[2024-01-24 13:12:52,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:52,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:52,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg666ea2c4-f36d-4d49-8258-de3aa2da5f77/dqc_reference
[2024-01-24 13:12:54,332] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:54,333] [INFO] Task started: Prodigal
[2024-01-24 13:12:54,333] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ee69625-3039-4779-9475-e473d61b886e/GCF_014201735.1_ASM1420173v1_genomic.fna.gz | prodigal -d GCF_014201735.1_ASM1420173v1_genomic.fna/cds.fna -a GCF_014201735.1_ASM1420173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:05,701] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:05,701] [INFO] Task started: HMMsearch
[2024-01-24 13:13:05,701] [INFO] Running command: hmmsearch --tblout GCF_014201735.1_ASM1420173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg666ea2c4-f36d-4d49-8258-de3aa2da5f77/dqc_reference/reference_markers.hmm GCF_014201735.1_ASM1420173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:06,098] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:06,099] [INFO] Found 6/6 markers.
[2024-01-24 13:13:06,139] [INFO] Query marker FASTA was written to GCF_014201735.1_ASM1420173v1_genomic.fna/markers.fasta
[2024-01-24 13:13:06,140] [INFO] Task started: Blastn
[2024-01-24 13:13:06,140] [INFO] Running command: blastn -query GCF_014201735.1_ASM1420173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg666ea2c4-f36d-4d49-8258-de3aa2da5f77/dqc_reference/reference_markers.fasta -out GCF_014201735.1_ASM1420173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:07,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:07,099] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:07,099] [INFO] Target genome list was writen to GCF_014201735.1_ASM1420173v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:07,114] [INFO] Task started: fastANI
[2024-01-24 13:13:07,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee69625-3039-4779-9475-e473d61b886e/GCF_014201735.1_ASM1420173v1_genomic.fna.gz --refList GCF_014201735.1_ASM1420173v1_genomic.fna/target_genomes.txt --output GCF_014201735.1_ASM1420173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:21,313] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:21,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg666ea2c4-f36d-4d49-8258-de3aa2da5f77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:21,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg666ea2c4-f36d-4d49-8258-de3aa2da5f77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:21,328] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:21,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:21,328] [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
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	100.0	1229	1229	95	conclusive
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	81.0082	572	1229	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	81.007	573	1229	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	80.2022	554	1229	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.1777	552	1229	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	79.9866	531	1229	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.7792	520	1229	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.7668	523	1229	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.6922	539	1229	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	79.6676	511	1229	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.4856	447	1229	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.4106	463	1229	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	79.2862	463	1229	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.2321	436	1229	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	79.1632	456	1229	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	76.7497	87	1229	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	76.473	139	1229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:21,330] [INFO] DFAST Taxonomy check result was written to GCF_014201735.1_ASM1420173v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:21,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:21,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:21,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg666ea2c4-f36d-4d49-8258-de3aa2da5f77/dqc_reference/checkm_data
[2024-01-24 13:13:21,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:21,372] [INFO] Task started: CheckM
[2024-01-24 13:13:21,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201735.1_ASM1420173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201735.1_ASM1420173v1_genomic.fna/checkm_input GCF_014201735.1_ASM1420173v1_genomic.fna/checkm_result
[2024-01-24 13:13:57,799] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:57,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:57,820] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:57,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:57,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201735.1_ASM1420173v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:57,821] [INFO] Task started: Blastn
[2024-01-24 13:13:57,821] [INFO] Running command: blastn -query GCF_014201735.1_ASM1420173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg666ea2c4-f36d-4d49-8258-de3aa2da5f77/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201735.1_ASM1420173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:59,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:59,234] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:59,234] [INFO] Target genome list was writen to GCF_014201735.1_ASM1420173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:59,268] [INFO] Task started: fastANI
[2024-01-24 13:13:59,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee69625-3039-4779-9475-e473d61b886e/GCF_014201735.1_ASM1420173v1_genomic.fna.gz --refList GCF_014201735.1_ASM1420173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201735.1_ASM1420173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:09,573] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:09,589] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:09,589] [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_014201735.1	s__Marinobacter oulmenensis	100.0	1229	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900114155.1	s__Marinobacter persicus	81.009	574	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002934325.1	s__Marinobacter persicus_A	80.8622	596	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002258215.1	s__Marinobacter vinifirmus	80.1861	556	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_900114925.1	s__Marinobacter pelagius	80.1653	552	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.1443	561	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	80.0584	448	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	79.7711	523	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007715.1	s__Marinobacter shengliensis	79.6886	538	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_001981305.1	s__Marinobacter lutaoensis	79.6661	512	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
GCF_001447155.2	s__Marinobacter sp001447155	79.6165	535	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013393545.1	s__Marinobacter sp013393545	79.5272	472	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	79.2568	467	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCA_014762755.1	s__Marinobacter sp014762755	79.2342	417	1229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,591] [INFO] GTDB search result was written to GCF_014201735.1_ASM1420173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:09,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:09,595] [INFO] DFAST_QC result json was written to GCF_014201735.1_ASM1420173v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:09,595] [INFO] DFAST_QC completed!
[2024-01-24 13:14:09,595] [INFO] Total running time: 0h1m17s