[2023-06-29 03:47:05,346] [INFO] DFAST_QC pipeline started.
[2023-06-29 03:47:05,349] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 03:47:05,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg13be81c1-78b2-4ac9-93fc-9c41bcd9f101/dqc_reference
[2023-06-29 03:47:06,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 03:47:06,592] [INFO] Task started: Prodigal
[2023-06-29 03:47:06,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg475a5524-87d5-4e37-be94-30be8626b837/GCA_027013095.1_ASM2701309v1_genomic.fna.gz | prodigal -d GCA_027013095.1_ASM2701309v1_genomic.fna/cds.fna -a GCA_027013095.1_ASM2701309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 03:47:15,527] [INFO] Task succeeded: Prodigal
[2023-06-29 03:47:15,527] [INFO] Task started: HMMsearch
[2023-06-29 03:47:15,527] [INFO] Running command: hmmsearch --tblout GCA_027013095.1_ASM2701309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13be81c1-78b2-4ac9-93fc-9c41bcd9f101/dqc_reference/reference_markers.hmm GCA_027013095.1_ASM2701309v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 03:47:15,821] [INFO] Task succeeded: HMMsearch
[2023-06-29 03:47:15,822] [INFO] Found 6/6 markers.
[2023-06-29 03:47:15,865] [INFO] Query marker FASTA was written to GCA_027013095.1_ASM2701309v1_genomic.fna/markers.fasta
[2023-06-29 03:47:15,866] [INFO] Task started: Blastn
[2023-06-29 03:47:15,866] [INFO] Running command: blastn -query GCA_027013095.1_ASM2701309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13be81c1-78b2-4ac9-93fc-9c41bcd9f101/dqc_reference/reference_markers.fasta -out GCA_027013095.1_ASM2701309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:47:16,707] [INFO] Task succeeded: Blastn
[2023-06-29 03:47:16,711] [INFO] Selected 31 target genomes.
[2023-06-29 03:47:16,711] [INFO] Target genome list was writen to GCA_027013095.1_ASM2701309v1_genomic.fna/target_genomes.txt
[2023-06-29 03:47:16,729] [INFO] Task started: fastANI
[2023-06-29 03:47:16,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg475a5524-87d5-4e37-be94-30be8626b837/GCA_027013095.1_ASM2701309v1_genomic.fna.gz --refList GCA_027013095.1_ASM2701309v1_genomic.fna/target_genomes.txt --output GCA_027013095.1_ASM2701309v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 03:47:40,958] [INFO] Task succeeded: fastANI
[2023-06-29 03:47:40,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13be81c1-78b2-4ac9-93fc-9c41bcd9f101/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 03:47:40,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13be81c1-78b2-4ac9-93fc-9c41bcd9f101/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 03:47:40,981] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 03:47:40,981] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 03:47:40,981] [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
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	77.013	163	939	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	76.9674	165	939	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.939	175	939	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	76.9156	161	939	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.8812	177	939	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	76.8453	223	939	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.8408	187	939	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	76.8269	199	939	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.8219	244	939	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	76.7781	164	939	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.7673	195	939	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.7473	143	939	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	76.736	169	939	95	below_threshold
Alkalilacustris brevis	strain=34079	GCA_003350345.1	2026338	2026338	type	True	76.6766	160	939	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	76.6718	165	939	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	76.6493	169	939	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	76.6437	142	939	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	76.6337	169	939	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	76.6153	181	939	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.6016	207	939	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.5843	171	939	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.581	195	939	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	76.5749	155	939	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.5551	179	939	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.5304	193	939	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.4882	152	939	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.4165	183	939	95	below_threshold
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	76.2966	167	939	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.2571	90	939	95	below_threshold
Ruegeria haliotis	strain=B1Z28	GCA_013377785.1	2747601	2747601	type	True	76.2241	118	939	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	75.9821	114	939	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 03:47:41,004] [INFO] DFAST Taxonomy check result was written to GCA_027013095.1_ASM2701309v1_genomic.fna/tc_result.tsv
[2023-06-29 03:47:41,005] [INFO] ===== Taxonomy check completed =====
[2023-06-29 03:47:41,005] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 03:47:41,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13be81c1-78b2-4ac9-93fc-9c41bcd9f101/dqc_reference/checkm_data
[2023-06-29 03:47:41,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 03:47:41,042] [INFO] Task started: CheckM
[2023-06-29 03:47:41,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027013095.1_ASM2701309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027013095.1_ASM2701309v1_genomic.fna/checkm_input GCA_027013095.1_ASM2701309v1_genomic.fna/checkm_result
[2023-06-29 03:48:11,943] [INFO] Task succeeded: CheckM
[2023-06-29 03:48:11,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 03:48:11,967] [INFO] ===== Completeness check finished =====
[2023-06-29 03:48:11,968] [INFO] ===== Start GTDB Search =====
[2023-06-29 03:48:11,968] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027013095.1_ASM2701309v1_genomic.fna/markers.fasta)
[2023-06-29 03:48:11,969] [INFO] Task started: Blastn
[2023-06-29 03:48:11,969] [INFO] Running command: blastn -query GCA_027013095.1_ASM2701309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13be81c1-78b2-4ac9-93fc-9c41bcd9f101/dqc_reference/reference_markers_gtdb.fasta -out GCA_027013095.1_ASM2701309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 03:48:13,399] [INFO] Task succeeded: Blastn
[2023-06-29 03:48:13,405] [INFO] Selected 29 target genomes.
