[2024-01-24 14:14:06,243] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:06,248] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:06,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f646e62-df00-40da-aa74-b7d6c1a18e40/dqc_reference
[2024-01-24 14:14:07,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,627] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg66b53ffc-347c-44bb-a390-e28f5ffe1289/GCF_004785685.1_ASM478568v1_genomic.fna.gz | prodigal -d GCF_004785685.1_ASM478568v1_genomic.fna/cds.fna -a GCF_004785685.1_ASM478568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:19,240] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:19,241] [INFO] Task started: HMMsearch
[2024-01-24 14:14:19,241] [INFO] Running command: hmmsearch --tblout GCF_004785685.1_ASM478568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f646e62-df00-40da-aa74-b7d6c1a18e40/dqc_reference/reference_markers.hmm GCF_004785685.1_ASM478568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:19,556] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:19,557] [INFO] Found 6/6 markers.
[2024-01-24 14:14:19,593] [INFO] Query marker FASTA was written to GCF_004785685.1_ASM478568v1_genomic.fna/markers.fasta
[2024-01-24 14:14:19,594] [INFO] Task started: Blastn
[2024-01-24 14:14:19,594] [INFO] Running command: blastn -query GCF_004785685.1_ASM478568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f646e62-df00-40da-aa74-b7d6c1a18e40/dqc_reference/reference_markers.fasta -out GCF_004785685.1_ASM478568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:20,399] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:20,402] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:20,403] [INFO] Target genome list was writen to GCF_004785685.1_ASM478568v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:20,457] [INFO] Task started: fastANI
[2024-01-24 14:14:20,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b53ffc-347c-44bb-a390-e28f5ffe1289/GCF_004785685.1_ASM478568v1_genomic.fna.gz --refList GCF_004785685.1_ASM478568v1_genomic.fna/target_genomes.txt --output GCF_004785685.1_ASM478568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:32,781] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:32,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f646e62-df00-40da-aa74-b7d6c1a18e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:32,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f646e62-df00-40da-aa74-b7d6c1a18e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:32,800] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:32,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:32,801] [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 confluentis	strain=HJM-18	GCA_004785685.1	1697557	1697557	type	True	100.0	1239	1239	95	conclusive
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	99.9992	1239	1239	95	conclusive
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	81.3333	782	1239	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	79.7685	533	1239	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.7057	579	1239	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	79.5589	503	1239	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	79.4996	539	1239	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	79.4727	498	1239	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.2866	495	1239	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	79.1949	459	1239	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.1748	503	1239	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	79.0501	459	1239	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.7729	464	1239	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	78.7463	470	1239	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.504	329	1239	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.4013	395	1239	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:32,803] [INFO] DFAST Taxonomy check result was written to GCF_004785685.1_ASM478568v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:32,803] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:32,803] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:32,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f646e62-df00-40da-aa74-b7d6c1a18e40/dqc_reference/checkm_data
[2024-01-24 14:14:32,805] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:32,851] [INFO] Task started: CheckM
[2024-01-24 14:14:32,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004785685.1_ASM478568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004785685.1_ASM478568v1_genomic.fna/checkm_input GCF_004785685.1_ASM478568v1_genomic.fna/checkm_result
[2024-01-24 14:15:09,437] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:09,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.15%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:09,467] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:09,468] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:09,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004785685.1_ASM478568v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:09,469] [INFO] Task started: Blastn
[2024-01-24 14:15:09,469] [INFO] Running command: blastn -query GCF_004785685.1_ASM478568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f646e62-df00-40da-aa74-b7d6c1a18e40/dqc_reference/reference_markers_gtdb.fasta -out GCF_004785685.1_ASM478568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:11,033] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:11,037] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:11,037] [INFO] Target genome list was writen to GCF_004785685.1_ASM478568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:11,055] [INFO] Task started: fastANI
[2024-01-24 14:15:11,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b53ffc-347c-44bb-a390-e28f5ffe1289/GCF_004785685.1_ASM478568v1_genomic.fna.gz --refList GCF_004785685.1_ASM478568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004785685.1_ASM478568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:25,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:25,417] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:25,417] [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_004785685.1	s__Marinobacter confluentis	100.0	1239	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008795985.1	s__Marinobacter halotolerans	81.3303	780	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686085.1	s__Marinobacter sp000686085	79.9306	607	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005298175.1	s__Marinobacter sp005298175	79.8341	600	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344045.1	s__Marinobacter vulgaris	79.7681	533	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008795955.1	s__Marinobacter sp008795955	79.6967	580	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000831005.1	s__Marinobacter salarius	79.6158	555	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.84	96.73	0.88	0.79	21	-
GCF_000170835.1	s__Marinobacter algicola	79.5213	538	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	79.453	500	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115175.1	s__Marinobacter gudaonensis	79.1748	503	1239	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	79.174	471	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCA_002726615.1	s__Marinobacter sp002726615	79.1197	366	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.30	0.75	0.64	3	-
GCF_003315345.1	s__Marinobacter pelagius_A	79.0927	482	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933295.1	s__Marinobacter flavimaris	79.0402	461	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_002934325.1	s__Marinobacter persicus_A	78.8995	363	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCA_000830985.1	s__Marinobacter similis	78.7729	464	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447155.2	s__Marinobacter sp001447155	78.7712	469	1239	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 14:15:25,419] [INFO] GTDB search result was written to GCF_004785685.1_ASM478568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:25,419] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:25,423] [INFO] DFAST_QC result json was written to GCF_004785685.1_ASM478568v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:25,424] [INFO] DFAST_QC completed!
[2024-01-24 14:15:25,424] [INFO] Total running time: 0h1m19s