[2024-01-24 14:13:01,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,577] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d0de53d-cdac-42f8-a364-b90d5e2af6f8/dqc_reference
[2024-01-24 14:13:02,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,783] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg73ca0051-8ea3-4d5e-8c8f-4a145623cb23/GCF_009496005.1_ASM949600v1_genomic.fna.gz | prodigal -d GCF_009496005.1_ASM949600v1_genomic.fna/cds.fna -a GCF_009496005.1_ASM949600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:17,197] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:17,197] [INFO] Task started: HMMsearch
[2024-01-24 14:13:17,197] [INFO] Running command: hmmsearch --tblout GCF_009496005.1_ASM949600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d0de53d-cdac-42f8-a364-b90d5e2af6f8/dqc_reference/reference_markers.hmm GCF_009496005.1_ASM949600v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:17,520] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:17,521] [INFO] Found 6/6 markers.
[2024-01-24 14:13:17,574] [INFO] Query marker FASTA was written to GCF_009496005.1_ASM949600v1_genomic.fna/markers.fasta
[2024-01-24 14:13:17,575] [INFO] Task started: Blastn
[2024-01-24 14:13:17,575] [INFO] Running command: blastn -query GCF_009496005.1_ASM949600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d0de53d-cdac-42f8-a364-b90d5e2af6f8/dqc_reference/reference_markers.fasta -out GCF_009496005.1_ASM949600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:18,392] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:18,396] [INFO] Selected 22 target genomes.
[2024-01-24 14:13:18,396] [INFO] Target genome list was writen to GCF_009496005.1_ASM949600v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:18,418] [INFO] Task started: fastANI
[2024-01-24 14:13:18,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg73ca0051-8ea3-4d5e-8c8f-4a145623cb23/GCF_009496005.1_ASM949600v1_genomic.fna.gz --refList GCF_009496005.1_ASM949600v1_genomic.fna/target_genomes.txt --output GCF_009496005.1_ASM949600v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:36,836] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:36,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d0de53d-cdac-42f8-a364-b90d5e2af6f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:36,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d0de53d-cdac-42f8-a364-b90d5e2af6f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:36,855] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:36,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:36,855] [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
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	100.0	1435	1438	95	conclusive
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	80.0665	638	1438	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	79.265	479	1438	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	79.235	475	1438	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	78.9779	415	1438	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	78.974	416	1438	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	78.7203	400	1438	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	78.6877	397	1438	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	78.646	454	1438	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	78.6432	402	1438	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.6119	458	1438	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	78.4726	389	1438	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.4141	464	1438	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.1463	396	1438	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	77.9502	251	1438	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.9075	176	1438	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.7226	236	1438	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.7151	248	1438	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.6199	255	1438	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	77.5169	181	1438	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.6813	247	1438	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	76.6499	190	1438	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:36,857] [INFO] DFAST Taxonomy check result was written to GCF_009496005.1_ASM949600v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:36,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:36,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:36,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d0de53d-cdac-42f8-a364-b90d5e2af6f8/dqc_reference/checkm_data
[2024-01-24 14:13:36,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:36,918] [INFO] Task started: CheckM
[2024-01-24 14:13:36,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009496005.1_ASM949600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009496005.1_ASM949600v1_genomic.fna/checkm_input GCF_009496005.1_ASM949600v1_genomic.fna/checkm_result
[2024-01-24 14:14:21,623] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:21,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:21,650] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:21,650] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:21,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009496005.1_ASM949600v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:21,651] [INFO] Task started: Blastn
[2024-01-24 14:14:21,651] [INFO] Running command: blastn -query GCF_009496005.1_ASM949600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d0de53d-cdac-42f8-a364-b90d5e2af6f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009496005.1_ASM949600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:22,726] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:22,729] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:22,729] [INFO] Target genome list was writen to GCF_009496005.1_ASM949600v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:22,740] [INFO] Task started: fastANI
[2024-01-24 14:14:22,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg73ca0051-8ea3-4d5e-8c8f-4a145623cb23/GCF_009496005.1_ASM949600v1_genomic.fna.gz --refList GCF_009496005.1_ASM949600v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009496005.1_ASM949600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:35,390] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:35,407] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:35,407] [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_009496005.1	s__Epibacterium litoralis	100.0	1435	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018678075.1	s__Epibacterium ulvae_A	81.248	822	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617595.1	s__Epibacterium aquimaris	80.075	637	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458415.1	s__Epibacterium multivorans	79.2847	477	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001518015.1	s__Epibacterium horizontis	79.0257	422	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	78.7268	424	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001681715.1	s__Epibacterium mobile	78.6982	396	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	97.01	96.41	0.91	0.87	56	-
GCF_000473325.1	s__Leisingera caerulea	78.6209	457	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	78.591	426	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_013317235.1	s__Leisingera sp013317235	78.5841	440	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	78.5076	422	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014065.1	s__Epibacterium sp000014065	78.4315	361	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152965.1	s__Pseudophaeobacter sp000152965	78.3699	361	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.26	98.26	0.93	0.93	2	-
GCA_013373325.1	s__Leisingera sp013373325	78.2944	368	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479575.1	s__Pseudophaeobacter sp905479575	78.1814	387	1438	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:35,409] [INFO] GTDB search result was written to GCF_009496005.1_ASM949600v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:35,410] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:35,414] [INFO] DFAST_QC result json was written to GCF_009496005.1_ASM949600v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:35,414] [INFO] DFAST_QC completed!
[2024-01-24 14:14:35,414] [INFO] Total running time: 0h1m34s