[2024-01-24 14:22:16,398] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:16,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:16,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a248b27-5d91-40f6-8ac5-1df9ebcd748d/dqc_reference
[2024-01-24 14:22:17,698] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:17,699] [INFO] Task started: Prodigal
[2024-01-24 14:22:17,699] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3602c61-856e-4b75-936e-90d2e4992e6c/GCF_010435915.1_ASM1043591v1_genomic.fna.gz | prodigal -d GCF_010435915.1_ASM1043591v1_genomic.fna/cds.fna -a GCF_010435915.1_ASM1043591v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:49,158] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:49,159] [INFO] Task started: HMMsearch
[2024-01-24 14:22:49,159] [INFO] Running command: hmmsearch --tblout GCF_010435915.1_ASM1043591v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a248b27-5d91-40f6-8ac5-1df9ebcd748d/dqc_reference/reference_markers.hmm GCF_010435915.1_ASM1043591v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:49,511] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:49,513] [INFO] Found 6/6 markers.
[2024-01-24 14:22:49,574] [INFO] Query marker FASTA was written to GCF_010435915.1_ASM1043591v1_genomic.fna/markers.fasta
[2024-01-24 14:22:49,574] [INFO] Task started: Blastn
[2024-01-24 14:22:49,574] [INFO] Running command: blastn -query GCF_010435915.1_ASM1043591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a248b27-5d91-40f6-8ac5-1df9ebcd748d/dqc_reference/reference_markers.fasta -out GCF_010435915.1_ASM1043591v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:50,166] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:50,171] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:50,171] [INFO] Target genome list was writen to GCF_010435915.1_ASM1043591v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:50,179] [INFO] Task started: fastANI
[2024-01-24 14:22:50,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3602c61-856e-4b75-936e-90d2e4992e6c/GCF_010435915.1_ASM1043591v1_genomic.fna.gz --refList GCF_010435915.1_ASM1043591v1_genomic.fna/target_genomes.txt --output GCF_010435915.1_ASM1043591v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:09,037] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:09,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a248b27-5d91-40f6-8ac5-1df9ebcd748d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:09,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a248b27-5d91-40f6-8ac5-1df9ebcd748d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:09,053] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:09,053] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:09,053] [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 terrae	strain=KCTC 52035	GCA_010435915.1	1968276	1968276	type	True	100.0	2482	2489	95	conclusive
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.8847	703	2489	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	77.7871	733	2489	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	77.6079	614	2489	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.3758	490	2489	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.3088	493	2489	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	77.2725	488	2489	95	below_threshold
Spirosoma aerolatum	strain=KACC 17939	GCA_002056795.1	1211326	1211326	type	True	77.0522	478	2489	95	below_threshold
Spirosoma pollinicola	strain=Ha7	GCA_002831565.1	2057025	2057025	type	True	77.004	379	2489	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	76.874	313	2489	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	76.8573	300	2489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:09,055] [INFO] DFAST Taxonomy check result was written to GCF_010435915.1_ASM1043591v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:09,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:09,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:09,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a248b27-5d91-40f6-8ac5-1df9ebcd748d/dqc_reference/checkm_data
[2024-01-24 14:23:09,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:09,122] [INFO] Task started: CheckM
[2024-01-24 14:23:09,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010435915.1_ASM1043591v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010435915.1_ASM1043591v1_genomic.fna/checkm_input GCF_010435915.1_ASM1043591v1_genomic.fna/checkm_result
[2024-01-24 14:24:36,049] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:36,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:36,079] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:36,079] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:36,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010435915.1_ASM1043591v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:36,080] [INFO] Task started: Blastn
[2024-01-24 14:24:36,081] [INFO] Running command: blastn -query GCF_010435915.1_ASM1043591v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a248b27-5d91-40f6-8ac5-1df9ebcd748d/dqc_reference/reference_markers_gtdb.fasta -out GCF_010435915.1_ASM1043591v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:36,850] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:36,855] [INFO] Selected 18 target genomes.
[2024-01-24 14:24:36,855] [INFO] Target genome list was writen to GCF_010435915.1_ASM1043591v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:36,875] [INFO] Task started: fastANI
[2024-01-24 14:24:36,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3602c61-856e-4b75-936e-90d2e4992e6c/GCF_010435915.1_ASM1043591v1_genomic.fna.gz --refList GCF_010435915.1_ASM1043591v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010435915.1_ASM1043591v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:03,774] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:03,787] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:03,787] [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_010435915.1	s__Spirosoma terrae	100.0	2482	2489	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	77.8847	703	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011604685.1	s__Spirosoma aureum	77.7919	732	2489	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	77.6079	614	2489	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	77.3644	492	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014117325.1	s__Spirosoma sp014117325	77.3349	487	2489	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	77.2822	467	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_014699005.1	s__Spirosoma profusum	77.2796	487	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965485.1	s__Spirosoma sp006965485	77.228	440	2489	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	77.1329	459	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112365.1	s__Spirosoma endophyticum	77.1104	477	2489	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	77.0413	480	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831565.1	s__Spirosoma pollinicola	76.9971	380	2489	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	76.867	314	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014282275.1	s__Spirosoma utsteinense	76.8573	300	2489	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.94	99.94	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:03,789] [INFO] GTDB search result was written to GCF_010435915.1_ASM1043591v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:03,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:03,793] [INFO] DFAST_QC result json was written to GCF_010435915.1_ASM1043591v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:03,793] [INFO] DFAST_QC completed!
[2024-01-24 14:25:03,793] [INFO] Total running time: 0h2m47s