[2024-01-24 13:12:52,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d9e33ce-003e-4a3b-9909-618b48387f56/dqc_reference
[2024-01-24 13:12:53,922] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:53,924] [INFO] Task started: Prodigal
[2024-01-24 13:12:53,924] [INFO] Running command: gunzip -c /var/lib/cwl/stg22b63444-fc36-48e2-ab94-bc8543416f7c/GCF_003663885.1_ASM366388v1_genomic.fna.gz | prodigal -d GCF_003663885.1_ASM366388v1_genomic.fna/cds.fna -a GCF_003663885.1_ASM366388v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:07,765] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:07,765] [INFO] Task started: HMMsearch
[2024-01-24 13:13:07,765] [INFO] Running command: hmmsearch --tblout GCF_003663885.1_ASM366388v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d9e33ce-003e-4a3b-9909-618b48387f56/dqc_reference/reference_markers.hmm GCF_003663885.1_ASM366388v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:08,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:08,156] [INFO] Found 6/6 markers.
[2024-01-24 13:13:08,195] [INFO] Query marker FASTA was written to GCF_003663885.1_ASM366388v1_genomic.fna/markers.fasta
[2024-01-24 13:13:08,195] [INFO] Task started: Blastn
[2024-01-24 13:13:08,195] [INFO] Running command: blastn -query GCF_003663885.1_ASM366388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d9e33ce-003e-4a3b-9909-618b48387f56/dqc_reference/reference_markers.fasta -out GCF_003663885.1_ASM366388v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:08,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:08,893] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:08,894] [INFO] Target genome list was writen to GCF_003663885.1_ASM366388v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:08,900] [INFO] Task started: fastANI
[2024-01-24 13:13:08,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg22b63444-fc36-48e2-ab94-bc8543416f7c/GCF_003663885.1_ASM366388v1_genomic.fna.gz --refList GCF_003663885.1_ASM366388v1_genomic.fna/target_genomes.txt --output GCF_003663885.1_ASM366388v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:21,610] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:21,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d9e33ce-003e-4a3b-9909-618b48387f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:21,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d9e33ce-003e-4a3b-9909-618b48387f56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:21,625] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:21,626] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:21,626] [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
Litoreibacter meonggei	strain=DSM 29466	GCA_003663885.1	1049199	1049199	type	True	100.0	1308	1309	95	conclusive
Litoreibacter ascidiaceicola	strain=DSM 100566	GCA_900129235.1	1486859	1486859	type	True	86.9803	836	1309	95	below_threshold
Litoreibacter halocynthiae	strain=DSM 29467	GCA_004365635.1	1242689	1242689	type	True	86.3636	862	1309	95	below_threshold
Litoreibacter arenae	strain=DSM 19593	GCA_000442275.2	491388	491388	type	True	83.1423	728	1309	95	below_threshold
Litoreibacter janthinus	strain=DSM 26921	GCA_900111945.1	670154	670154	type	True	81.2765	737	1309	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	80.9853	684	1309	95	below_threshold
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	78.9568	544	1309	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.2858	141	1309	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.2038	161	1309	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.2004	205	1309	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.1876	190	1309	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	77.1444	189	1309	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	77.1444	189	1309	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	77.0277	192	1309	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.9866	192	1309	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.7393	169	1309	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.5854	159	1309	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.4739	171	1309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:21,628] [INFO] DFAST Taxonomy check result was written to GCF_003663885.1_ASM366388v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:21,629] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:21,629] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:21,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d9e33ce-003e-4a3b-9909-618b48387f56/dqc_reference/checkm_data
[2024-01-24 13:13:21,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:21,677] [INFO] Task started: CheckM
[2024-01-24 13:13:21,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003663885.1_ASM366388v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003663885.1_ASM366388v1_genomic.fna/checkm_input GCF_003663885.1_ASM366388v1_genomic.fna/checkm_result
[2024-01-24 13:14:03,665] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:03,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,685] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:03,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:03,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003663885.1_ASM366388v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:03,687] [INFO] Task started: Blastn
[2024-01-24 13:14:03,687] [INFO] Running command: blastn -query GCF_003663885.1_ASM366388v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d9e33ce-003e-4a3b-9909-618b48387f56/dqc_reference/reference_markers_gtdb.fasta -out GCF_003663885.1_ASM366388v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:04,768] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:04,772] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:04,772] [INFO] Target genome list was writen to GCF_003663885.1_ASM366388v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:04,781] [INFO] Task started: fastANI
[2024-01-24 13:14:04,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg22b63444-fc36-48e2-ab94-bc8543416f7c/GCF_003663885.1_ASM366388v1_genomic.fna.gz --refList GCF_003663885.1_ASM366388v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003663885.1_ASM366388v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:14,796] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:14,808] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:14,808] [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_003663885.1	s__Litoreibacter meonggei	100.0	1308	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129235.1	s__Litoreibacter ascidiaceicola	86.9952	835	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365635.1	s__Litoreibacter halocynthiae	86.3387	864	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442275.2	s__Litoreibacter arenae	83.1423	728	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111945.1	s__Litoreibacter janthinus	81.2765	737	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107015.1	s__Litoreibacter albidus	80.9949	683	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054285.1	s__Litoreibacter ponti	78.9725	544	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.2135	204	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	77.1736	191	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001258055.1	s__Phaeobacter italicus	77.1444	189	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.0579	250	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_017743735.1	s__Shimia sp017743735	77.0547	181	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCA_013215215.1	s__Cognatishimia sp013215215	76.9649	137	1309	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:14,810] [INFO] GTDB search result was written to GCF_003663885.1_ASM366388v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:14,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:14,815] [INFO] DFAST_QC result json was written to GCF_003663885.1_ASM366388v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:14,816] [INFO] DFAST_QC completed!
[2024-01-24 13:14:14,816] [INFO] Total running time: 0h1m22s