[2024-01-24 11:43:25,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg14263521-008d-4dd7-a681-f09671d0e6c2/dqc_reference
[2024-01-24 11:43:30,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,059] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg27bcd22f-4e06-4443-a4d0-7ccb42cd1bc9/GCF_018457175.1_ASM1845717v1_genomic.fna.gz | prodigal -d GCF_018457175.1_ASM1845717v1_genomic.fna/cds.fna -a GCF_018457175.1_ASM1845717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:41,637] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:41,637] [INFO] Task started: HMMsearch
[2024-01-24 11:43:41,638] [INFO] Running command: hmmsearch --tblout GCF_018457175.1_ASM1845717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14263521-008d-4dd7-a681-f09671d0e6c2/dqc_reference/reference_markers.hmm GCF_018457175.1_ASM1845717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:41,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:41,919] [INFO] Found 6/6 markers.
[2024-01-24 11:43:41,957] [INFO] Query marker FASTA was written to GCF_018457175.1_ASM1845717v1_genomic.fna/markers.fasta
[2024-01-24 11:43:41,958] [INFO] Task started: Blastn
[2024-01-24 11:43:41,958] [INFO] Running command: blastn -query GCF_018457175.1_ASM1845717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14263521-008d-4dd7-a681-f09671d0e6c2/dqc_reference/reference_markers.fasta -out GCF_018457175.1_ASM1845717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:42,670] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:42,674] [INFO] Selected 28 target genomes.
[2024-01-24 11:43:42,674] [INFO] Target genome list was writen to GCF_018457175.1_ASM1845717v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:42,684] [INFO] Task started: fastANI
[2024-01-24 11:43:42,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg27bcd22f-4e06-4443-a4d0-7ccb42cd1bc9/GCF_018457175.1_ASM1845717v1_genomic.fna.gz --refList GCF_018457175.1_ASM1845717v1_genomic.fna/target_genomes.txt --output GCF_018457175.1_ASM1845717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:00,284] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:00,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14263521-008d-4dd7-a681-f09671d0e6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:00,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14263521-008d-4dd7-a681-f09671d0e6c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:00,304] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:00,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:00,304] [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
Pseudohalocynthiibacter aestuariivivens	strain=BS-W9	GCA_018457175.1	1591409	1591409	type	True	100.0	1277	1279	95	conclusive
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.3001	86	1279	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	77.107	137	1279	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	76.7331	100	1279	95	below_threshold
Ruegeria haliotis	strain=B1Z28	GCA_013377785.1	2747601	2747601	type	True	76.6729	93	1279	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	76.6708	102	1279	95	below_threshold
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	76.6523	114	1279	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	76.6032	73	1279	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.5241	80	1279	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	76.5165	100	1279	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	76.4766	100	1279	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	76.47	110	1279	95	below_threshold
Actibacterium pelagium	strain=CGMCC 1.16012	GCA_014644355.1	2029103	2029103	type	True	76.4572	100	1279	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	76.4123	77	1279	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.3967	100	1279	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	76.3315	83	1279	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.3191	108	1279	95	below_threshold
Pontivivens insulae	strain=DSM 103361	GCA_003385715.1	1639689	1639689	type	True	76.305	53	1279	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	76.2558	68	1279	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.2383	54	1279	95	below_threshold
Planktotalea frisia	strain=SH6-1	GCA_001890925.1	696762	696762	type	True	76.234	69	1279	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.2065	81	1279	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	76.0293	64	1279	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	76.015	68	1279	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	75.9154	91	1279	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:00,306] [INFO] DFAST Taxonomy check result was written to GCF_018457175.1_ASM1845717v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:00,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:00,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:00,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14263521-008d-4dd7-a681-f09671d0e6c2/dqc_reference/checkm_data
[2024-01-24 11:44:00,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:00,349] [INFO] Task started: CheckM
[2024-01-24 11:44:00,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018457175.1_ASM1845717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018457175.1_ASM1845717v1_genomic.fna/checkm_input GCF_018457175.1_ASM1845717v1_genomic.fna/checkm_result
[2024-01-24 11:44:37,829] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:37,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:37,850] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:37,850] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:37,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018457175.1_ASM1845717v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:37,851] [INFO] Task started: Blastn
[2024-01-24 11:44:37,851] [INFO] Running command: blastn -query GCF_018457175.1_ASM1845717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14263521-008d-4dd7-a681-f09671d0e6c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_018457175.1_ASM1845717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:39,067] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:39,072] [INFO] Selected 28 target genomes.
[2024-01-24 11:44:39,072] [INFO] Target genome list was writen to GCF_018457175.1_ASM1845717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:39,092] [INFO] Task started: fastANI
[2024-01-24 11:44:39,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg27bcd22f-4e06-4443-a4d0-7ccb42cd1bc9/GCF_018457175.1_ASM1845717v1_genomic.fna.gz --refList GCF_018457175.1_ASM1845717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018457175.1_ASM1845717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:57,026] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:57,049] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:57,049] [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_018457175.1	s__Pseudohalocynthiibacter aestuariivivens	100.0	1277	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudohalocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900188035.1	s__Puniceibacterium sediminis	77.3001	86	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544895.1	s__Profundibacter amoris	77.0873	138	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352045.1	s__JL08 sp003352045	76.8308	133	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JL08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494385.1	s__Profundibacter sp015494385	76.8265	113	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318255.1	s__Ruegeria sp003318255	76.6906	79	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001518015.1	s__Epibacterium horizontis	76.6889	96	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013377785.1	s__Ruegeria haliotis	76.667	92	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743705.1	s__Ruegeria halocynthiae_B	76.6302	112	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018524345.1	s__KMM-3653 sp018524345	76.5445	72	1279	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_009363715.1	s__Roseovarius sp009363715	76.5322	75	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	76.5177	88	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900172215.1	s__Ruegeria meonggei	76.5095	99	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	76.4721	82	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCA_002748285.1	s__Profundibacter sp002748285	76.4502	85	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016123485.1	s__Halocynthiibacter sp016123485	76.444	134	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	76.4087	98	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	76.3191	108	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_007923445.1	s__Puniceibacterium confluentis	76.2992	82	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001879715.1	s__Nioella nitratireducens	76.298	83	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129875.1	s__Marivita hallyeonensis	76.2712	66	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551805.1	s__Yoonia sp003551805	76.227	67	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	98.26	98.25	0.80	0.77	3	-
GCA_017390475.1	s__Yoonia sp017390475	76.2079	92	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002340515.1	s__Aliiroseovarius sp002340515	76.0914	67	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128995.1	s__Loktanella atrilutea	76.015	68	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003254465.1	s__Fluviibacterium sp003254465	75.9958	63	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854675.1	s__Sulfitobacter sp017854675	75.9111	68	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003355.1	s__Donghicola tyrosinivorans	75.8813	90	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:57,051] [INFO] GTDB search result was written to GCF_018457175.1_ASM1845717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:57,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:57,057] [INFO] DFAST_QC result json was written to GCF_018457175.1_ASM1845717v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:57,057] [INFO] DFAST_QC completed!
[2024-01-24 11:44:57,057] [INFO] Total running time: 0h1m32s