[2024-01-24 14:19:45,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,039] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,040] [INFO] DQC Reference Directory: /var/lib/cwl/stgebcb8f3d-5716-4137-8bd1-d4f4f3a4673a/dqc_reference
[2024-01-24 14:19:46,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:46,790] [INFO] Task started: Prodigal
[2024-01-24 14:19:46,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg6916123b-14ea-490c-9f53-634cbcc697da/GCF_000019225.1_ASM1922v1_genomic.fna.gz | prodigal -d GCF_000019225.1_ASM1922v1_genomic.fna/cds.fna -a GCF_000019225.1_ASM1922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:16,233] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:16,233] [INFO] Task started: HMMsearch
[2024-01-24 14:20:16,234] [INFO] Running command: hmmsearch --tblout GCF_000019225.1_ASM1922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebcb8f3d-5716-4137-8bd1-d4f4f3a4673a/dqc_reference/reference_markers.hmm GCF_000019225.1_ASM1922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:16,750] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:16,751] [INFO] Found 6/6 markers.
[2024-01-24 14:20:16,825] [INFO] Query marker FASTA was written to GCF_000019225.1_ASM1922v1_genomic.fna/markers.fasta
[2024-01-24 14:20:16,826] [INFO] Task started: Blastn
[2024-01-24 14:20:16,826] [INFO] Running command: blastn -query GCF_000019225.1_ASM1922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebcb8f3d-5716-4137-8bd1-d4f4f3a4673a/dqc_reference/reference_markers.fasta -out GCF_000019225.1_ASM1922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:17,854] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:17,857] [INFO] Selected 24 target genomes.
[2024-01-24 14:20:17,858] [INFO] Target genome list was writen to GCF_000019225.1_ASM1922v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:17,873] [INFO] Task started: fastANI
[2024-01-24 14:20:17,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg6916123b-14ea-490c-9f53-634cbcc697da/GCF_000019225.1_ASM1922v1_genomic.fna.gz --refList GCF_000019225.1_ASM1922v1_genomic.fna/target_genomes.txt --output GCF_000019225.1_ASM1922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:34,552] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:34,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebcb8f3d-5716-4137-8bd1-d4f4f3a4673a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:34,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebcb8f3d-5716-4137-8bd1-d4f4f3a4673a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:34,564] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:34,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:34,565] [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
Cellvibrio japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	100.0	1522	1525	95	conclusive
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	77.817	197	1525	95	below_threshold
Simiduia agarivorans	strain=SA1 = DSM 21679	GCA_000305785.2	447471	447471	type	True	77.7431	92	1525	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	77.7194	91	1525	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	77.3055	83	1525	95	below_threshold
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	76.9398	130	1525	95	below_threshold
Simiduia agarivorans	strain=DSM 21679	GCA_000420285.1	447471	447471	type	True	76.9396	88	1525	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.9367	80	1525	95	below_threshold
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	76.923	166	1525	95	below_threshold
Pseudomonas fluvialis	strain=CCM 8778	GCA_014635625.1	1793966	1793966	suspected-type	True	76.493	53	1525	95	below_threshold
Aestuariicella albida	strain=HHU G3-2	GCA_018863235.1	2842452	2842452	type	True	76.2848	70	1525	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	76.0885	74	1525	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	76.0856	50	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:34,567] [INFO] DFAST Taxonomy check result was written to GCF_000019225.1_ASM1922v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:34,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:34,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:34,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebcb8f3d-5716-4137-8bd1-d4f4f3a4673a/dqc_reference/checkm_data
[2024-01-24 14:20:34,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:34,618] [INFO] Task started: CheckM
[2024-01-24 14:20:34,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000019225.1_ASM1922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000019225.1_ASM1922v1_genomic.fna/checkm_input GCF_000019225.1_ASM1922v1_genomic.fna/checkm_result
[2024-01-24 14:21:37,480] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:37,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:37,504] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:37,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:37,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000019225.1_ASM1922v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:37,505] [INFO] Task started: Blastn
[2024-01-24 14:21:37,505] [INFO] Running command: blastn -query GCF_000019225.1_ASM1922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebcb8f3d-5716-4137-8bd1-d4f4f3a4673a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000019225.1_ASM1922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:38,661] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:38,664] [INFO] Selected 20 target genomes.
[2024-01-24 14:21:38,664] [INFO] Target genome list was writen to GCF_000019225.1_ASM1922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:38,681] [INFO] Task started: fastANI
[2024-01-24 14:21:38,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg6916123b-14ea-490c-9f53-634cbcc697da/GCF_000019225.1_ASM1922v1_genomic.fna.gz --refList GCF_000019225.1_ASM1922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000019225.1_ASM1922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:54,055] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:54,076] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:54,076] [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_000019225.1	s__Cellvibrio japonicus	100.0	1523	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_008806975.1	s__Cellvibrio sp008806975	78.4538	348	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001183545.1	s__Cellvibrio sp001183545	78.2339	343	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806955.1	s__Cellvibrio sp000263355	78.1294	371	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCF_000766945.1	s__Cellvibrio mixtus_A	78.0351	337	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007605.1	s__Cellvibrio sp002007605	78.0153	410	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	97.66	97.66	0.90	0.90	2	-
GCF_004363885.1	s__Cellvibrio sp004363885	77.8568	339	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003056245.1	s__Cellvibrio sp003056245	77.8208	327	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483365.1	s__Cellvibrio sp002483365	77.8043	327	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000305785.2	s__Simiduia agarivorans	77.7514	93	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Simiduia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015182315.1	s__Cellvibrio polysaccharolyticus	77.7275	195	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483145.1	s__Cellvibrio sp002483145	77.6805	347	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858205.1	s__Cellvibrio sp903858205	77.6261	254	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953825.1	s__Cellvibrio sp000953825	77.6144	326	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003524365.1	s__Cellvibrio sp003524365	77.4389	263	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002162135.1	s__Cellvibrio sp002162135	77.2701	250	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076275.1	s__Microbulbifer sp003076275	77.1018	71	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712405.1	s__Cellvibrio sp016712405	76.9544	133	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:54,078] [INFO] GTDB search result was written to GCF_000019225.1_ASM1922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:54,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:54,082] [INFO] DFAST_QC result json was written to GCF_000019225.1_ASM1922v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:54,082] [INFO] DFAST_QC completed!
[2024-01-24 14:21:54,082] [INFO] Total running time: 0h2m9s