[2023-06-19 14:15:42,192] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:15:42,195] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:15:42,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg643d7b3f-3a99-44c0-ad2a-f28382b25f84/dqc_reference
[2023-06-19 14:15:43,465] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:15:43,466] [INFO] Task started: Prodigal
[2023-06-19 14:15:43,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c9213b2-33fe-4d39-9ff9-90e912470727/GCA_018607905.1_ASM1860790v1_genomic.fna.gz | prodigal -d GCA_018607905.1_ASM1860790v1_genomic.fna/cds.fna -a GCA_018607905.1_ASM1860790v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:15:53,674] [INFO] Task succeeded: Prodigal
[2023-06-19 14:15:53,674] [INFO] Task started: HMMsearch
[2023-06-19 14:15:53,674] [INFO] Running command: hmmsearch --tblout GCA_018607905.1_ASM1860790v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg643d7b3f-3a99-44c0-ad2a-f28382b25f84/dqc_reference/reference_markers.hmm GCA_018607905.1_ASM1860790v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:15:53,978] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:15:53,980] [INFO] Found 6/6 markers.
[2023-06-19 14:15:54,011] [INFO] Query marker FASTA was written to GCA_018607905.1_ASM1860790v1_genomic.fna/markers.fasta
[2023-06-19 14:15:54,011] [INFO] Task started: Blastn
[2023-06-19 14:15:54,011] [INFO] Running command: blastn -query GCA_018607905.1_ASM1860790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg643d7b3f-3a99-44c0-ad2a-f28382b25f84/dqc_reference/reference_markers.fasta -out GCA_018607905.1_ASM1860790v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:15:54,750] [INFO] Task succeeded: Blastn
[2023-06-19 14:15:54,760] [INFO] Selected 30 target genomes.
[2023-06-19 14:15:54,760] [INFO] Target genome list was writen to GCA_018607905.1_ASM1860790v1_genomic.fna/target_genomes.txt
[2023-06-19 14:15:54,769] [INFO] Task started: fastANI
[2023-06-19 14:15:54,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c9213b2-33fe-4d39-9ff9-90e912470727/GCA_018607905.1_ASM1860790v1_genomic.fna.gz --refList GCA_018607905.1_ASM1860790v1_genomic.fna/target_genomes.txt --output GCA_018607905.1_ASM1860790v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:16:14,802] [INFO] Task succeeded: fastANI
[2023-06-19 14:16:14,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg643d7b3f-3a99-44c0-ad2a-f28382b25f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:16:14,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg643d7b3f-3a99-44c0-ad2a-f28382b25f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:16:14,819] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:16:14,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:16:14,820] [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
Amylibacter kogurei	strain=4G11	GCA_002742285.1	1889778	1889778	type	True	76.4977	105	1016	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	76.3235	88	1016	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.1494	64	1016	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	76.1223	69	1016	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.1033	91	1016	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.0936	90	1016	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	76.0156	58	1016	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.0005	68	1016	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	75.9835	73	1016	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	75.9363	72	1016	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	75.9363	72	1016	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	75.9039	74	1016	95	below_threshold
Falsihalocynthiibacter arcticus	strain=PAMC 20958	GCA_000812665.2	1579316	1579316	type	True	75.9023	57	1016	95	below_threshold
Nereida ignava	strain=DSM 16309	GCA_900114125.1	282199	282199	type	True	75.8735	60	1016	95	below_threshold
Nereida ignava	strain=CECT 5292	GCA_001049735.1	282199	282199	type	True	75.8704	60	1016	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	75.8563	64	1016	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	75.5672	51	1016	95	below_threshold
Aquimixticola soesokkakensis	strain=CECT 8620	GCA_900172375.1	1519096	1519096	type	True	75.5312	55	1016	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	75.4832	63	1016	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	75.4456	61	1016	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.1332	50	1016	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:16:14,822] [INFO] DFAST Taxonomy check result was written to GCA_018607905.1_ASM1860790v1_genomic.fna/tc_result.tsv
[2023-06-19 14:16:14,823] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:16:14,823] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:16:14,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg643d7b3f-3a99-44c0-ad2a-f28382b25f84/dqc_reference/checkm_data
[2023-06-19 14:16:14,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:16:14,860] [INFO] Task started: CheckM
[2023-06-19 14:16:14,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607905.1_ASM1860790v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607905.1_ASM1860790v1_genomic.fna/checkm_input GCA_018607905.1_ASM1860790v1_genomic.fna/checkm_result
[2023-06-19 14:16:49,168] [INFO] Task succeeded: CheckM
[2023-06-19 14:16:49,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:16:49,199] [INFO] ===== Completeness check finished =====
[2023-06-19 14:16:49,200] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:16:49,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607905.1_ASM1860790v1_genomic.fna/markers.fasta)
[2023-06-19 14:16:49,200] [INFO] Task started: Blastn
[2023-06-19 14:16:49,201] [INFO] Running command: blastn -query GCA_018607905.1_ASM1860790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg643d7b3f-3a99-44c0-ad2a-f28382b25f84/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607905.1_ASM1860790v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:16:50,325] [INFO] Task succeeded: Blastn
[2023-06-19 14:16:50,331] [INFO] Selected 24 target genomes.
[2023-06-19 14:16:50,331] [INFO] Target genome list was writen to GCA_018607905.1_ASM1860790v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:16:50,344] [INFO] Task started: fastANI
[2023-06-19 14:16:50,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c9213b2-33fe-4d39-9ff9-90e912470727/GCA_018607905.1_ASM1860790v1_genomic.fna.gz --refList GCA_018607905.1_ASM1860790v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607905.1_ASM1860790v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:17:05,822] [INFO] Task succeeded: fastANI
[2023-06-19 14:17:05,849] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:17:05,849] [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
GCA_018607905.1	s__Amylibacter sp002387535	100.0	1008	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	99.84	99.84	0.91	0.91	2	conclusive
GCF_014643735.1	s__Amylibacter cionae	77.5929	276	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719615.1	s__Amylibacter sediminis	77.428	253	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018223125.1	s__Amylibacter sp018223125	77.2067	255	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860325.1	s__Amylibacter lutimaris	77.1797	256	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003447515.1	s__Amylibacter sp003447515	76.9138	162	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002732995.1	s__Profundibacter sp002732995	76.3235	68	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458335.1	s__Cognatishimia activa	76.1388	63	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	99.97	99.97	0.99	0.99	2	-
GCA_017854675.1	s__Sulfitobacter sp017854675	76.0973	80	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401045.1	s__Amylibacter sp002401045	76.0628	50	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469545.1	s__Amylibacter sp002469545	76.056	55	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amylibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	75.9614	70	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	75.9187	70	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000812665.2	s__Halocynthiibacter_B arcticus	75.9023	57	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313015.1	s__OMPR01 sp900313015	75.7027	70	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__OMPR01	95.0	97.69	97.65	0.92	0.91	5	-
GCF_000511355.1	s__Leisingera methylohalidivorans	75.5423	50	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172375.1	s__Aquimixticola soesokkakensis	75.4746	54	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aquimixticola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 14:17:05,851] [INFO] GTDB search result was written to GCA_018607905.1_ASM1860790v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:17:05,852] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:17:05,857] [INFO] DFAST_QC result json was written to GCA_018607905.1_ASM1860790v1_genomic.fna/dqc_result.json
[2023-06-19 14:17:05,857] [INFO] DFAST_QC completed!
[2023-06-19 14:17:05,857] [INFO] Total running time: 0h1m24s