[2024-01-24 12:14:34,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,154] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,154] [INFO] DQC Reference Directory: /var/lib/cwl/stg725a6a39-6460-416f-84b9-943fcf196a5a/dqc_reference
[2024-01-24 12:14:35,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,528] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,528] [INFO] Running command: gunzip -c /var/lib/cwl/stga84eba97-0b1c-4320-87da-5411acf5e6bc/GCF_003205515.1_ASM320551v1_genomic.fna.gz | prodigal -d GCF_003205515.1_ASM320551v1_genomic.fna/cds.fna -a GCF_003205515.1_ASM320551v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:46,450] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:46,451] [INFO] Task started: HMMsearch
[2024-01-24 12:14:46,451] [INFO] Running command: hmmsearch --tblout GCF_003205515.1_ASM320551v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg725a6a39-6460-416f-84b9-943fcf196a5a/dqc_reference/reference_markers.hmm GCF_003205515.1_ASM320551v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:46,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:46,766] [INFO] Found 6/6 markers.
[2024-01-24 12:14:46,793] [INFO] Query marker FASTA was written to GCF_003205515.1_ASM320551v1_genomic.fna/markers.fasta
[2024-01-24 12:14:46,793] [INFO] Task started: Blastn
[2024-01-24 12:14:46,793] [INFO] Running command: blastn -query GCF_003205515.1_ASM320551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg725a6a39-6460-416f-84b9-943fcf196a5a/dqc_reference/reference_markers.fasta -out GCF_003205515.1_ASM320551v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:47,527] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:47,530] [INFO] Selected 29 target genomes.
[2024-01-24 12:14:47,530] [INFO] Target genome list was writen to GCF_003205515.1_ASM320551v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:47,560] [INFO] Task started: fastANI
[2024-01-24 12:14:47,560] [INFO] Running command: fastANI --query /var/lib/cwl/stga84eba97-0b1c-4320-87da-5411acf5e6bc/GCF_003205515.1_ASM320551v1_genomic.fna.gz --refList GCF_003205515.1_ASM320551v1_genomic.fna/target_genomes.txt --output GCF_003205515.1_ASM320551v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:09,332] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:09,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg725a6a39-6460-416f-84b9-943fcf196a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:09,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg725a6a39-6460-416f-84b9-943fcf196a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:09,349] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:09,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:09,349] [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
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	100.0	1127	1129	95	conclusive
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	78.5632	191	1129	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	78.5051	189	1129	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.7992	290	1129	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	77.7514	277	1129	95	below_threshold
Thalassobius mediterraneus	strain=CECT 5383	GCA_001458435.1	340021	340021	type	True	77.6979	228	1129	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	77.6061	223	1129	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	77.5783	221	1129	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	77.4576	213	1129	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.3901	219	1129	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.3777	222	1129	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.3362	246	1129	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.2665	176	1129	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	77.2622	232	1129	95	below_threshold
Ruegeria haliotis	strain=B1Z28	GCA_013377785.1	2747601	2747601	type	True	77.2503	144	1129	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.0788	172	1129	95	below_threshold
Shimia gijangensis	strain=DSM 100564	GCA_900142085.1	1470563	1470563	type	True	77.0735	162	1129	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.0226	206	1129	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	76.9334	191	1129	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	76.7931	218	1129	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.7884	173	1129	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.7658	211	1129	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.7234	208	1129	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	76.6267	202	1129	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.6022	131	1129	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	76.5852	146	1129	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.533	145	1129	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	76.3172	122	1129	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.0395	131	1129	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:09,350] [INFO] DFAST Taxonomy check result was written to GCF_003205515.1_ASM320551v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:09,351] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:09,351] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:09,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg725a6a39-6460-416f-84b9-943fcf196a5a/dqc_reference/checkm_data
[2024-01-24 12:15:09,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:09,388] [INFO] Task started: CheckM
[2024-01-24 12:15:09,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003205515.1_ASM320551v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003205515.1_ASM320551v1_genomic.fna/checkm_input GCF_003205515.1_ASM320551v1_genomic.fna/checkm_result
[2024-01-24 12:15:41,783] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:41,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,795] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:41,795] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:41,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003205515.1_ASM320551v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:41,796] [INFO] Task started: Blastn
[2024-01-24 12:15:41,796] [INFO] Running command: blastn -query GCF_003205515.1_ASM320551v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg725a6a39-6460-416f-84b9-943fcf196a5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003205515.1_ASM320551v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:43,073] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:43,075] [INFO] Selected 25 target genomes.
[2024-01-24 12:15:43,075] [INFO] Target genome list was writen to GCF_003205515.1_ASM320551v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:43,101] [INFO] Task started: fastANI
[2024-01-24 12:15:43,101] [INFO] Running command: fastANI --query /var/lib/cwl/stga84eba97-0b1c-4320-87da-5411acf5e6bc/GCF_003205515.1_ASM320551v1_genomic.fna.gz --refList GCF_003205515.1_ASM320551v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003205515.1_ASM320551v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:59,128] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:59,142] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:59,143] [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_003205515.1	s__Litorivita pollutaquae	100.0	1127	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorivita	95.0	98.23	98.23	0.93	0.93	2	conclusive
GCF_001458175.1	s__Shimia marina	78.5051	189	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.3416	298	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_002366795.1	s__UBA3069 sp002366795	77.9338	335	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	77.9039	325	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003316635.1	s__Roseovarius dicentrarchi	77.5973	219	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014901205.1	s__Fluviibacterium sp014901205	77.5539	193	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.4465	229	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_001458255.1	s__Thalassobius autumnalis	77.3649	223	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_016888515.1	s__Shimia_A biformata	77.2932	263	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	77.283	175	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377785.1	s__Ruegeria haliotis	77.2503	144	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223085.1	s__Shimia sp018223085	77.1713	220	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	77.1275	234	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCF_003122245.1	s__Roseovarius sp003122245	77.1235	211	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018524345.1	s__KMM-3653 sp018524345	77.0944	199	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMM-3653	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	77.0788	172	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282555.1	s__EhC02 sp002282555	77.0412	133	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	76.9935	176	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	76.8841	204	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_004959925.1	s__Pseudooceanicola onchidii	76.7915	217	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544895.1	s__Profundibacter amoris	76.7234	208	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214575.1	s__Parasedimentitalea sp013214575	76.6779	188	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494385.1	s__Profundibacter sp015494385	76.5422	153	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688285.1	s__Rhodophyticola porphyridii	76.5309	144	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:59,144] [INFO] GTDB search result was written to GCF_003205515.1_ASM320551v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:59,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:59,148] [INFO] DFAST_QC result json was written to GCF_003205515.1_ASM320551v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:59,148] [INFO] DFAST_QC completed!
[2024-01-24 12:15:59,148] [INFO] Total running time: 0h1m25s