[2023-03-15 13:20:53,690] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:53,690] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:53,690] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f38928f-4810-42b6-9295-140803d5455d/dqc_reference
[2023-03-15 13:20:54,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:54,863] [INFO] Task started: Prodigal
[2023-03-15 13:20:54,863] [INFO] Running command: cat /var/lib/cwl/stg5715f3fb-be61-4753-a7bd-4a4541e01d34/OceanDNA-b30569.fa | prodigal -d OceanDNA-b30569/cds.fna -a OceanDNA-b30569/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:10,902] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:10,902] [INFO] Task started: HMMsearch
[2023-03-15 13:21:10,902] [INFO] Running command: hmmsearch --tblout OceanDNA-b30569/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f38928f-4810-42b6-9295-140803d5455d/dqc_reference/reference_markers.hmm OceanDNA-b30569/protein.faa > /dev/null
[2023-03-15 13:21:11,211] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:11,211] [INFO] Found 6/6 markers.
[2023-03-15 13:21:11,236] [INFO] Query marker FASTA was written to OceanDNA-b30569/markers.fasta
[2023-03-15 13:21:11,237] [INFO] Task started: Blastn
[2023-03-15 13:21:11,237] [INFO] Running command: blastn -query OceanDNA-b30569/markers.fasta -db /var/lib/cwl/stg1f38928f-4810-42b6-9295-140803d5455d/dqc_reference/reference_markers.fasta -out OceanDNA-b30569/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:11,930] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:11,932] [INFO] Selected 37 target genomes.
[2023-03-15 13:21:11,932] [INFO] Target genome list was writen to OceanDNA-b30569/target_genomes.txt
[2023-03-15 13:21:11,956] [INFO] Task started: fastANI
[2023-03-15 13:21:11,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg5715f3fb-be61-4753-a7bd-4a4541e01d34/OceanDNA-b30569.fa --refList OceanDNA-b30569/target_genomes.txt --output OceanDNA-b30569/fastani_result.tsv --threads 1
[2023-03-15 13:21:36,654] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:36,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f38928f-4810-42b6-9295-140803d5455d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:36,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f38928f-4810-42b6-9295-140803d5455d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:36,673] [INFO] Found 35 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 13:21:36,673] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 13:21:36,673] [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
Thalassococcus halodurans	strain=DSM 26915	GCA_900108225.1	373675	373675	type	True	95.2681	767	809	95	conclusive
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	77.6297	155	809	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	77.6169	155	809	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	77.5848	180	809	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.5029	95	809	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.3842	190	809	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.3209	164	809	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.2964	146	809	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	77.2413	192	809	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.2058	133	809	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.177	218	809	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	77.1628	193	809	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.1613	221	809	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	77.08	180	809	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.052	195	809	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	76.969	156	809	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	76.969	167	809	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	76.9617	167	809	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	76.9601	168	809	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	76.7919	133	809	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	76.7798	135	809	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	76.7373	181	809	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	76.6398	151	809	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	76.611	133	809	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.539	162	809	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	76.5182	128	809	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	76.4712	142	809	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	76.4049	116	809	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	76.3678	117	809	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	76.3496	85	809	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.2803	88	809	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.1355	83	809	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	76.056	84	809	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	75.9817	125	809	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	75.774	77	809	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:36,674] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30569/tc_result.tsv
[2023-03-15 13:21:36,674] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:36,674] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:36,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f38928f-4810-42b6-9295-140803d5455d/dqc_reference/checkm_data
[2023-03-15 13:21:36,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:36,680] [INFO] Task started: CheckM
[2023-03-15 13:21:36,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30569/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30569/checkm_input OceanDNA-b30569/checkm_result
[2023-03-15 13:22:19,910] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:19,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.63%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:19,913] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:19,914] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:19,914] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30569/markers.fasta)
[2023-03-15 13:22:19,914] [INFO] Task started: Blastn
[2023-03-15 13:22:19,914] [INFO] Running command: blastn -query OceanDNA-b30569/markers.fasta -db /var/lib/cwl/stg1f38928f-4810-42b6-9295-140803d5455d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30569/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:20,909] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:20,910] [INFO] Selected 36 target genomes.
[2023-03-15 13:22:20,911] [INFO] Target genome list was writen to OceanDNA-b30569/target_genomes_gtdb.txt
[2023-03-15 13:22:21,000] [INFO] Task started: fastANI
[2023-03-15 13:22:21,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg5715f3fb-be61-4753-a7bd-4a4541e01d34/OceanDNA-b30569.fa --refList OceanDNA-b30569/target_genomes_gtdb.txt --output OceanDNA-b30569/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:47,041] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:47,062] [INFO] Found 36 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:22:47,063] [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_900108225.1	s__Thalassococcus halodurans	95.2681	767	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassococcus	95.0	96.13	96.13	0.95	0.95	2	conclusive
GCF_900172225.1	s__Ruegeria_E litorea	77.3209	164	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	77.2723	235	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	77.2207	221	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	77.2058	133	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	77.2007	161	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_900101505.1	s__Mameliella alba	77.177	218	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCA_016806125.1	s__AWRV01 sp000504185	77.1746	185	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.1706	117	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	77.1582	146	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	77.1505	174	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	77.081	182	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_017743935.1	s__Ruegeria_E sp017743935	77.0709	174	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959925.1	s__Pseudooceanicola onchidii	77.0691	180	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.064	194	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	77.0574	177	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143635.1	s__FREY01 sp900143635	77.0494	164	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__FREY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	77.0276	176	809	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_001038505.1	s__Puniceibacterium sp001038505	77.0223	181	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	77.0124	204	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_013032855.1	s__Ruegeria arenilitoris	76.9972	183	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_002814095.1	s__Sagittula sp002814095	76.9949	192	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001258055.1	s__Phaeobacter italicus	76.9697	155	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCF_014196795.1	s__Sagittula marina	76.9617	167	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458415.1	s__Epibacterium multivorans	76.9601	168	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCA_014872815.1	s__Shimia sp014872815	76.9288	135	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	97.10	97.10	0.91	0.91	2	-
GCF_014884385.1	s__Pseudophaeobacter_A sp014884385	76.8866	153	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	99.80	99.80	0.96	0.96	2	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.8813	166	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	76.8706	179	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.832	172	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001975705.1	s__Salipiger abyssi	76.7969	175	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	76.7462	135	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002407245.1	s__Phaeobacter piscinae	76.611	133	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	76.4049	116	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_014196805.1	s__Sulfitobacter undariae	76.056	84	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	75.8566	101	809	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:47,063] [INFO] GTDB search result was written to OceanDNA-b30569/result_gtdb.tsv
[2023-03-15 13:22:47,064] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:47,069] [INFO] DFAST_QC result json was written to OceanDNA-b30569/dqc_result.json
[2023-03-15 13:22:47,069] [INFO] DFAST_QC completed!
[2023-03-15 13:22:47,069] [INFO] Total running time: 0h1m53s