[2023-03-16 12:37:44,825] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:37:44,825] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:37:44,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg273adfa6-7045-41c5-aa03-ccaef5bc454b/dqc_reference
[2023-03-16 12:37:45,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:37:45,956] [INFO] Task started: Prodigal
[2023-03-16 12:37:45,956] [INFO] Running command: cat /var/lib/cwl/stg959f5815-95e6-49c5-894f-d5a19a543a69/OceanDNA-b27608.fa | prodigal -d OceanDNA-b27608/cds.fna -a OceanDNA-b27608/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:38:07,222] [INFO] Task succeeded: Prodigal
[2023-03-16 12:38:07,222] [INFO] Task started: HMMsearch
[2023-03-16 12:38:07,222] [INFO] Running command: hmmsearch --tblout OceanDNA-b27608/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg273adfa6-7045-41c5-aa03-ccaef5bc454b/dqc_reference/reference_markers.hmm OceanDNA-b27608/protein.faa > /dev/null
[2023-03-16 12:38:07,418] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:38:07,419] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg959f5815-95e6-49c5-894f-d5a19a543a69/OceanDNA-b27608.fa]
[2023-03-16 12:38:07,441] [INFO] Query marker FASTA was written to OceanDNA-b27608/markers.fasta
[2023-03-16 12:38:07,441] [INFO] Task started: Blastn
[2023-03-16 12:38:07,442] [INFO] Running command: blastn -query OceanDNA-b27608/markers.fasta -db /var/lib/cwl/stg273adfa6-7045-41c5-aa03-ccaef5bc454b/dqc_reference/reference_markers.fasta -out OceanDNA-b27608/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:38:08,109] [INFO] Task succeeded: Blastn
[2023-03-16 12:38:08,110] [INFO] Selected 28 target genomes.
[2023-03-16 12:38:08,110] [INFO] Target genome list was writen to OceanDNA-b27608/target_genomes.txt
[2023-03-16 12:38:08,124] [INFO] Task started: fastANI
[2023-03-16 12:38:08,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg959f5815-95e6-49c5-894f-d5a19a543a69/OceanDNA-b27608.fa --refList OceanDNA-b27608/target_genomes.txt --output OceanDNA-b27608/fastani_result.tsv --threads 1
[2023-03-16 12:38:27,091] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:27,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg273adfa6-7045-41c5-aa03-ccaef5bc454b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:38:27,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg273adfa6-7045-41c5-aa03-ccaef5bc454b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:38:27,106] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:38:27,106] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:38:27,106] [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	83.0598	784	1096	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.7712	357	1096	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.7517	370	1096	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.7263	391	1096	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.6979	360	1096	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	77.6098	270	1096	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	77.5527	278	1096	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.5299	330	1096	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.3887	261	1096	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.3655	263	1096	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.3587	312	1096	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.3461	260	1096	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.3248	268	1096	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	77.3192	266	1096	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	77.2691	265	1096	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.2076	296	1096	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	77.1879	280	1096	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.1319	230	1096	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.9534	248	1096	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.7801	214	1096	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	76.6483	126	1096	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.6341	230	1096	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.524	183	1096	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	76.4688	154	1096	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.4249	161	1096	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.2914	131	1096	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:38:27,106] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27608/tc_result.tsv
[2023-03-16 12:38:27,106] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:38:27,106] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:38:27,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg273adfa6-7045-41c5-aa03-ccaef5bc454b/dqc_reference/checkm_data
[2023-03-16 12:38:27,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:38:27,114] [INFO] Task started: CheckM
[2023-03-16 12:38:27,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27608/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27608/checkm_input OceanDNA-b27608/checkm_result
[2023-03-16 12:39:46,444] [INFO] Task succeeded: CheckM
[2023-03-16 12:39:46,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:39:46,448] [INFO] ===== Completeness check finished =====
[2023-03-16 12:39:46,448] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:39:46,448] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27608/markers.fasta)
[2023-03-16 12:39:46,450] [INFO] Task started: Blastn
[2023-03-16 12:39:46,450] [INFO] Running command: blastn -query OceanDNA-b27608/markers.fasta -db /var/lib/cwl/stg273adfa6-7045-41c5-aa03-ccaef5bc454b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27608/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:39:47,571] [INFO] Task succeeded: Blastn
[2023-03-16 12:39:47,572] [INFO] Selected 26 target genomes.
[2023-03-16 12:39:47,573] [INFO] Target genome list was writen to OceanDNA-b27608/target_genomes_gtdb.txt
[2023-03-16 12:39:47,916] [INFO] Task started: fastANI
[2023-03-16 12:39:47,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg959f5815-95e6-49c5-894f-d5a19a543a69/OceanDNA-b27608.fa --refList OceanDNA-b27608/target_genomes_gtdb.txt --output OceanDNA-b27608/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:40:06,974] [INFO] Task succeeded: fastANI
[2023-03-16 12:40:06,989] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:40:06,989] [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_001262635.1	s__Aestuariivita boseongensis	83.0598	784	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401465.1	s__Aestuariivita sp018401465	78.1594	431	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	78.0634	326	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.7671	338	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.7517	370	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.7289	390	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCA_003511785.1	s__UBA7951 sp003511785	77.7039	231	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.6979	360	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	77.6938	342	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000814025.1	s__Tateyamaria sp000814025	77.6573	320	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216475.1	s__GCA-004216475 sp004216475	77.6506	382	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-004216475	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	77.6098	270	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_013031405.1	s__Ruegeria sp013031405	77.5773	378	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	77.5722	303	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_001969365.1	s__Tateyamaria omphalii_A	77.4488	336	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	77.446	284	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_008728195.1	s__Roseovarius indicus	77.3543	264	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900172255.1	s__Roseovarius halotolerans	77.3192	266	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	77.3122	319	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_002917925.1	s__Roseovarius confluentis	77.2702	264	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCA_013214665.1	s__JABSSA01 sp013214665	77.2594	203	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	77.2551	265	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_900142765.1	s__Roseovarius litoreus	77.2165	295	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_001458295.1	s__Ruegeria denitrificans	77.2	228	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814005.1	s__Ruegeria sp000814005	77.1001	222	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172215.1	s__Ruegeria meonggei	77.0983	246	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:40:06,990] [INFO] GTDB search result was written to OceanDNA-b27608/result_gtdb.tsv
[2023-03-16 12:40:06,990] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:40:06,992] [INFO] DFAST_QC result json was written to OceanDNA-b27608/dqc_result.json
[2023-03-16 12:40:06,992] [INFO] DFAST_QC completed!
[2023-03-16 12:40:06,993] [INFO] Total running time: 0h2m22s