[2023-03-16 15:26:08,855] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,855] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f657f52-7f64-4c9e-b821-21e09d39121c/dqc_reference
[2023-03-16 15:26:11,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:11,535] [INFO] Task started: Prodigal
[2023-03-16 15:26:11,535] [INFO] Running command: cat /var/lib/cwl/stgcdeee401-536c-4f54-83c6-0204d5e18222/OceanDNA-b28646.fa | prodigal -d OceanDNA-b28646/cds.fna -a OceanDNA-b28646/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:27,519] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:27,519] [INFO] Task started: HMMsearch
[2023-03-16 15:26:27,519] [INFO] Running command: hmmsearch --tblout OceanDNA-b28646/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f657f52-7f64-4c9e-b821-21e09d39121c/dqc_reference/reference_markers.hmm OceanDNA-b28646/protein.faa > /dev/null
[2023-03-16 15:26:28,190] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:28,191] [INFO] Found 6/6 markers.
[2023-03-16 15:26:28,212] [INFO] Query marker FASTA was written to OceanDNA-b28646/markers.fasta
[2023-03-16 15:26:28,212] [INFO] Task started: Blastn
[2023-03-16 15:26:28,212] [INFO] Running command: blastn -query OceanDNA-b28646/markers.fasta -db /var/lib/cwl/stg8f657f52-7f64-4c9e-b821-21e09d39121c/dqc_reference/reference_markers.fasta -out OceanDNA-b28646/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:30,022] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:30,023] [INFO] Selected 38 target genomes.
[2023-03-16 15:26:30,023] [INFO] Target genome list was writen to OceanDNA-b28646/target_genomes.txt
[2023-03-16 15:26:30,047] [INFO] Task started: fastANI
[2023-03-16 15:26:30,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdeee401-536c-4f54-83c6-0204d5e18222/OceanDNA-b28646.fa --refList OceanDNA-b28646/target_genomes.txt --output OceanDNA-b28646/fastani_result.tsv --threads 1
[2023-03-16 15:27:00,686] [INFO] Task succeeded: fastANI
[2023-03-16 15:27:00,686] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f657f52-7f64-4c9e-b821-21e09d39121c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:27:00,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f657f52-7f64-4c9e-b821-21e09d39121c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:27:00,700] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:27:00,700] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 15:27:00,700] [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
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	76.6635	79	800	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.6441	70	800	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	76.6063	80	800	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.5274	57	800	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.4983	58	800	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.4866	64	800	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.4696	55	800	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	76.4276	53	800	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	76.3855	51	800	95	below_threshold
Pelagimonas varians	strain=DSM 23678	GCA_003208435.1	696760	696760	type	True	76.3465	56	800	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.2751	82	800	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.2475	53	800	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.2412	59	800	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.2305	55	800	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.1895	69	800	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	76.1543	73	800	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	76.1527	55	800	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	76.0982	53	800	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	76.0761	72	800	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	75.9838	57	800	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	75.9772	64	800	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	75.9438	55	800	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	75.8767	63	800	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	75.859	61	800	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.5971	54	800	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:27:00,700] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28646/tc_result.tsv
[2023-03-16 15:27:00,700] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:27:00,701] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:27:00,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f657f52-7f64-4c9e-b821-21e09d39121c/dqc_reference/checkm_data
[2023-03-16 15:27:00,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:27:00,706] [INFO] Task started: CheckM
[2023-03-16 15:27:00,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28646/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28646/checkm_input OceanDNA-b28646/checkm_result
[2023-03-16 15:27:40,823] [INFO] Task succeeded: CheckM
[2023-03-16 15:27:40,824] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 15:27:40,826] [INFO] ===== Completeness check finished =====
[2023-03-16 15:27:40,826] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:27:40,826] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28646/markers.fasta)
[2023-03-16 15:27:40,828] [INFO] Task started: Blastn
[2023-03-16 15:27:40,828] [INFO] Running command: blastn -query OceanDNA-b28646/markers.fasta -db /var/lib/cwl/stg8f657f52-7f64-4c9e-b821-21e09d39121c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28646/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:27:41,901] [INFO] Task succeeded: Blastn
[2023-03-16 15:27:41,902] [INFO] Selected 25 target genomes.
[2023-03-16 15:27:41,902] [INFO] Target genome list was writen to OceanDNA-b28646/target_genomes_gtdb.txt
[2023-03-16 15:27:42,323] [INFO] Task started: fastANI
[2023-03-16 15:27:42,323] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdeee401-536c-4f54-83c6-0204d5e18222/OceanDNA-b28646.fa --refList OceanDNA-b28646/target_genomes_gtdb.txt --output OceanDNA-b28646/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:27:56,944] [INFO] Task succeeded: fastANI
[2023-03-16 15:27:56,955] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 15:27:56,955] [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_902512685.1	s__CABZJG01 sp902512685	97.7772	456	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.75	97.42	0.59	0.54	7	conclusive
GCA_902525995.1	s__CABZJG01 sp902525995	86.065	304	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726375.1	s__CABZJG01 sp002726375	85.8505	425	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CABZJG01	95.0	97.70	96.98	0.64	0.64	3	-
GCA_001642945.1	s__LGRT01 sp001642945	77.0172	103	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	-
GCA_002684375.1	s__CPC320 sp002684375	76.7048	65	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.52	98.26	0.79	0.72	8	-
GCF_900115165.1	s__Roseovarius lutimaris	76.6409	68	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900327775.1	s__Roseovarius sp900327775	76.5775	51	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458195.1	s__Ruegeria atlantica	76.4696	55	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.59	95.51	0.84	0.83	3	-
GCA_001510135.1	s__LFER01 sp001510135	76.3191	71	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LFER01	95.0	98.63	96.26	0.85	0.78	7	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	76.2305	55	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900172335.1	s__Roseovarius albus	76.23	58	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814005.1	s__Ruegeria sp000814005	76.1608	51	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	76.1531	68	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032505.1	s__Ruegeria atlantica_F	76.1403	56	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	76.0901	50	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.0781	65	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_900142085.1	s__Shimia gijangensis	76.0488	52	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473205.1	s__Pseudophaeobacter arcticus	75.9346	63	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002087335.1	s__Pseudophaeobacter leonis	75.8318	62	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:27:56,955] [INFO] GTDB search result was written to OceanDNA-b28646/result_gtdb.tsv
[2023-03-16 15:27:56,955] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:27:56,958] [INFO] DFAST_QC result json was written to OceanDNA-b28646/dqc_result.json
[2023-03-16 15:27:56,958] [INFO] DFAST_QC completed!
[2023-03-16 15:27:56,958] [INFO] Total running time: 0h1m48s