[2023-03-19 04:43:18,620] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,621] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,621] [INFO] DQC Reference Directory: /var/lib/cwl/stg02fdee2e-d753-4446-a360-69266e7f0ef7/dqc_reference
[2023-03-19 04:43:19,867] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,867] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,867] [INFO] Running command: cat /var/lib/cwl/stg31719fd6-fd52-442d-87f4-435f2689b343/OceanDNA-b29508.fa | prodigal -d OceanDNA-b29508/cds.fna -a OceanDNA-b29508/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:49,585] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:49,586] [INFO] Task started: HMMsearch
[2023-03-19 04:43:49,586] [INFO] Running command: hmmsearch --tblout OceanDNA-b29508/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02fdee2e-d753-4446-a360-69266e7f0ef7/dqc_reference/reference_markers.hmm OceanDNA-b29508/protein.faa > /dev/null
[2023-03-19 04:43:49,810] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:49,810] [INFO] Found 6/6 markers.
[2023-03-19 04:43:49,841] [INFO] Query marker FASTA was written to OceanDNA-b29508/markers.fasta
[2023-03-19 04:43:49,842] [INFO] Task started: Blastn
[2023-03-19 04:43:49,843] [INFO] Running command: blastn -query OceanDNA-b29508/markers.fasta -db /var/lib/cwl/stg02fdee2e-d753-4446-a360-69266e7f0ef7/dqc_reference/reference_markers.fasta -out OceanDNA-b29508/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:50,631] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:50,632] [INFO] Selected 26 target genomes.
[2023-03-19 04:43:50,632] [INFO] Target genome list was writen to OceanDNA-b29508/target_genomes.txt
[2023-03-19 04:43:50,647] [INFO] Task started: fastANI
[2023-03-19 04:43:50,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg31719fd6-fd52-442d-87f4-435f2689b343/OceanDNA-b29508.fa --refList OceanDNA-b29508/target_genomes.txt --output OceanDNA-b29508/fastani_result.tsv --threads 1
[2023-03-19 04:44:11,107] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:11,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02fdee2e-d753-4446-a360-69266e7f0ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:44:11,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02fdee2e-d753-4446-a360-69266e7f0ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:44:11,122] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:44:11,122] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:44:11,122] [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
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	81.8887	991	1601	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.6504	477	1601	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.5342	501	1601	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.5259	504	1601	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.4269	455	1601	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	78.3965	463	1601	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.3844	523	1601	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.3707	454	1601	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.1472	442	1601	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	78.1389	468	1601	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.1383	410	1601	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.0912	412	1601	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.008	369	1601	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.9279	489	1601	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.8953	488	1601	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	77.8097	369	1601	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	77.8029	376	1601	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.6859	465	1601	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.6556	385	1601	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	77.5717	351	1601	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5158	321	1601	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.441	340	1601	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.2677	319	1601	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	77.2479	291	1601	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.9891	262	1601	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	76.6788	217	1601	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:44:11,122] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29508/tc_result.tsv
[2023-03-19 04:44:11,122] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:44:11,122] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:44:11,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02fdee2e-d753-4446-a360-69266e7f0ef7/dqc_reference/checkm_data
[2023-03-19 04:44:11,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:44:11,129] [INFO] Task started: CheckM
[2023-03-19 04:44:11,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29508/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29508/checkm_input OceanDNA-b29508/checkm_result
[2023-03-19 04:45:23,353] [INFO] Task succeeded: CheckM
[2023-03-19 04:45:23,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:45:23,722] [INFO] ===== Completeness check finished =====
[2023-03-19 04:45:23,722] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:45:23,723] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29508/markers.fasta)
[2023-03-19 04:45:23,724] [INFO] Task started: Blastn
[2023-03-19 04:45:23,724] [INFO] Running command: blastn -query OceanDNA-b29508/markers.fasta -db /var/lib/cwl/stg02fdee2e-d753-4446-a360-69266e7f0ef7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29508/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:45:25,015] [INFO] Task succeeded: Blastn
[2023-03-19 04:45:25,016] [INFO] Selected 17 target genomes.
[2023-03-19 04:45:25,016] [INFO] Target genome list was writen to OceanDNA-b29508/target_genomes_gtdb.txt
[2023-03-19 04:45:25,029] [INFO] Task started: fastANI
[2023-03-19 04:45:25,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg31719fd6-fd52-442d-87f4-435f2689b343/OceanDNA-b29508.fa --refList OceanDNA-b29508/target_genomes_gtdb.txt --output OceanDNA-b29508/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:45:40,590] [INFO] Task succeeded: fastANI
[2023-03-19 04:45:40,600] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:45:40,600] [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_003646465.1	s__Chachezhania antarctica	84.7176	1034	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765275.1	s__Chachezhania sp009765275	81.9243	986	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	79.2003	621	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	79.0018	636	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.8648	524	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.6839	474	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	78.5904	511	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.5451	499	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005938225.1	s__Arenibacterium halophilum	78.5334	461	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_001205715.1	s__Pseudaestuariivita atlantica	78.4373	467	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	78.3791	442	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.3785	453	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	78.2619	452	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.193	476	1601	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_900101475.1	s__Ruegeria_B marina	78.1329	468	1601	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_003054175.1	s__Allosediminivita pacifica	78.0706	415	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Allosediminivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002300555.1	s__Salipiger sp002300555	77.8594	369	1601	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:45:40,601] [INFO] GTDB search result was written to OceanDNA-b29508/result_gtdb.tsv
[2023-03-19 04:45:40,601] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:45:40,603] [INFO] DFAST_QC result json was written to OceanDNA-b29508/dqc_result.json
[2023-03-19 04:45:40,603] [INFO] DFAST_QC completed!
[2023-03-19 04:45:40,603] [INFO] Total running time: 0h2m22s