[2024-01-24 14:30:31,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:31,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:31,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg56b8e51f-aa4d-467d-a1b1-d7bcb8e7992f/dqc_reference
[2024-01-24 14:30:33,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:33,802] [INFO] Task started: Prodigal
[2024-01-24 14:30:33,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f9920b3-bd5c-4bdb-bcbb-b128c84bd1f7/GCF_011604685.1_ASM1160468v1_genomic.fna.gz | prodigal -d GCF_011604685.1_ASM1160468v1_genomic.fna/cds.fna -a GCF_011604685.1_ASM1160468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:15,829] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:15,829] [INFO] Task started: HMMsearch
[2024-01-24 14:31:15,829] [INFO] Running command: hmmsearch --tblout GCF_011604685.1_ASM1160468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56b8e51f-aa4d-467d-a1b1-d7bcb8e7992f/dqc_reference/reference_markers.hmm GCF_011604685.1_ASM1160468v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:16,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:16,337] [INFO] Found 6/6 markers.
[2024-01-24 14:31:16,417] [INFO] Query marker FASTA was written to GCF_011604685.1_ASM1160468v1_genomic.fna/markers.fasta
[2024-01-24 14:31:16,418] [INFO] Task started: Blastn
[2024-01-24 14:31:16,418] [INFO] Running command: blastn -query GCF_011604685.1_ASM1160468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56b8e51f-aa4d-467d-a1b1-d7bcb8e7992f/dqc_reference/reference_markers.fasta -out GCF_011604685.1_ASM1160468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:17,157] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:17,164] [INFO] Selected 16 target genomes.
[2024-01-24 14:31:17,164] [INFO] Target genome list was writen to GCF_011604685.1_ASM1160468v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:17,178] [INFO] Task started: fastANI
[2024-01-24 14:31:17,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f9920b3-bd5c-4bdb-bcbb-b128c84bd1f7/GCF_011604685.1_ASM1160468v1_genomic.fna.gz --refList GCF_011604685.1_ASM1160468v1_genomic.fna/target_genomes.txt --output GCF_011604685.1_ASM1160468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:40,518] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:40,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56b8e51f-aa4d-467d-a1b1-d7bcb8e7992f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:40,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56b8e51f-aa4d-467d-a1b1-d7bcb8e7992f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:40,540] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:40,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:40,541] [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
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	100.0	2965	2966	95	conclusive
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	92.8636	2672	2966	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	78.9654	993	2966	95	below_threshold
Spirosoma terrae	strain=KCTC 52035	GCA_010435915.1	1968276	1968276	type	True	77.8312	731	2966	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.7545	709	2966	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.7333	489	2966	95	below_threshold
Spirosoma pollinicola	strain=Ha7	GCA_002831565.1	2057025	2057025	type	True	77.707	547	2966	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.4498	532	2966	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.3982	564	2966	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.2167	490	2966	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.1884	527	2966	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.1533	359	2966	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.1054	358	2966	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	76.9278	372	2966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:40,568] [INFO] DFAST Taxonomy check result was written to GCF_011604685.1_ASM1160468v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:40,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:40,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:40,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56b8e51f-aa4d-467d-a1b1-d7bcb8e7992f/dqc_reference/checkm_data
[2024-01-24 14:31:40,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:40,649] [INFO] Task started: CheckM
[2024-01-24 14:31:40,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011604685.1_ASM1160468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011604685.1_ASM1160468v1_genomic.fna/checkm_input GCF_011604685.1_ASM1160468v1_genomic.fna/checkm_result
[2024-01-24 14:33:30,545] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:30,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:30,571] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:30,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:30,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011604685.1_ASM1160468v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:30,572] [INFO] Task started: Blastn
[2024-01-24 14:33:30,572] [INFO] Running command: blastn -query GCF_011604685.1_ASM1160468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56b8e51f-aa4d-467d-a1b1-d7bcb8e7992f/dqc_reference/reference_markers_gtdb.fasta -out GCF_011604685.1_ASM1160468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:31,445] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:31,448] [INFO] Selected 14 target genomes.
[2024-01-24 14:33:31,448] [INFO] Target genome list was writen to GCF_011604685.1_ASM1160468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:31,462] [INFO] Task started: fastANI
[2024-01-24 14:33:31,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f9920b3-bd5c-4bdb-bcbb-b128c84bd1f7/GCF_011604685.1_ASM1160468v1_genomic.fna.gz --refList GCF_011604685.1_ASM1160468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011604685.1_ASM1160468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:51,930] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:51,947] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:51,948] [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_011604685.1	s__Spirosoma aureum	100.0	2964	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010233585.1	s__Spirosoma endbachense	92.8599	2673	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010747415.1	s__Spirosoma agri	78.9681	991	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010435915.1	s__Spirosoma terrae	77.8453	728	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000024525.1	s__Spirosoma linguale	77.7622	532	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009754945.1	s__Spirosoma sp009754945	77.7571	707	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	77.7265	490	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230225.1	s__Spirosoma fluviale	77.4441	533	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699035.1	s__Spirosoma validum	77.3986	564	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374025.1	s__Spirosoma panaciterrae	77.2025	489	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699005.1	s__Spirosoma profusum	77.1938	528	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870035.1	s__Spirosoma lacussanchae	77.1494	358	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.0982	359	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_000374065.1	s__Spirosoma luteum	76.9181	371	2966	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:33:51,949] [INFO] GTDB search result was written to GCF_011604685.1_ASM1160468v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:51,950] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:51,954] [INFO] DFAST_QC result json was written to GCF_011604685.1_ASM1160468v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:51,954] [INFO] DFAST_QC completed!
[2024-01-24 14:33:51,954] [INFO] Total running time: 0h3m21s