[2023-03-19 03:50:09,666] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:09,666] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:09,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b94e4a2-e7b2-41df-9521-14c31f485385/dqc_reference
[2023-03-19 03:50:10,747] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:10,747] [INFO] Task started: Prodigal
[2023-03-19 03:50:10,747] [INFO] Running command: cat /var/lib/cwl/stg98ce7b8e-4d64-4b97-b530-ccf2bb0fe8b7/OceanDNA-b27568.fa | prodigal -d OceanDNA-b27568/cds.fna -a OceanDNA-b27568/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:35,520] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:35,521] [INFO] Task started: HMMsearch
[2023-03-19 03:50:35,521] [INFO] Running command: hmmsearch --tblout OceanDNA-b27568/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b94e4a2-e7b2-41df-9521-14c31f485385/dqc_reference/reference_markers.hmm OceanDNA-b27568/protein.faa > /dev/null
[2023-03-19 03:50:35,776] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:35,777] [INFO] Found 6/6 markers.
[2023-03-19 03:50:35,806] [INFO] Query marker FASTA was written to OceanDNA-b27568/markers.fasta
[2023-03-19 03:50:35,806] [INFO] Task started: Blastn
[2023-03-19 03:50:35,806] [INFO] Running command: blastn -query OceanDNA-b27568/markers.fasta -db /var/lib/cwl/stg6b94e4a2-e7b2-41df-9521-14c31f485385/dqc_reference/reference_markers.fasta -out OceanDNA-b27568/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:36,490] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:36,491] [INFO] Selected 34 target genomes.
[2023-03-19 03:50:36,491] [INFO] Target genome list was writen to OceanDNA-b27568/target_genomes.txt
[2023-03-19 03:50:36,509] [INFO] Task started: fastANI
[2023-03-19 03:50:36,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg98ce7b8e-4d64-4b97-b530-ccf2bb0fe8b7/OceanDNA-b27568.fa --refList OceanDNA-b27568/target_genomes.txt --output OceanDNA-b27568/fastani_result.tsv --threads 1
[2023-03-19 03:50:58,374] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:58,374] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b94e4a2-e7b2-41df-9521-14c31f485385/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:58,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b94e4a2-e7b2-41df-9521-14c31f485385/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:58,392] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:58,392] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:50:58,392] [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
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.7318	275	1253	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.5372	171	1253	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.4542	172	1253	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.2788	251	1253	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.2427	213	1253	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.2169	223	1253	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.1907	218	1253	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.1295	236	1253	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.103	202	1253	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.1007	266	1253	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.09	221	1253	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.0818	161	1253	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.0629	206	1253	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	77.0588	162	1253	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.057	210	1253	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	77.0373	209	1253	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.0346	276	1253	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.0019	226	1253	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.9658	249	1253	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.9417	166	1253	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	76.9342	236	1253	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.8867	163	1253	95	below_threshold
Ruegeria profundi	strain=ZGT108	GCA_001507545.1	1685378	1685378	type	True	76.8784	174	1253	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.7601	99	1253	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	76.692	212	1253	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	76.6819	212	1253	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.6779	191	1253	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.6694	143	1253	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	76.6606	172	1253	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.2644	117	1253	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.2122	96	1253	95	below_threshold
Paracoccus halophilus	strain=CGMCC 1.6117	GCA_900111785.1	376733	376733	type	True	76.1589	115	1253	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.1074	126	1253	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	76.1006	115	1253	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:50:58,392] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27568/tc_result.tsv
[2023-03-19 03:50:58,392] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:58,392] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:58,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b94e4a2-e7b2-41df-9521-14c31f485385/dqc_reference/checkm_data
[2023-03-19 03:50:58,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:58,398] [INFO] Task started: CheckM
[2023-03-19 03:50:58,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27568/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27568/checkm_input OceanDNA-b27568/checkm_result
[2023-03-19 03:52:00,817] [INFO] Task succeeded: CheckM
[2023-03-19 03:52:00,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:52:00,820] [INFO] ===== Completeness check finished =====
[2023-03-19 03:52:00,821] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:52:00,821] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27568/markers.fasta)
[2023-03-19 03:52:00,821] [INFO] Task started: Blastn
[2023-03-19 03:52:00,821] [INFO] Running command: blastn -query OceanDNA-b27568/markers.fasta -db /var/lib/cwl/stg6b94e4a2-e7b2-41df-9521-14c31f485385/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27568/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:52:01,906] [INFO] Task succeeded: Blastn
[2023-03-19 03:52:01,907] [INFO] Selected 27 target genomes.
[2023-03-19 03:52:01,907] [INFO] Target genome list was writen to OceanDNA-b27568/target_genomes_gtdb.txt
[2023-03-19 03:52:01,927] [INFO] Task started: fastANI
[2023-03-19 03:52:01,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg98ce7b8e-4d64-4b97-b530-ccf2bb0fe8b7/OceanDNA-b27568.fa --refList OceanDNA-b27568/target_genomes_gtdb.txt --output OceanDNA-b27568/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:52:21,866] [INFO] Task succeeded: fastANI
[2023-03-19 03:52:21,881] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:52:21,882] [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_013214665.1	s__JABSSA01 sp013214665	99.3741	1041	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001262635.1	s__Aestuariivita boseongensis	77.7318	275	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.5656	272	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	77.3997	272	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	77.2962	227	1253	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_004358185.1	s__Antarcticimicrobium luteum	77.2169	223	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743995.1	s__Ruegeria sp017743995	77.1885	217	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.1295	236	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031245.1	s__Ruegeria lacuscaerulensis_C	77.1241	199	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	77.0451	211	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.0439	275	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_001650875.1	s__Sulfitobacter sp001650875	77.0325	244	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	77.0111	208	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.0037	259	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000473145.1	s__Leisingera daeponensis	76.9911	227	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_900129345.1	s__Ruegeria intermedia	76.9658	249	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811755.1	s__Roseobacter cerasinus	76.9337	237	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032005.1	s__Ruegeria atlantica_A	76.9274	202	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.11	97.00	0.94	0.90	12	-
GCF_000813965.1	s__Leisingera sp000813965	76.8968	205	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285415.1	s__Actibacterium pelagium	76.8867	163	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009363615.1	s__Ruegeria sp009363615	76.8183	230	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
GCF_003352065.1	s__Sulfitobacter sp003352065	76.8032	198	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	76.6842	214	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014045.1	s__Roseobacter denitrificans	76.6819	212	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900129875.1	s__Marivita hallyeonensis	76.6606	172	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	76.651	203	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	76.4579	197	1253	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:52:21,882] [INFO] GTDB search result was written to OceanDNA-b27568/result_gtdb.tsv
[2023-03-19 03:52:21,882] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:52:21,885] [INFO] DFAST_QC result json was written to OceanDNA-b27568/dqc_result.json
[2023-03-19 03:52:21,885] [INFO] DFAST_QC completed!
[2023-03-19 03:52:21,885] [INFO] Total running time: 0h2m12s