[2024-01-24 12:53:57,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:57,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:57,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg86886f39-3944-44dd-b514-f995ee7ae2dd/dqc_reference
[2024-01-24 12:53:58,461] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,462] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,462] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bb15572-dab5-4aa7-b66e-6157b8d52b8c/GCF_030409725.1_ASM3040972v1_genomic.fna.gz | prodigal -d GCF_030409725.1_ASM3040972v1_genomic.fna/cds.fna -a GCF_030409725.1_ASM3040972v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:06,564] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:06,565] [INFO] Task started: HMMsearch
[2024-01-24 12:54:06,565] [INFO] Running command: hmmsearch --tblout GCF_030409725.1_ASM3040972v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86886f39-3944-44dd-b514-f995ee7ae2dd/dqc_reference/reference_markers.hmm GCF_030409725.1_ASM3040972v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:06,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:06,851] [INFO] Found 6/6 markers.
[2024-01-24 12:54:06,883] [INFO] Query marker FASTA was written to GCF_030409725.1_ASM3040972v1_genomic.fna/markers.fasta
[2024-01-24 12:54:06,883] [INFO] Task started: Blastn
[2024-01-24 12:54:06,883] [INFO] Running command: blastn -query GCF_030409725.1_ASM3040972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86886f39-3944-44dd-b514-f995ee7ae2dd/dqc_reference/reference_markers.fasta -out GCF_030409725.1_ASM3040972v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:07,654] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:07,657] [INFO] Selected 29 target genomes.
[2024-01-24 12:54:07,658] [INFO] Target genome list was writen to GCF_030409725.1_ASM3040972v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:07,670] [INFO] Task started: fastANI
[2024-01-24 12:54:07,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb15572-dab5-4aa7-b66e-6157b8d52b8c/GCF_030409725.1_ASM3040972v1_genomic.fna.gz --refList GCF_030409725.1_ASM3040972v1_genomic.fna/target_genomes.txt --output GCF_030409725.1_ASM3040972v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:26,864] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:26,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86886f39-3944-44dd-b514-f995ee7ae2dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:26,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86886f39-3944-44dd-b514-f995ee7ae2dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:26,876] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:26,877] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:26,877] [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
Thalassotalea mangrovi	strain=ZS-4	GCA_005116735.1	2572245	2572245	type	True	78.7495	118	1082	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	78.567	95	1082	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	78.4173	99	1082	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	78.4054	142	1082	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	78.3181	140	1082	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.8738	85	1082	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.8643	84	1082	95	below_threshold
Thalassomonas actiniarum	strain=A5K-106	GCA_000948975.1	485447	485447	type	True	77.7542	75	1082	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.4898	72	1082	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	77.3866	55	1082	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.2072	77	1082	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	76.8172	56	1082	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	76.8165	59	1082	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	76.7744	59	1082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:26,879] [INFO] DFAST Taxonomy check result was written to GCF_030409725.1_ASM3040972v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:26,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:26,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:26,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86886f39-3944-44dd-b514-f995ee7ae2dd/dqc_reference/checkm_data
[2024-01-24 12:54:26,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:26,916] [INFO] Task started: CheckM
[2024-01-24 12:54:26,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409725.1_ASM3040972v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409725.1_ASM3040972v1_genomic.fna/checkm_input GCF_030409725.1_ASM3040972v1_genomic.fna/checkm_result
[2024-01-24 12:54:54,747] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:54,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:54,767] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:54,767] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:54,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409725.1_ASM3040972v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:54,768] [INFO] Task started: Blastn
[2024-01-24 12:54:54,768] [INFO] Running command: blastn -query GCF_030409725.1_ASM3040972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86886f39-3944-44dd-b514-f995ee7ae2dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409725.1_ASM3040972v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:55,920] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:55,925] [INFO] Selected 25 target genomes.
[2024-01-24 12:54:55,925] [INFO] Target genome list was writen to GCF_030409725.1_ASM3040972v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:55,964] [INFO] Task started: fastANI
[2024-01-24 12:54:55,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bb15572-dab5-4aa7-b66e-6157b8d52b8c/GCF_030409725.1_ASM3040972v1_genomic.fna.gz --refList GCF_030409725.1_ASM3040972v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409725.1_ASM3040972v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:10,125] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:10,139] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:55:10,139] [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_004752005.1	s__Thalassotalea_A sp004752005	79.0912	315	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	95.63	95.63	0.92	0.92	2	-
GCF_005116735.1	s__Thalassotalea_A mangrovi	78.7697	118	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097525.1	s__Thalassotalea_A sp007097525	78.5794	127	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197775.1	s__Thalassotalea_A sp007197775	78.5785	142	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111755.1	s__Thalassotalea_D agarivorans	78.5246	96	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744155.1	s__Thalassotalea sp017744155	78.3634	113	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001831495.1	s__Thalassotalea_A crassostreae	78.2909	141	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003390375.1	s__Thalassotalea euphylliae_A	77.9588	119	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	77.9422	128	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005843925.1	s__Thalassotalea_A litorea	77.94	135	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	77.8928	88	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439335.1	s__Litorilituus lipolyticus	77.8829	84	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898095.1	s__Thalassotalea sp014898095	77.7569	126	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764205.1	s__Thalassotalea_A sp000764205	77.7014	179	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	77.3295	88	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	77.2821	59	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_002076895.1	s__Cognaticolwellia beringensis	77.2661	92	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401725.1	s__GCA-2401725 sp002401725	76.4224	65	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:10,141] [INFO] GTDB search result was written to GCF_030409725.1_ASM3040972v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:10,142] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:10,145] [INFO] DFAST_QC result json was written to GCF_030409725.1_ASM3040972v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:10,145] [INFO] DFAST_QC completed!
[2024-01-24 12:55:10,145] [INFO] Total running time: 0h1m13s