[2023-03-15 17:12:23,171] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:12:23,174] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:12:23,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f5ecb80-6a2d-4388-adc7-ad6040db65f6/dqc_reference
[2023-03-15 17:12:29,488] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:12:29,489] [INFO] Task started: Prodigal
[2023-03-15 17:12:29,489] [INFO] Running command: cat /var/lib/cwl/stgb2a5dbcf-0553-45eb-bb0e-b8030abda079/OceanDNA-b6632.fa | prodigal -d OceanDNA-b6632/cds.fna -a OceanDNA-b6632/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:12:47,841] [INFO] Task succeeded: Prodigal
[2023-03-15 17:12:47,841] [INFO] Task started: HMMsearch
[2023-03-15 17:12:47,841] [INFO] Running command: hmmsearch --tblout OceanDNA-b6632/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f5ecb80-6a2d-4388-adc7-ad6040db65f6/dqc_reference/reference_markers.hmm OceanDNA-b6632/protein.faa > /dev/null
[2023-03-15 17:12:48,194] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:12:48,194] [INFO] Found 6/6 markers.
[2023-03-15 17:12:48,249] [INFO] Query marker FASTA was written to OceanDNA-b6632/markers.fasta
[2023-03-15 17:12:48,250] [INFO] Task started: Blastn
[2023-03-15 17:12:48,250] [INFO] Running command: blastn -query OceanDNA-b6632/markers.fasta -db /var/lib/cwl/stg7f5ecb80-6a2d-4388-adc7-ad6040db65f6/dqc_reference/reference_markers.fasta -out OceanDNA-b6632/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:12:52,551] [INFO] Task succeeded: Blastn
[2023-03-15 17:12:52,555] [INFO] Selected 26 target genomes.
[2023-03-15 17:12:52,555] [INFO] Target genome list was writen to OceanDNA-b6632/target_genomes.txt
[2023-03-15 17:12:52,614] [INFO] Task started: fastANI
[2023-03-15 17:12:52,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a5dbcf-0553-45eb-bb0e-b8030abda079/OceanDNA-b6632.fa --refList OceanDNA-b6632/target_genomes.txt --output OceanDNA-b6632/fastani_result.tsv --threads 1
[2023-03-15 17:13:08,428] [INFO] Task succeeded: fastANI
[2023-03-15 17:13:08,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f5ecb80-6a2d-4388-adc7-ad6040db65f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:13:08,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f5ecb80-6a2d-4388-adc7-ad6040db65f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:13:08,451] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:13:08,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:13:08,451] [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
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	94.2442	741	858	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.1432	93	858	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.1144	126	858	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.9976	119	858	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	76.9496	88	858	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.9129	125	858	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.8861	99	858	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.8694	187	858	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.8692	185	858	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.8502	58	858	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.7528	76	858	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.7279	70	858	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	76.6244	100	858	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5974	93	858	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	76.5763	101	858	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	76.526	75	858	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.5104	136	858	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.486	69	858	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.4734	125	858	95	below_threshold
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	76.4253	52	858	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	76.4186	70	858	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.1254	70	858	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	75.9265	57	858	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	75.9129	68	858	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	75.904	58	858	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:13:08,453] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6632/tc_result.tsv
[2023-03-15 17:13:08,456] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:13:08,456] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:13:08,456] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f5ecb80-6a2d-4388-adc7-ad6040db65f6/dqc_reference/checkm_data
[2023-03-15 17:13:08,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:13:08,464] [INFO] Task started: CheckM
[2023-03-15 17:13:08,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6632/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6632/checkm_input OceanDNA-b6632/checkm_result
[2023-03-15 17:13:58,605] [INFO] Task succeeded: CheckM
[2023-03-15 17:13:58,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:13:58,680] [INFO] ===== Completeness check finished =====
[2023-03-15 17:13:58,680] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:13:58,680] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6632/markers.fasta)
[2023-03-15 17:13:58,682] [INFO] Task started: Blastn
[2023-03-15 17:13:58,682] [INFO] Running command: blastn -query OceanDNA-b6632/markers.fasta -db /var/lib/cwl/stg7f5ecb80-6a2d-4388-adc7-ad6040db65f6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6632/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:13:59,791] [INFO] Task succeeded: Blastn
[2023-03-15 17:13:59,793] [INFO] Selected 27 target genomes.
[2023-03-15 17:13:59,793] [INFO] Target genome list was writen to OceanDNA-b6632/target_genomes_gtdb.txt
[2023-03-15 17:13:59,843] [INFO] Task started: fastANI
[2023-03-15 17:13:59,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2a5dbcf-0553-45eb-bb0e-b8030abda079/OceanDNA-b6632.fa --refList OceanDNA-b6632/target_genomes_gtdb.txt --output OceanDNA-b6632/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:14:14,418] [INFO] Task succeeded: fastANI
[2023-03-15 17:14:14,433] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:14:14,433] [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_002694465.1	s__IN17 sp002694465	98.1805	806	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	conclusive
GCA_002707025.1	s__IN17 sp002707025	78.3298	254	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCA_002360635.1	s__Marixanthomonas sp002360635	77.4994	144	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCF_003688405.1	s__Ulvibacter antarcticus	77.0954	127	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707745.1	s__Marinirhabdus sp002707745	77.0739	104	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	-
GCF_001641085.1	s__Aequorivita soesokkakensis	77.0123	112	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_002375695.1	s__Aequorivita sp002375695	76.982	130	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCA_013002065.1	s__SMXJ01 sp013002065	76.9685	140	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375495.1	s__Marinirhabdus sp002375495	76.9329	129	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCA_002384055.1	s__BACL21 sp002384055	76.9304	63	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__BACL21	95.0	99.79	99.68	0.93	0.91	4	-
GCF_900102055.1	s__Ulvibacter litoralis	76.8694	187	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_006346335.1	s__Aequorivita sinensis	76.8675	125	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.8588	98	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827225.1	s__SMXJ01 sp009827225	76.7754	115	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489465.1	s__Aequorivita sp900489465	76.7229	139	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	76.5747	94	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	76.5743	104	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440705.1	s__IN17 sp002440705	76.5611	133	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.92	99.92	0.93	0.93	2	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	76.5379	68	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265385.1	s__Aequorivita sublithincola	76.5258	135	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366675.1	s__Xanthomarina sp002366675	76.5037	62	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009014635.1	s__Patiriisocius marinistellae	76.4734	125	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	76.3315	95	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	76.2002	91	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	75.935	67	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	75.9036	100	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCA_905479815.1	s__Psychroserpens sp905479815	75.7496	61	858	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:14:14,436] [INFO] GTDB search result was written to OceanDNA-b6632/result_gtdb.tsv
[2023-03-15 17:14:14,441] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:14:14,445] [INFO] DFAST_QC result json was written to OceanDNA-b6632/dqc_result.json
[2023-03-15 17:14:14,445] [INFO] DFAST_QC completed!
[2023-03-15 17:14:14,446] [INFO] Total running time: 0h1m51s