[2024-01-24 13:40:42,625] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:42,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:42,630] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc218768-5b9d-4a05-845d-bd52bb955071/dqc_reference
[2024-01-24 13:40:44,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,030] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg6122bd3d-8a16-4a48-9ebd-879e2e0dc6b2/GCF_003063625.1_ASM306362v1_genomic.fna.gz | prodigal -d GCF_003063625.1_ASM306362v1_genomic.fna/cds.fna -a GCF_003063625.1_ASM306362v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:57,106] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:57,107] [INFO] Task started: HMMsearch
[2024-01-24 13:40:57,107] [INFO] Running command: hmmsearch --tblout GCF_003063625.1_ASM306362v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc218768-5b9d-4a05-845d-bd52bb955071/dqc_reference/reference_markers.hmm GCF_003063625.1_ASM306362v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:57,535] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:57,536] [INFO] Found 6/6 markers.
[2024-01-24 13:40:57,588] [INFO] Query marker FASTA was written to GCF_003063625.1_ASM306362v1_genomic.fna/markers.fasta
[2024-01-24 13:40:57,588] [INFO] Task started: Blastn
[2024-01-24 13:40:57,588] [INFO] Running command: blastn -query GCF_003063625.1_ASM306362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc218768-5b9d-4a05-845d-bd52bb955071/dqc_reference/reference_markers.fasta -out GCF_003063625.1_ASM306362v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:58,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:58,407] [INFO] Selected 23 target genomes.
[2024-01-24 13:40:58,408] [INFO] Target genome list was writen to GCF_003063625.1_ASM306362v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:58,415] [INFO] Task started: fastANI
[2024-01-24 13:40:58,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg6122bd3d-8a16-4a48-9ebd-879e2e0dc6b2/GCF_003063625.1_ASM306362v1_genomic.fna.gz --refList GCF_003063625.1_ASM306362v1_genomic.fna/target_genomes.txt --output GCF_003063625.1_ASM306362v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:19,349] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:19,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc218768-5b9d-4a05-845d-bd52bb955071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:19,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc218768-5b9d-4a05-845d-bd52bb955071/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:19,364] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:19,364] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:19,364] [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
Saccharobesus litoralis	strain=CCB-QB4	GCA_003063625.1	2172099	2172099	type	True	100.0	1952	1956	95	conclusive
Vibrio porteresiae	strain=MSSRF30	GCA_024347055.1	435912	435912	type	True	79.5903	52	1956	95	below_threshold
Shewanella livingstonensis	strain=LMG 19866	GCA_003855395.1	150120	150120	type	True	78.8175	66	1956	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	78.4328	67	1956	95	below_threshold
Algibacillus agarilyticus	strain=RQJ05	GCA_003286125.1	2234133	2234133	type	True	78.3434	298	1956	95	below_threshold
Marinifaba aquimaris	strain=SM1970	GCA_013328345.1	2741323	2741323	type	True	78.156	158	1956	95	below_threshold
Gayadomonas joobiniege	strain=G7	GCA_000300815.1	1234606	1234606	type	True	78.087	105	1956	95	below_threshold
Catenovulum agarivorans	strain=YM01	GCA_000281085.1	1172192	1172192	type	True	78.0126	181	1956	95	below_threshold
Pseudoalteromonas rubra	strain=DSM 6842	GCA_000238295.4	43658	43658	suspected-type	True	77.7522	52	1956	95	below_threshold
Pseudoalteromonas prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	77.7316	90	1956	95	below_threshold
Catenovulum maritimum	strain=Q1	GCA_001050375.1	1513271	1513271	type	True	77.6931	149	1956	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.0335	67	1956	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	76.5086	79	1956	95	below_threshold
Shewanella psychromarinicola	strain=JCM 32090	GCA_023283865.1	2487742	2487742	type	True	76.4998	55	1956	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	76.4983	61	1956	95	below_threshold
Pseudoalteromonas denitrificans	strain=DSM 6059	GCA_900112265.1	43656	43656	type	True	76.4637	70	1956	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	76.4588	62	1956	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	76.4297	79	1956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,366] [INFO] DFAST Taxonomy check result was written to GCF_003063625.1_ASM306362v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:19,366] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:19,366] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:19,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc218768-5b9d-4a05-845d-bd52bb955071/dqc_reference/checkm_data
[2024-01-24 13:41:19,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:19,424] [INFO] Task started: CheckM
[2024-01-24 13:41:19,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003063625.1_ASM306362v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003063625.1_ASM306362v1_genomic.fna/checkm_input GCF_003063625.1_ASM306362v1_genomic.fna/checkm_result
[2024-01-24 13:42:03,030] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:03,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:03,052] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:03,053] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:03,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003063625.1_ASM306362v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:03,054] [INFO] Task started: Blastn
[2024-01-24 13:42:03,054] [INFO] Running command: blastn -query GCF_003063625.1_ASM306362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc218768-5b9d-4a05-845d-bd52bb955071/dqc_reference/reference_markers_gtdb.fasta -out GCF_003063625.1_ASM306362v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:04,152] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:04,156] [INFO] Selected 22 target genomes.
[2024-01-24 13:42:04,156] [INFO] Target genome list was writen to GCF_003063625.1_ASM306362v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:04,178] [INFO] Task started: fastANI
[2024-01-24 13:42:04,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg6122bd3d-8a16-4a48-9ebd-879e2e0dc6b2/GCF_003063625.1_ASM306362v1_genomic.fna.gz --refList GCF_003063625.1_ASM306362v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003063625.1_ASM306362v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:24,480] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:24,500] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:24,500] [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_003063625.1	s__Algibacillus sp003063625	100.0	1952	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Algibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001547935.1	s__Vibrio tritonius	79.7663	54	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850255.1	s__Pseudoalteromonas sp002850255	79.3394	80	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.4968	98.33	98.31	0.92	0.91	5	-
GCF_003855155.1	s__Shewanella sp002836275	78.4998	67	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	78.491	91	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286125.1	s__Algibacillus agarilyticus	78.371	306	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Algibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855395.1	s__Shewanella livingstonensis	78.343	64	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	78.2797	91	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_000300815.1	s__Catenovulum joobiniege	78.2385	106	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328345.1	s__Marinifaba aquimaris	78.1545	158	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Marinifaba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898095.1	s__Thalassotalea sp014898095	78.1101	88	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281085.1	s__Catenovulum agarivorans	77.9936	182	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000568405.1	s__Catenovulum agarivorans_A	77.8283	155	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050375.1	s__Catenovulum maritimum	77.6931	149	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	77.0335	67	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	76.9907	89	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153325.1	s__Photobacterium sp000153325	76.9344	58	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001565895.1	s__Paraglaciecola hydrolytica	76.5075	62	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378905.1	s__Paraglaciecola sp011378905	76.3021	51	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	75.6565	67	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:24,502] [INFO] GTDB search result was written to GCF_003063625.1_ASM306362v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:24,503] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:24,507] [INFO] DFAST_QC result json was written to GCF_003063625.1_ASM306362v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:24,507] [INFO] DFAST_QC completed!
[2024-01-24 13:42:24,507] [INFO] Total running time: 0h1m42s