[2023-06-18 13:03:40,621] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:03:40,624] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:03:40,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bc34779-dce7-4b91-8459-253a9395dbfa/dqc_reference
[2023-06-18 13:03:41,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:03:41,899] [INFO] Task started: Prodigal
[2023-06-18 13:03:41,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg457b9a63-ba35-4d43-81a4-df64815e2c6a/GCA_018675475.1_ASM1867547v1_genomic.fna.gz | prodigal -d GCA_018675475.1_ASM1867547v1_genomic.fna/cds.fna -a GCA_018675475.1_ASM1867547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:03:49,831] [INFO] Task succeeded: Prodigal
[2023-06-18 13:03:49,832] [INFO] Task started: HMMsearch
[2023-06-18 13:03:49,832] [INFO] Running command: hmmsearch --tblout GCA_018675475.1_ASM1867547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bc34779-dce7-4b91-8459-253a9395dbfa/dqc_reference/reference_markers.hmm GCA_018675475.1_ASM1867547v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:03:50,088] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:03:50,090] [INFO] Found 6/6 markers.
[2023-06-18 13:03:50,128] [INFO] Query marker FASTA was written to GCA_018675475.1_ASM1867547v1_genomic.fna/markers.fasta
[2023-06-18 13:03:50,128] [INFO] Task started: Blastn
[2023-06-18 13:03:50,128] [INFO] Running command: blastn -query GCA_018675475.1_ASM1867547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc34779-dce7-4b91-8459-253a9395dbfa/dqc_reference/reference_markers.fasta -out GCA_018675475.1_ASM1867547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:03:50,817] [INFO] Task succeeded: Blastn
[2023-06-18 13:03:50,828] [INFO] Selected 34 target genomes.
[2023-06-18 13:03:50,829] [INFO] Target genome list was writen to GCA_018675475.1_ASM1867547v1_genomic.fna/target_genomes.txt
[2023-06-18 13:03:50,861] [INFO] Task started: fastANI
[2023-06-18 13:03:50,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg457b9a63-ba35-4d43-81a4-df64815e2c6a/GCA_018675475.1_ASM1867547v1_genomic.fna.gz --refList GCA_018675475.1_ASM1867547v1_genomic.fna/target_genomes.txt --output GCA_018675475.1_ASM1867547v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:04:13,195] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:13,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bc34779-dce7-4b91-8459-253a9395dbfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:04:13,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bc34779-dce7-4b91-8459-253a9395dbfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:04:13,222] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:04:13,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 13:04:13,222] [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 lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.5009	72	881	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.4828	57	881	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	76.4728	54	881	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	76.4343	74	881	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.4025	55	881	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.3929	60	881	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.354	56	881	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	76.3185	56	881	95	below_threshold
Cognatishimia maritima	strain=DSM 28223	GCA_900129685.1	870908	870908	type	True	76.2943	51	881	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	76.1331	75	881	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.1209	80	881	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.0845	53	881	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	76.0838	53	881	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.0593	59	881	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	76.0415	65	881	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	76.0337	78	881	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	76.0144	58	881	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	75.9501	72	881	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	75.9501	72	881	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	75.9289	50	881	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	75.8984	54	881	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	75.8922	59	881	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	75.8262	75	881	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.8117	52	881	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	75.7951	51	881	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	75.6369	63	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 13:04:13,226] [INFO] DFAST Taxonomy check result was written to GCA_018675475.1_ASM1867547v1_genomic.fna/tc_result.tsv
[2023-06-18 13:04:13,229] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:04:13,229] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:04:13,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bc34779-dce7-4b91-8459-253a9395dbfa/dqc_reference/checkm_data
[2023-06-18 13:04:13,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:04:13,270] [INFO] Task started: CheckM
[2023-06-18 13:04:13,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018675475.1_ASM1867547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018675475.1_ASM1867547v1_genomic.fna/checkm_input GCA_018675475.1_ASM1867547v1_genomic.fna/checkm_result
[2023-06-18 13:04:42,111] [INFO] Task succeeded: CheckM
[2023-06-18 13:04:42,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:04:42,145] [INFO] ===== Completeness check finished =====
[2023-06-18 13:04:42,146] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:04:42,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018675475.1_ASM1867547v1_genomic.fna/markers.fasta)
[2023-06-18 13:04:42,147] [INFO] Task started: Blastn
[2023-06-18 13:04:42,147] [INFO] Running command: blastn -query GCA_018675475.1_ASM1867547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc34779-dce7-4b91-8459-253a9395dbfa/dqc_reference/reference_markers_gtdb.fasta -out GCA_018675475.1_ASM1867547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:04:43,308] [INFO] Task succeeded: Blastn
[2023-06-18 13:04:43,313] [INFO] Selected 22 target genomes.
[2023-06-18 13:04:43,314] [INFO] Target genome list was writen to GCA_018675475.1_ASM1867547v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:04:43,332] [INFO] Task started: fastANI
[2023-06-18 13:04:43,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg457b9a63-ba35-4d43-81a4-df64815e2c6a/GCA_018675475.1_ASM1867547v1_genomic.fna.gz --refList GCA_018675475.1_ASM1867547v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018675475.1_ASM1867547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:04:56,091] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:56,113] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:04:56,114] [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	97.7379	498	881	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	86.2108	317	881	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	85.9501	466	881	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	77.2874	126	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	-
GCF_900327775.1	s__Roseovarius sp900327775	76.5537	56	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172295.1	s__Roseovarius litorisediminis	76.4067	75	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510135.1	s__LFER01 sp001510135	76.3243	80	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LFER01	95.0	98.63	96.26	0.85	0.78	7	-
GCF_900142085.1	s__Shimia gijangensis	76.2695	56	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.2437	65	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_011601345.1	s__Roseovarius gahaiensis	76.1641	76	881	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	76.0845	53	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.59	95.51	0.84	0.83	3	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	76.0111	59	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013032445.1	s__Ruegeria arenilitoris_F	75.9202	51	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743735.1	s__Shimia sp017743735	75.9197	70	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	75.8262	75	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814005.1	s__Ruegeria sp000814005	75.8198	51	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637725.1	s__Marivita lacus	75.7951	51	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	75.7116	55	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-18 13:04:56,118] [INFO] GTDB search result was written to GCA_018675475.1_ASM1867547v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:04:56,122] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:04:56,129] [INFO] DFAST_QC result json was written to GCA_018675475.1_ASM1867547v1_genomic.fna/dqc_result.json
[2023-06-18 13:04:56,130] [INFO] DFAST_QC completed!
[2023-06-18 13:04:56,130] [INFO] Total running time: 0h1m16s