[2023-06-29 03:48:13,405] [INFO] Target genome list was writen to GCA_027013095.1_ASM2701309v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 03:48:13,442] [INFO] Task started: fastANI
[2023-06-29 03:48:13,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg475a5524-87d5-4e37-be94-30be8626b837/GCA_027013095.1_ASM2701309v1_genomic.fna.gz --refList GCA_027013095.1_ASM2701309v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027013095.1_ASM2701309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 03:48:30,348] [INFO] Task succeeded: fastANI
[2023-06-29 03:48:30,385] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 03:48:30,385] [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_015487165.1	s__UBA5972 sp015487165	78.7589	364	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151535.1	s__UBA5972 sp013151535	77.2199	260	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	76.9867	170	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491895.1	s__WFVA01 sp015491895	76.9757	159	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WFVA01	95.0	99.60	99.57	0.92	0.91	3	-
GCA_013151335.1	s__UBA5972 sp013151335	76.9342	246	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	76.9251	176	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_000744955.1	s__Actibacterium sp000744955	76.9068	212	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	76.9042	236	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	76.8601	232	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	76.8453	223	939	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_014359745.1	s__JACIYW01 sp014359745	76.8042	163	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACIYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	76.7793	195	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_013093415.1	s__Halovulum dunhuangense	76.7473	143	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003172915.1	s__Fluviibacterium sp003172915	76.7383	108	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237555.1	s__Antarctobacter heliothermus_B	76.7297	131	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	97.31	97.29	0.90	0.89	3	-
GCF_003344785.1	s__Puniceibacterium profundi	76.6995	149	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350345.1	s__Rhodobaculum breve	76.6627	161	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908165.1	s__Frigidibacter albus	76.6607	168	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCF_002504165.1	s__Pacificitalea manganoxidans	76.6437	142	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	-
GCA_011048875.1	s__Rhodovulum sp011048875	76.6085	148	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	76.6024	207	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	76.575	189	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	76.5749	155	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	76.51	182	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078595.1	s__Rhodobacter_B lobularis	76.3417	166	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430125.1	s__UBA5972 sp002430125	76.337	146	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	99.40	99.40	0.79	0.79	2	-
GCF_001719615.1	s__Amylibacter sediminis	76.2657	127	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	76.0916	136	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007128865.1	s__Rhodobaculum sp007128865	75.9751	88	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	97.54	97.54	0.66	0.66	2	-
--------------------------------------------------------------------------------
[2023-06-29 03:48:30,388] [INFO] GTDB search result was written to GCA_027013095.1_ASM2701309v1_genomic.fna/result_gtdb.tsv
[2023-06-29 03:48:30,388] [INFO] ===== GTDB Search completed =====
[2023-06-29 03:48:30,396] [INFO] DFAST_QC result json was written to GCA_027013095.1_ASM2701309v1_genomic.fna/dqc_result.json
[2023-06-29 03:48:30,397] [INFO] DFAST_QC completed!
[2023-06-29 03:48:30,397] [INFO] Total running time: 0h1m25s