[2024-01-24 10:57:26,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a0f8272-6128-42ce-b4a2-d474cd84b884/dqc_reference
[2024-01-24 10:57:27,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:27,909] [INFO] Task started: Prodigal
[2024-01-24 10:57:27,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb374112-a37a-4d2c-bcf4-923ea8915df9/GCF_005116735.1_ASM511673v1_genomic.fna.gz | prodigal -d GCF_005116735.1_ASM511673v1_genomic.fna/cds.fna -a GCF_005116735.1_ASM511673v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:36,617] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:36,618] [INFO] Task started: HMMsearch
[2024-01-24 10:57:36,618] [INFO] Running command: hmmsearch --tblout GCF_005116735.1_ASM511673v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a0f8272-6128-42ce-b4a2-d474cd84b884/dqc_reference/reference_markers.hmm GCF_005116735.1_ASM511673v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:36,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:36,891] [INFO] Found 6/6 markers.
[2024-01-24 10:57:36,948] [INFO] Query marker FASTA was written to GCF_005116735.1_ASM511673v1_genomic.fna/markers.fasta
[2024-01-24 10:57:36,949] [INFO] Task started: Blastn
[2024-01-24 10:57:36,949] [INFO] Running command: blastn -query GCF_005116735.1_ASM511673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a0f8272-6128-42ce-b4a2-d474cd84b884/dqc_reference/reference_markers.fasta -out GCF_005116735.1_ASM511673v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:37,747] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:37,750] [INFO] Selected 27 target genomes.
[2024-01-24 10:57:37,751] [INFO] Target genome list was writen to GCF_005116735.1_ASM511673v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:37,794] [INFO] Task started: fastANI
[2024-01-24 10:57:37,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb374112-a37a-4d2c-bcf4-923ea8915df9/GCF_005116735.1_ASM511673v1_genomic.fna.gz --refList GCF_005116735.1_ASM511673v1_genomic.fna/target_genomes.txt --output GCF_005116735.1_ASM511673v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:56,940] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:56,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a0f8272-6128-42ce-b4a2-d474cd84b884/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:56,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a0f8272-6128-42ce-b4a2-d474cd84b884/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:56,952] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:56,953] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:56,953] [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	100.0	1202	1205	95	conclusive
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	78.5227	96	1205	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	78.5189	98	1205	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.8586	80	1205	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	77.5971	81	1205	95	below_threshold
Thalassomonas actiniarum	strain=A5K-106	GCA_000948975.1	485447	485447	type	True	77.5617	111	1205	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.3371	74	1205	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.1791	75	1205	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	77.0658	68	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:56,955] [INFO] DFAST Taxonomy check result was written to GCF_005116735.1_ASM511673v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:56,956] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:56,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:56,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a0f8272-6128-42ce-b4a2-d474cd84b884/dqc_reference/checkm_data
[2024-01-24 10:57:56,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:57,005] [INFO] Task started: CheckM
[2024-01-24 10:57:57,005] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116735.1_ASM511673v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116735.1_ASM511673v1_genomic.fna/checkm_input GCF_005116735.1_ASM511673v1_genomic.fna/checkm_result
[2024-01-24 10:58:28,397] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:28,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:28,415] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:28,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:28,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116735.1_ASM511673v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:28,416] [INFO] Task started: Blastn
[2024-01-24 10:58:28,416] [INFO] Running command: blastn -query GCF_005116735.1_ASM511673v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a0f8272-6128-42ce-b4a2-d474cd84b884/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116735.1_ASM511673v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:29,605] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:29,608] [INFO] Selected 14 target genomes.
[2024-01-24 10:58:29,609] [INFO] Target genome list was writen to GCF_005116735.1_ASM511673v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:29,618] [INFO] Task started: fastANI
[2024-01-24 10:58:29,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb374112-a37a-4d2c-bcf4-923ea8915df9/GCF_005116735.1_ASM511673v1_genomic.fna.gz --refList GCF_005116735.1_ASM511673v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005116735.1_ASM511673v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:39,337] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:39,347] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:39,348] [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_005116735.1	s__Thalassotalea_A mangrovi	100.0	1202	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007197775.1	s__Thalassotalea_A sp007197775	80.7834	556	1205	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_005843925.1	s__Thalassotalea_A litorea	79.7392	468	1205	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_001831495.1	s__Thalassotalea_A crassostreae	78.5189	98	1205	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_004752005.1	s__Thalassotalea_A sp004752005	78.4428	132	1205	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_007097525.1	s__Thalassotalea_A sp007097525	78.3951	107	1205	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_014656435.1	s__Thalassotalea_C marina	77.8586	80	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	77.774	102	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162925.1	s__Thalassotalea_A sp002162925	77.7379	129	1205	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_000764205.1	s__Thalassotalea_A sp000764205	77.5011	159	1205	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_007954275.1	s__Colwellia demingiae	77.0659	68	1205	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:39,352] [INFO] GTDB search result was written to GCF_005116735.1_ASM511673v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:39,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:39,358] [INFO] DFAST_QC result json was written to GCF_005116735.1_ASM511673v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:39,358] [INFO] DFAST_QC completed!
[2024-01-24 10:58:39,358] [INFO] Total running time: 0h1m13s