[2024-01-24 14:28:15,632] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,634] [INFO] DQC Reference Directory: /var/lib/cwl/stge74e1541-9c1c-474e-a4aa-1ef2035f83a4/dqc_reference
[2024-01-24 14:28:17,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,938] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,939] [INFO] Running command: gunzip -c /var/lib/cwl/stga572f44f-3af1-4832-b07a-46594f0f7df2/GCF_019264345.1_ASM1926434v1_genomic.fna.gz | prodigal -d GCF_019264345.1_ASM1926434v1_genomic.fna/cds.fna -a GCF_019264345.1_ASM1926434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:30,653] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:30,654] [INFO] Task started: HMMsearch
[2024-01-24 14:28:30,654] [INFO] Running command: hmmsearch --tblout GCF_019264345.1_ASM1926434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge74e1541-9c1c-474e-a4aa-1ef2035f83a4/dqc_reference/reference_markers.hmm GCF_019264345.1_ASM1926434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:30,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:30,942] [INFO] Found 6/6 markers.
[2024-01-24 14:28:30,980] [INFO] Query marker FASTA was written to GCF_019264345.1_ASM1926434v1_genomic.fna/markers.fasta
[2024-01-24 14:28:30,980] [INFO] Task started: Blastn
[2024-01-24 14:28:30,981] [INFO] Running command: blastn -query GCF_019264345.1_ASM1926434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge74e1541-9c1c-474e-a4aa-1ef2035f83a4/dqc_reference/reference_markers.fasta -out GCF_019264345.1_ASM1926434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:31,827] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:31,831] [INFO] Selected 19 target genomes.
[2024-01-24 14:28:31,831] [INFO] Target genome list was writen to GCF_019264345.1_ASM1926434v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:32,119] [INFO] Task started: fastANI
[2024-01-24 14:28:32,120] [INFO] Running command: fastANI --query /var/lib/cwl/stga572f44f-3af1-4832-b07a-46594f0f7df2/GCF_019264345.1_ASM1926434v1_genomic.fna.gz --refList GCF_019264345.1_ASM1926434v1_genomic.fna/target_genomes.txt --output GCF_019264345.1_ASM1926434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:48,674] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:48,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge74e1541-9c1c-474e-a4aa-1ef2035f83a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:48,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge74e1541-9c1c-474e-a4aa-1ef2035f83a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:48,689] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:48,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:48,690] [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 arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	100.0	1366	1367	95	conclusive
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	81.3327	794	1367	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	81.2999	825	1367	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	81.2769	783	1367	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	80.7616	721	1367	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	80.6932	719	1367	95	below_threshold
Marinobacter salinus	strain=Hb8	GCA_001854125.1	1874317	1874317	type	True	80.6856	708	1367	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	80.6849	733	1367	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.6214	686	1367	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	80.607	740	1367	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	79.9925	574	1367	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	79.9219	572	1367	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.9152	569	1367	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	79.8617	607	1367	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.8483	548	1367	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.5512	591	1367	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.5163	564	1367	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.3309	550	1367	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.3698	82	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:48,692] [INFO] DFAST Taxonomy check result was written to GCF_019264345.1_ASM1926434v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:48,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:48,693] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:48,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge74e1541-9c1c-474e-a4aa-1ef2035f83a4/dqc_reference/checkm_data
[2024-01-24 14:28:48,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:48,734] [INFO] Task started: CheckM
[2024-01-24 14:28:48,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019264345.1_ASM1926434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019264345.1_ASM1926434v1_genomic.fna/checkm_input GCF_019264345.1_ASM1926434v1_genomic.fna/checkm_result
[2024-01-24 14:29:29,804] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:29,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:29,823] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:29,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:29,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019264345.1_ASM1926434v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:29,824] [INFO] Task started: Blastn
[2024-01-24 14:29:29,824] [INFO] Running command: blastn -query GCF_019264345.1_ASM1926434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge74e1541-9c1c-474e-a4aa-1ef2035f83a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_019264345.1_ASM1926434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:31,237] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:31,241] [INFO] Selected 21 target genomes.
[2024-01-24 14:29:31,241] [INFO] Target genome list was writen to GCF_019264345.1_ASM1926434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:31,263] [INFO] Task started: fastANI
[2024-01-24 14:29:31,264] [INFO] Running command: fastANI --query /var/lib/cwl/stga572f44f-3af1-4832-b07a-46594f0f7df2/GCF_019264345.1_ASM1926434v1_genomic.fna.gz --refList GCF_019264345.1_ASM1926434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019264345.1_ASM1926434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:47,746] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:47,765] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:29:47,765] [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_000830985.1	s__Marinobacter similis	81.3327	794	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871205.1	s__Marinobacter alexandrii	81.2892	827	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
GCF_016820575.1	s__Marinobacter sediminum	81.2855	782	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	80.7712	731	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.7417	669	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	80.702	718	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_002933295.1	s__Marinobacter flavimaris	80.6815	733	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_009617755.1	s__Marinobacter salsuginis	80.6362	733	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCF_900114925.1	s__Marinobacter pelagius	80.6313	685	1367	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	80.5959	741	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188315.1	s__Marinobacter sp900188315	80.5325	692	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	80.4545	698	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCA_018623515.1	s__Marinobacter sp018623515	80.4054	563	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003030785.1	s__Marinobacter sp003030785	80.3062	422	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	80.2614	624	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000397065.2	s__Marinobacter lipolyticus	79.984	576	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	79.96	624	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	79.9591	516	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708045.1	s__Marinobacter nitratireducens	79.8637	606	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.86	98.83	0.90	0.89	3	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.8326	547	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_001447155.2	s__Marinobacter sp001447155	79.4512	565	1367	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 14:29:47,767] [INFO] GTDB search result was written to GCF_019264345.1_ASM1926434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:47,768] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:47,773] [INFO] DFAST_QC result json was written to GCF_019264345.1_ASM1926434v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:47,773] [INFO] DFAST_QC completed!
[2024-01-24 14:29:47,773] [INFO] Total running time: 0h1m32s