[2024-01-24 13:27:46,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,432] [INFO] DQC Reference Directory: /var/lib/cwl/stgf844f0b4-0d9d-48a9-8598-35bd5476f396/dqc_reference
[2024-01-24 13:27:47,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,854] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg00c7d520-bae7-4fae-a534-ab83624b85f9/GCF_014636685.1_ASM1463668v1_genomic.fna.gz | prodigal -d GCF_014636685.1_ASM1463668v1_genomic.fna/cds.fna -a GCF_014636685.1_ASM1463668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:05,760] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:05,761] [INFO] Task started: HMMsearch
[2024-01-24 13:28:05,761] [INFO] Running command: hmmsearch --tblout GCF_014636685.1_ASM1463668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf844f0b4-0d9d-48a9-8598-35bd5476f396/dqc_reference/reference_markers.hmm GCF_014636685.1_ASM1463668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:06,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:06,155] [INFO] Found 6/6 markers.
[2024-01-24 13:28:06,204] [INFO] Query marker FASTA was written to GCF_014636685.1_ASM1463668v1_genomic.fna/markers.fasta
[2024-01-24 13:28:06,204] [INFO] Task started: Blastn
[2024-01-24 13:28:06,204] [INFO] Running command: blastn -query GCF_014636685.1_ASM1463668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf844f0b4-0d9d-48a9-8598-35bd5476f396/dqc_reference/reference_markers.fasta -out GCF_014636685.1_ASM1463668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:06,894] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:06,898] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:06,898] [INFO] Target genome list was writen to GCF_014636685.1_ASM1463668v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:06,906] [INFO] Task started: fastANI
[2024-01-24 13:28:06,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c7d520-bae7-4fae-a534-ab83624b85f9/GCF_014636685.1_ASM1463668v1_genomic.fna.gz --refList GCF_014636685.1_ASM1463668v1_genomic.fna/target_genomes.txt --output GCF_014636685.1_ASM1463668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:20,069] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:20,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf844f0b4-0d9d-48a9-8598-35bd5476f396/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:20,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf844f0b4-0d9d-48a9-8598-35bd5476f396/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:20,085] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:20,085] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:20,085] [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
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	100.0	1832	1834	95	conclusive
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	99.9956	1812	1834	95	conclusive
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	77.2891	258	1834	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	77.1725	260	1834	95	below_threshold
Dokdonia sinensis	strain=SH27	GCA_003688895.1	2479847	2479847	type	True	77.1222	209	1834	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.0083	99	1834	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.9061	114	1834	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.856	72	1834	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.6579	92	1834	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.6435	121	1834	95	below_threshold
Mangrovimonas xylaniphaga	strain=ST2L12	GCA_001280435.1	1645915	1645915	type	True	76.6323	70	1834	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.629	114	1834	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.6185	133	1834	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.5285	121	1834	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	76.4939	141	1834	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.4844	140	1834	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.4587	117	1834	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.3802	148	1834	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.8528	62	1834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:20,087] [INFO] DFAST Taxonomy check result was written to GCF_014636685.1_ASM1463668v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:20,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:20,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:20,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf844f0b4-0d9d-48a9-8598-35bd5476f396/dqc_reference/checkm_data
[2024-01-24 13:28:20,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:20,139] [INFO] Task started: CheckM
[2024-01-24 13:28:20,139] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636685.1_ASM1463668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636685.1_ASM1463668v1_genomic.fna/checkm_input GCF_014636685.1_ASM1463668v1_genomic.fna/checkm_result
[2024-01-24 13:29:14,686] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:14,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:14,711] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:14,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:14,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636685.1_ASM1463668v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:14,712] [INFO] Task started: Blastn
[2024-01-24 13:29:14,712] [INFO] Running command: blastn -query GCF_014636685.1_ASM1463668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf844f0b4-0d9d-48a9-8598-35bd5476f396/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636685.1_ASM1463668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:15,628] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:15,632] [INFO] Selected 16 target genomes.
[2024-01-24 13:29:15,632] [INFO] Target genome list was writen to GCF_014636685.1_ASM1463668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:15,655] [INFO] Task started: fastANI
[2024-01-24 13:29:15,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c7d520-bae7-4fae-a534-ab83624b85f9/GCF_014636685.1_ASM1463668v1_genomic.fna.gz --refList GCF_014636685.1_ASM1463668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636685.1_ASM1463668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:27,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:27,177] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:27,177] [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_900188275.1	s__Dokdonia pacifica	99.9956	1812	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_011762485.1	s__Yeosuana marina	77.2906	131	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095655.1	s__Dokdonia sp003095655	77.2899	254	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653755.1	s__Dokdonia donghaensis	77.2732	258	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
GCF_000212355.1	s__Dokdonia sp000212355	77.2316	256	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	98.49	98.49	0.97	0.97	2	-
GCF_003688895.1	s__Dokdonia sinensis	77.1345	208	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355805.1	s__Dokdonia sp000355805	77.1231	244	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.9655	132	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827465.1	s__Dokdonia sp007827465	76.9046	215	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	76.725	142	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007489275.1	s__Aquimarina algiphila	76.6331	156	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.5212	145	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	76.4809	139	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	76.4446	112	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	76.3759	147	1834	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:27,181] [INFO] GTDB search result was written to GCF_014636685.1_ASM1463668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:27,182] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:27,194] [INFO] DFAST_QC result json was written to GCF_014636685.1_ASM1463668v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:27,194] [INFO] DFAST_QC completed!
[2024-01-24 13:29:27,194] [INFO] Total running time: 0h1m41s