[2024-01-25 17:38:05,395] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:05,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:05,396] [INFO] DQC Reference Directory: /var/lib/cwl/stg41bf58eb-1b20-4a3d-b513-958ac0e1de9c/dqc_reference
[2024-01-25 17:38:06,583] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:06,584] [INFO] Task started: Prodigal
[2024-01-25 17:38:06,584] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2fc0f14-fd48-4341-b725-9ee78e476f4d/GCF_014117325.1_ASM1411732v1_genomic.fna.gz | prodigal -d GCF_014117325.1_ASM1411732v1_genomic.fna/cds.fna -a GCF_014117325.1_ASM1411732v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:38,885] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:38,885] [INFO] Task started: HMMsearch
[2024-01-25 17:38:38,885] [INFO] Running command: hmmsearch --tblout GCF_014117325.1_ASM1411732v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41bf58eb-1b20-4a3d-b513-958ac0e1de9c/dqc_reference/reference_markers.hmm GCF_014117325.1_ASM1411732v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:39,221] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:39,223] [INFO] Found 6/6 markers.
[2024-01-25 17:38:39,288] [INFO] Query marker FASTA was written to GCF_014117325.1_ASM1411732v1_genomic.fna/markers.fasta
[2024-01-25 17:38:39,288] [INFO] Task started: Blastn
[2024-01-25 17:38:39,288] [INFO] Running command: blastn -query GCF_014117325.1_ASM1411732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41bf58eb-1b20-4a3d-b513-958ac0e1de9c/dqc_reference/reference_markers.fasta -out GCF_014117325.1_ASM1411732v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:39,882] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:39,886] [INFO] Selected 19 target genomes.
[2024-01-25 17:38:39,886] [INFO] Target genome list was writen to GCF_014117325.1_ASM1411732v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:39,908] [INFO] Task started: fastANI
[2024-01-25 17:38:39,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2fc0f14-fd48-4341-b725-9ee78e476f4d/GCF_014117325.1_ASM1411732v1_genomic.fna.gz --refList GCF_014117325.1_ASM1411732v1_genomic.fna/target_genomes.txt --output GCF_014117325.1_ASM1411732v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:09,021] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:09,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41bf58eb-1b20-4a3d-b513-958ac0e1de9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:09,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41bf58eb-1b20-4a3d-b513-958ac0e1de9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:09,032] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:39:09,032] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:39:09,032] [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 arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	81.6123	1739	2951	95	below_threshold
Spirosoma pollinicola	strain=Ha7	GCA_002831565.1	2057025	2057025	type	True	78.2652	804	2951	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	78.0082	659	2951	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.9328	697	2951	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	77.876	770	2951	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.8227	638	2951	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.8078	724	2951	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.7772	768	2951	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	77.7164	592	2951	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.6061	646	2951	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.568	616	2951	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	77.5464	524	2951	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	77.424	509	2951	95	below_threshold
Spirosoma spitsbergense	strain=DSM 19989	GCA_000374085.1	431554	431554	type	True	77.3796	562	2951	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	76.9693	342	2951	95	below_threshold
Larkinella terrae	strain=KCTC 52001	GCA_009668025.1	2025311	2025311	type	True	76.8069	212	2951	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	75.917	131	2951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:09,033] [INFO] DFAST Taxonomy check result was written to GCF_014117325.1_ASM1411732v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:09,034] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:09,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:09,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41bf58eb-1b20-4a3d-b513-958ac0e1de9c/dqc_reference/checkm_data
[2024-01-25 17:39:09,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:09,113] [INFO] Task started: CheckM
[2024-01-25 17:39:09,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014117325.1_ASM1411732v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014117325.1_ASM1411732v1_genomic.fna/checkm_input GCF_014117325.1_ASM1411732v1_genomic.fna/checkm_result
[2024-01-25 17:40:35,466] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:35,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:35,512] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:35,512] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:35,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014117325.1_ASM1411732v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:35,514] [INFO] Task started: Blastn
[2024-01-25 17:40:35,514] [INFO] Running command: blastn -query GCF_014117325.1_ASM1411732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41bf58eb-1b20-4a3d-b513-958ac0e1de9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014117325.1_ASM1411732v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:36,325] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:36,328] [INFO] Selected 12 target genomes.
[2024-01-25 17:40:36,328] [INFO] Target genome list was writen to GCF_014117325.1_ASM1411732v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:36,344] [INFO] Task started: fastANI
[2024-01-25 17:40:36,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2fc0f14-fd48-4341-b725-9ee78e476f4d/GCF_014117325.1_ASM1411732v1_genomic.fna.gz --refList GCF_014117325.1_ASM1411732v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014117325.1_ASM1411732v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:58,781] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:58,790] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:58,790] [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_014117325.1	s__Spirosoma sp014117325	100.0	2945	2951	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_009754945.1	s__Spirosoma sp009754945	81.597	1742	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003259005.1	s__Spirosoma sp003259005	80.7937	1573	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006965485.1	s__Spirosoma sp006965485	80.5697	1513	2951	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	78.1541	690	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898575.1	s__Spirosoma sp001898575	78.0646	771	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900230225.1	s__Spirosoma fluviale	78.0047	658	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974425.1	s__Spirosoma radiotolerans	77.9201	701	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112365.1	s__Spirosoma endophyticum	77.862	776	2951	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	77.7987	726	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002056795.1	s__Spirosoma aerolatum	77.768	768	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010233585.1	s__Spirosoma endbachense	77.5959	648	2951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:58,791] [INFO] GTDB search result was written to GCF_014117325.1_ASM1411732v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:58,792] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:58,796] [INFO] DFAST_QC result json was written to GCF_014117325.1_ASM1411732v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:58,796] [INFO] DFAST_QC completed!
[2024-01-25 17:40:58,796] [INFO] Total running time: 0h2m53s