[2023-03-15 07:29:11,756] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg7738b928-f6df-4c8c-bdec-194da5b49227/dqc_reference
[2023-03-15 07:29:13,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,591] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,591] [INFO] Running command: cat /var/lib/cwl/stg6396bd56-efc4-431e-b3ad-6da9c33b3c60/OceanDNA-b30021.fa | prodigal -d OceanDNA-b30021/cds.fna -a OceanDNA-b30021/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:28,801] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:28,801] [INFO] Task started: HMMsearch
[2023-03-15 07:29:28,801] [INFO] Running command: hmmsearch --tblout OceanDNA-b30021/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7738b928-f6df-4c8c-bdec-194da5b49227/dqc_reference/reference_markers.hmm OceanDNA-b30021/protein.faa > /dev/null
[2023-03-15 07:29:28,995] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:28,995] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6396bd56-efc4-431e-b3ad-6da9c33b3c60/OceanDNA-b30021.fa]
[2023-03-15 07:29:29,016] [INFO] Query marker FASTA was written to OceanDNA-b30021/markers.fasta
[2023-03-15 07:29:29,018] [INFO] Task started: Blastn
[2023-03-15 07:29:29,018] [INFO] Running command: blastn -query OceanDNA-b30021/markers.fasta -db /var/lib/cwl/stg7738b928-f6df-4c8c-bdec-194da5b49227/dqc_reference/reference_markers.fasta -out OceanDNA-b30021/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:29,608] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:29,609] [INFO] Selected 23 target genomes.
[2023-03-15 07:29:29,609] [INFO] Target genome list was writen to OceanDNA-b30021/target_genomes.txt
[2023-03-15 07:29:29,623] [INFO] Task started: fastANI
[2023-03-15 07:29:29,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg6396bd56-efc4-431e-b3ad-6da9c33b3c60/OceanDNA-b30021.fa --refList OceanDNA-b30021/target_genomes.txt --output OceanDNA-b30021/fastani_result.tsv --threads 1
[2023-03-15 07:29:45,786] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:45,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7738b928-f6df-4c8c-bdec-194da5b49227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:45,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7738b928-f6df-4c8c-bdec-194da5b49227/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:45,798] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:45,799] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:29:45,799] [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	77.2728	181	833	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	76.98	185	833	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.9782	155	833	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.977	154	833	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	76.8649	133	833	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	76.7036	116	833	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	76.6012	102	833	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	76.5976	123	833	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	76.5514	140	833	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.5364	141	833	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	76.4591	122	833	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	76.4559	121	833	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.4495	141	833	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.4206	110	833	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	76.3942	67	833	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	76.3942	67	833	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	76.3547	113	833	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.3388	60	833	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.3047	91	833	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.1276	78	833	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	75.8356	52	833	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:29:45,799] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30021/tc_result.tsv
[2023-03-15 07:29:45,799] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:45,799] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:45,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7738b928-f6df-4c8c-bdec-194da5b49227/dqc_reference/checkm_data
[2023-03-15 07:29:45,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:45,805] [INFO] Task started: CheckM
[2023-03-15 07:29:45,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30021/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30021/checkm_input OceanDNA-b30021/checkm_result
[2023-03-15 07:30:27,182] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:27,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:27,185] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:27,185] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:27,185] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30021/markers.fasta)
[2023-03-15 07:30:27,186] [INFO] Task started: Blastn
[2023-03-15 07:30:27,186] [INFO] Running command: blastn -query OceanDNA-b30021/markers.fasta -db /var/lib/cwl/stg7738b928-f6df-4c8c-bdec-194da5b49227/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30021/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:28,115] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:28,116] [INFO] Selected 25 target genomes.
[2023-03-15 07:30:28,116] [INFO] Target genome list was writen to OceanDNA-b30021/target_genomes_gtdb.txt
[2023-03-15 07:30:28,128] [INFO] Task started: fastANI
[2023-03-15 07:30:28,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg6396bd56-efc4-431e-b3ad-6da9c33b3c60/OceanDNA-b30021.fa --refList OceanDNA-b30021/target_genomes_gtdb.txt --output OceanDNA-b30021/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:45,641] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:45,655] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:30:45,655] [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_005938225.1	s__Arenibacterium halophilum	77.2519	182	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_013032445.1	s__Ruegeria arenilitoris_F	77.1609	122	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	77.0505	122	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.0491	137	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	76.9922	184	833	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_004216475.1	s__GCA-004216475 sp004216475	76.9021	129	833	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_015644665.1	s__Roseobacter sp015644665	76.893	119	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	76.8869	133	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_010500245.1	s__Ruegeria_B sp010500245	76.8867	166	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	76.8805	132	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	76.8055	122	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473225.1	s__Sedimentitalea nanhaiensis	76.723	144	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001730095.1	s__Leisingera sp001730095	76.6767	132	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.6355	129	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_013033515.1	s__Ruegeria sp013033515	76.6278	148	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.60	97.60	0.95	0.93	6	-
GCF_900108275.1	s__Jhaorihella thermophila	76.5806	133	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	76.5569	158	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	76.531	140	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	76.516	89	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013035315.1	s__Ruegeria arenilitoris_D	76.505	132	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.80	95.80	0.90	0.90	2	-
GCA_017854855.1	s__Sulfitobacter sp017854855	76.49	110	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192475.1	s__Ruegeria conchae	76.4591	122	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013031245.1	s__Ruegeria lacuscaerulensis_C	76.3767	138	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042605.1	s__IMCC34051 sp013042605	76.2286	76	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
GCF_014337925.1	s__Roseobacter litoralis_A	75.8613	102	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:45,655] [INFO] GTDB search result was written to OceanDNA-b30021/result_gtdb.tsv
[2023-03-15 07:30:45,655] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:45,658] [INFO] DFAST_QC result json was written to OceanDNA-b30021/dqc_result.json
[2023-03-15 07:30:45,658] [INFO] DFAST_QC completed!
[2023-03-15 07:30:45,658] [INFO] Total running time: 0h1m34s