[2024-01-25 18:09:05,888] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:05,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:05,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg6669118d-9494-4263-8772-69258ddfbd05/dqc_reference
[2024-01-25 18:09:07,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:07,058] [INFO] Task started: Prodigal
[2024-01-25 18:09:07,058] [INFO] Running command: gunzip -c /var/lib/cwl/stga1426c34-a964-4ab7-a7ee-49273c0c1560/GCF_001043175.1_ASM104317v1_genomic.fna.gz | prodigal -d GCF_001043175.1_ASM104317v1_genomic.fna/cds.fna -a GCF_001043175.1_ASM104317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:17,341] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:17,342] [INFO] Task started: HMMsearch
[2024-01-25 18:09:17,342] [INFO] Running command: hmmsearch --tblout GCF_001043175.1_ASM104317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6669118d-9494-4263-8772-69258ddfbd05/dqc_reference/reference_markers.hmm GCF_001043175.1_ASM104317v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:17,588] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:17,589] [INFO] Found 6/6 markers.
[2024-01-25 18:09:17,630] [INFO] Query marker FASTA was written to GCF_001043175.1_ASM104317v1_genomic.fna/markers.fasta
[2024-01-25 18:09:17,630] [INFO] Task started: Blastn
[2024-01-25 18:09:17,630] [INFO] Running command: blastn -query GCF_001043175.1_ASM104317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6669118d-9494-4263-8772-69258ddfbd05/dqc_reference/reference_markers.fasta -out GCF_001043175.1_ASM104317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:18,326] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:18,328] [INFO] Selected 22 target genomes.
[2024-01-25 18:09:18,329] [INFO] Target genome list was writen to GCF_001043175.1_ASM104317v1_genomic.fna/target_genomes.txt
[2024-01-25 18:09:18,347] [INFO] Task started: fastANI
[2024-01-25 18:09:18,348] [INFO] Running command: fastANI --query /var/lib/cwl/stga1426c34-a964-4ab7-a7ee-49273c0c1560/GCF_001043175.1_ASM104317v1_genomic.fna.gz --refList GCF_001043175.1_ASM104317v1_genomic.fna/target_genomes.txt --output GCF_001043175.1_ASM104317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:09:34,019] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:34,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6669118d-9494-4263-8772-69258ddfbd05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:09:34,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6669118d-9494-4263-8772-69258ddfbd05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:09:34,032] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:09:34,032] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:09:34,033] [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 psychrophilus	strain=20041	GCA_001043175.1	330734	330734	type	True	100.0	1332	1332	95	conclusive
Marinobacter gelidimuriae	strain=BF04_CF-4	GCA_000372805.1	2739064	2739064	type	True	91.7271	837	1332	95	below_threshold
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	79.2468	353	1332	95	below_threshold
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	78.6992	329	1332	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	78.098	282	1332	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	77.9992	263	1332	95	below_threshold
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	77.8525	184	1332	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	77.8494	253	1332	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	77.7935	290	1332	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	77.7676	244	1332	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	77.7214	242	1332	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	77.7025	265	1332	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	77.6307	248	1332	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	77.6199	276	1332	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	77.485	256	1332	95	below_threshold
Marinobacter changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	77.3827	196	1332	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	77.3481	248	1332	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	77.3419	190	1332	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	77.3167	166	1332	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.0242	50	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:09:34,034] [INFO] DFAST Taxonomy check result was written to GCF_001043175.1_ASM104317v1_genomic.fna/tc_result.tsv
[2024-01-25 18:09:34,034] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:09:34,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:09:34,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6669118d-9494-4263-8772-69258ddfbd05/dqc_reference/checkm_data
[2024-01-25 18:09:34,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:09:34,077] [INFO] Task started: CheckM
[2024-01-25 18:09:34,077] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001043175.1_ASM104317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001043175.1_ASM104317v1_genomic.fna/checkm_input GCF_001043175.1_ASM104317v1_genomic.fna/checkm_result
[2024-01-25 18:10:07,583] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:07,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:07,623] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:07,623] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:07,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001043175.1_ASM104317v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:07,624] [INFO] Task started: Blastn
[2024-01-25 18:10:07,624] [INFO] Running command: blastn -query GCF_001043175.1_ASM104317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6669118d-9494-4263-8772-69258ddfbd05/dqc_reference/reference_markers_gtdb.fasta -out GCF_001043175.1_ASM104317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:08,839] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:08,842] [INFO] Selected 10 target genomes.
[2024-01-25 18:10:08,842] [INFO] Target genome list was writen to GCF_001043175.1_ASM104317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:08,864] [INFO] Task started: fastANI
[2024-01-25 18:10:08,864] [INFO] Running command: fastANI --query /var/lib/cwl/stga1426c34-a964-4ab7-a7ee-49273c0c1560/GCF_001043175.1_ASM104317v1_genomic.fna.gz --refList GCF_001043175.1_ASM104317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001043175.1_ASM104317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:17,321] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:17,328] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:17,329] [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_001043175.1	s__Marinobacter psychrophilus	100.0	1331	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.61	96.50	0.89	0.87	4	conclusive
GCF_000169375.1	s__Marinobacter sp000169375	93.1469	1067	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372805.1	s__Marinobacter gelidimuriae	91.7271	837	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563885.1	s__Marinobacter sp002563885	90.0749	1000	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.52	0.89	0.89	2	-
GCF_007671675.1	s__Marinobacter maritimus	78.698	330	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
GCF_016820575.1	s__Marinobacter sediminum	78.0145	260	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	77.7505	246	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933275.1	s__Marinobacter maroccanus	77.6288	276	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017301335.1	s__Marinobacter sp017301335	77.527	237	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009193265.1	s__Marinobacter changyiensis	77.3827	196	1332	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:17,330] [INFO] GTDB search result was written to GCF_001043175.1_ASM104317v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:17,330] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:17,335] [INFO] DFAST_QC result json was written to GCF_001043175.1_ASM104317v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:17,335] [INFO] DFAST_QC completed!
[2024-01-25 18:10:17,335] [INFO] Total running time: 0h1m11s