.1911	71	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	76.1541	121	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.1138	110	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_903914075.1	s__Ruegeria sp903914075	76.0902	72	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.16	95.09	0.87	0.84	7	-
GCF_000737065.1	s__Thioclava atlantica	76.0721	95	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	76.0657	69	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_900110425.1	s__Salinihabitans flavidus	76.0226	94	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salinihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	76.0137	87	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003254295.1	s__Rhodobacter capsulatus	75.9392	88	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.61	98.47	0.97	0.92	5	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	75.914	92	861	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:45:14,162] [INFO] GTDB search result was written to OceanDNA-b30165/result_gtdb.tsv
[2023-03-15 05:45:14,163] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:45:14,166] [INFO] DFAST_QC result json was written to OceanDNA-b30165/dqc_result.json
[2023-03-15 05:45:14,166] [INFO] DFAST_QC completed!
[2023-03-15 05:45:14,166] [INFO] Total running time: 0h1m35s