[2024-01-25 17:38:20,764] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:20,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:20,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dbfecd5-4bde-425b-b1ab-601ad0b08a5b/dqc_reference
[2024-01-25 17:38:21,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:21,908] [INFO] Task started: Prodigal
[2024-01-25 17:38:21,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ce9a42a-8573-4d79-a86a-06123dfa7ae1/GCF_014191715.1_ASM1419171v1_genomic.fna.gz | prodigal -d GCF_014191715.1_ASM1419171v1_genomic.fna/cds.fna -a GCF_014191715.1_ASM1419171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:30,657] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:30,657] [INFO] Task started: HMMsearch
[2024-01-25 17:38:30,658] [INFO] Running command: hmmsearch --tblout GCF_014191715.1_ASM1419171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dbfecd5-4bde-425b-b1ab-601ad0b08a5b/dqc_reference/reference_markers.hmm GCF_014191715.1_ASM1419171v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:30,878] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:30,879] [INFO] Found 6/6 markers.
[2024-01-25 17:38:30,909] [INFO] Query marker FASTA was written to GCF_014191715.1_ASM1419171v1_genomic.fna/markers.fasta
[2024-01-25 17:38:30,909] [INFO] Task started: Blastn
[2024-01-25 17:38:30,909] [INFO] Running command: blastn -query GCF_014191715.1_ASM1419171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dbfecd5-4bde-425b-b1ab-601ad0b08a5b/dqc_reference/reference_markers.fasta -out GCF_014191715.1_ASM1419171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:31,638] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:31,641] [INFO] Selected 28 target genomes.
[2024-01-25 17:38:31,642] [INFO] Target genome list was writen to GCF_014191715.1_ASM1419171v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:31,649] [INFO] Task started: fastANI
[2024-01-25 17:38:31,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ce9a42a-8573-4d79-a86a-06123dfa7ae1/GCF_014191715.1_ASM1419171v1_genomic.fna.gz --refList GCF_014191715.1_ASM1419171v1_genomic.fna/target_genomes.txt --output GCF_014191715.1_ASM1419171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:51,455] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:51,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dbfecd5-4bde-425b-b1ab-601ad0b08a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:51,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dbfecd5-4bde-425b-b1ab-601ad0b08a5b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:51,470] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:51,470] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:51,470] [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
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	100.0	1159	1159	95	conclusive
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.7993	131	1159	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.5565	135	1159	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	77.4895	164	1159	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.3696	120	1159	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	77.3654	137	1159	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	77.0868	89	1159	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	77.0829	89	1159	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	76.9408	66	1159	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	76.927	66	1159	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	76.7732	83	1159	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	76.6931	67	1159	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	76.6467	76	1159	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.6042	107	1159	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.5736	63	1159	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	76.547	72	1159	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.5171	85	1159	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	76.5093	81	1159	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	76.5021	84	1159	95	below_threshold
Pseudohaliea rubra	strain=DSM 19751	GCA_000764025.1	475795	475795	type	True	76.3457	58	1159	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	76.2837	65	1159	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.2778	69	1159	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	76.2669	72	1159	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.1964	78	1159	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	76.1932	69	1159	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	75.9419	60	1159	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:51,472] [INFO] DFAST Taxonomy check result was written to GCF_014191715.1_ASM1419171v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:51,473] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:51,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:51,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dbfecd5-4bde-425b-b1ab-601ad0b08a5b/dqc_reference/checkm_data
[2024-01-25 17:38:51,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:51,513] [INFO] Task started: CheckM
[2024-01-25 17:38:51,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191715.1_ASM1419171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191715.1_ASM1419171v1_genomic.fna/checkm_input GCF_014191715.1_ASM1419171v1_genomic.fna/checkm_result
[2024-01-25 17:39:20,825] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:20,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:20,853] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:20,854] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:20,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191715.1_ASM1419171v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:20,854] [INFO] Task started: Blastn
[2024-01-25 17:39:20,854] [INFO] Running command: blastn -query GCF_014191715.1_ASM1419171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dbfecd5-4bde-425b-b1ab-601ad0b08a5b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191715.1_ASM1419171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:22,222] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:22,225] [INFO] Selected 22 target genomes.
[2024-01-25 17:39:22,225] [INFO] Target genome list was writen to GCF_014191715.1_ASM1419171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:22,257] [INFO] Task started: fastANI
[2024-01-25 17:39:22,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ce9a42a-8573-4d79-a86a-06123dfa7ae1/GCF_014191715.1_ASM1419171v1_genomic.fna.gz --refList GCF_014191715.1_ASM1419171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191715.1_ASM1419171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:36,923] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:36,937] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:36,937] [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_014191715.1	s__Litorivivens lipolytica	100.0	1159	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002710725.1	s__Litorivivens sp002710725	81.0282	497	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415025.1	s__Litorivivens sp002415025	77.8596	333	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	99.88	99.82	0.96	0.94	3	-
GCF_000420325.1	s__Spongiibacter tropicus	77.4895	164	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_016132545.1	s__CSC3-9 sp016132545	77.3858	136	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	77.3244	122	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422345.1	s__Spongiibacter marinus_A	77.2896	105	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	77.0644	140	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	76.9769	65	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCF_001641755.2	s__Microbulbifer flavimaris	76.9675	81	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	76.828	53	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003597125.1	s__Alcanivorax profundi	76.6931	67	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
GCF_003457605.1	s__Halioglobus sediminis	76.6433	104	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651805.1	s__Marinobacterium_A aestuarii	76.5744	71	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	76.5624	83	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340525.1	s__Chromatocurvus halotolerans	76.4988	55	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002699145.1	s__Halioglobus sp002699145	76.4705	86	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_017776525.1	s__Marinobacterium alkalitolerans	76.1932	69	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	76.1642	78	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067195.1	s__Marortus sp018067195	76.089	74	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206575.1	s__Salinicola endophyticus	75.9647	59	1159	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.06	99.06	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:36,939] [INFO] GTDB search result was written to GCF_014191715.1_ASM1419171v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:36,939] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:36,944] [INFO] DFAST_QC result json was written to GCF_014191715.1_ASM1419171v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:36,945] [INFO] DFAST_QC completed!
[2024-01-25 17:39:36,945] [INFO] Total running time: 0h1m16s