[2024-01-24 15:18:19,423] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,425] [INFO] DQC Reference Directory: /var/lib/cwl/stge2658520-a673-441a-a1f7-ae37ea307dd4/dqc_reference
[2024-01-24 15:18:20,586] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,587] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,587] [INFO] Running command: gunzip -c /var/lib/cwl/stg6676a1e1-6370-40a1-8e9e-ae7f861b78fe/GCF_003086355.1_ASM308635v2_genomic.fna.gz | prodigal -d GCF_003086355.1_ASM308635v2_genomic.fna/cds.fna -a GCF_003086355.1_ASM308635v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:25,727] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:25,728] [INFO] Task started: HMMsearch
[2024-01-24 15:18:25,728] [INFO] Running command: hmmsearch --tblout GCF_003086355.1_ASM308635v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2658520-a673-441a-a1f7-ae37ea307dd4/dqc_reference/reference_markers.hmm GCF_003086355.1_ASM308635v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:25,994] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:25,996] [INFO] Found 6/6 markers.
[2024-01-24 15:18:26,018] [INFO] Query marker FASTA was written to GCF_003086355.1_ASM308635v2_genomic.fna/markers.fasta
[2024-01-24 15:18:26,019] [INFO] Task started: Blastn
[2024-01-24 15:18:26,019] [INFO] Running command: blastn -query GCF_003086355.1_ASM308635v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge2658520-a673-441a-a1f7-ae37ea307dd4/dqc_reference/reference_markers.fasta -out GCF_003086355.1_ASM308635v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:26,614] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:26,619] [INFO] Selected 22 target genomes.
[2024-01-24 15:18:26,620] [INFO] Target genome list was writen to GCF_003086355.1_ASM308635v2_genomic.fna/target_genomes.txt
[2024-01-24 15:18:26,633] [INFO] Task started: fastANI
[2024-01-24 15:18:26,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg6676a1e1-6370-40a1-8e9e-ae7f861b78fe/GCF_003086355.1_ASM308635v2_genomic.fna.gz --refList GCF_003086355.1_ASM308635v2_genomic.fna/target_genomes.txt --output GCF_003086355.1_ASM308635v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:37,834] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:37,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2658520-a673-441a-a1f7-ae37ea307dd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:37,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2658520-a673-441a-a1f7-ae37ea307dd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:37,861] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:37,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:37,861] [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
Streptococcus chenjunshii	strain=Z15	GCA_003086355.2	2173853	2173853	type	True	100.0	811	814	95	conclusive
Streptococcus pantholopis	strain=TA 26	GCA_001642085.1	1811193	1811193	type	True	82.3376	515	814	95	below_threshold
Streptococcus pseudoporcinus	strain=NCTC13786	GCA_900637075.1	361101	361101	type	True	79.3373	63	814	95	below_threshold
Streptococcus pseudoporcinus	strain=LQ 940-04	GCA_000188035.3	361101	361101	type	True	78.9621	62	814	95	below_threshold
Streptococcus agalactiae	strain=NCTC8181	GCA_900458965.1	1311	1311	suspected-type	True	78.7829	71	814	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1018	GCA_016403165.1	150055	150055	type	True	78.7052	80	814	95	below_threshold
Streptococcus sobrinus	strain=SL1	GCA_003172995.1	1310	1310	type	True	78.6629	69	814	95	below_threshold
Streptococcus ferus	strain=NCTC12278	GCA_900475025.1	1345	1345	type	True	78.1911	91	814	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	77.3146	74	814	95	below_threshold
Streptococcus ferus	strain=DSM 20646	GCA_000372425.1	1345	1345	type	True	77.2726	85	814	95	below_threshold
Streptococcus ratti	strain=FA-1	GCA_000286075.1	1341	1341	suspected-type	True	77.2531	122	814	95	below_threshold
Streptococcus caballi	strain=DSM 19004	GCA_000379985.1	439220	439220	type	True	77.2509	94	814	95	below_threshold
Streptococcus agalactiae	strain=ATCC 13813	GCA_000186445.1	1311	1311	type	True	77.2061	63	814	95	below_threshold
Streptococcus ratti	strain=DSM 20564	GCA_000347915.1	1341	1341	suspected-type	True	77.1183	113	814	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	77.0472	65	814	95	below_threshold
Streptococcus sobrinus	strain=DSM 20742	GCA_000686605.1	1310	1310	type	True	76.9757	64	814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:37,863] [INFO] DFAST Taxonomy check result was written to GCF_003086355.1_ASM308635v2_genomic.fna/tc_result.tsv
[2024-01-24 15:18:37,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:37,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:37,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2658520-a673-441a-a1f7-ae37ea307dd4/dqc_reference/checkm_data
[2024-01-24 15:18:37,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:37,896] [INFO] Task started: CheckM
[2024-01-24 15:18:37,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003086355.1_ASM308635v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003086355.1_ASM308635v2_genomic.fna/checkm_input GCF_003086355.1_ASM308635v2_genomic.fna/checkm_result
[2024-01-24 15:19:00,672] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:00,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:00,690] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:00,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:00,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003086355.1_ASM308635v2_genomic.fna/markers.fasta)
[2024-01-24 15:19:00,692] [INFO] Task started: Blastn
[2024-01-24 15:19:00,692] [INFO] Running command: blastn -query GCF_003086355.1_ASM308635v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge2658520-a673-441a-a1f7-ae37ea307dd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003086355.1_ASM308635v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:01,485] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:01,488] [INFO] Selected 21 target genomes.
[2024-01-24 15:19:01,489] [INFO] Target genome list was writen to GCF_003086355.1_ASM308635v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:01,505] [INFO] Task started: fastANI
[2024-01-24 15:19:01,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg6676a1e1-6370-40a1-8e9e-ae7f861b78fe/GCF_003086355.1_ASM308635v2_genomic.fna.gz --refList GCF_003086355.1_ASM308635v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003086355.1_ASM308635v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:12,516] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:12,531] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:12,531] [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_003086355.1	s__Streptococcus chenjunshii	100.0	812	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_001642085.1	s__Streptococcus pantholopis	82.349	511	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188035.1	s__Streptococcus pseudoporcinus	79.0743	62	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.36	97.79	0.89	0.85	10	-
GCF_001431045.1	s__Streptococcus orisasini	78.2606	133	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013343115.1	s__Streptococcus sanguinis_H	78.1491	66	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.75	95.06	0.92	0.88	13	-
GCF_002355215.1	s__Streptococcus troglodytae	78.0024	99	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006739205.1	s__Streptococcus mutans	77.9026	109	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.12	98.73	0.95	0.87	261	-
GCF_012277075.1	s__Streptococcus alactolyticus	77.8814	63	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.29	98.88	0.94	0.83	11	-
GCF_000380105.1	s__Streptococcus orisratti	77.8597	117	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423745.1	s__Streptococcus plurextorum	77.4549	53	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376985.1	s__Streptococcus henryi	77.3146	74	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_000286075.1	s__Streptococcus ratti	77.2742	121	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_000372425.1	s__Streptococcus ferus	77.2726	85	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001937065.1	s__Streptococcus sp001937065	77.2613	113	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186445.1	s__Streptococcus agalactiae	77.2061	63	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_011038795.1	s__Streptococcus sp011038795	77.174	76	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	99.03	0.90	0.90	2	-
GCF_000379985.1	s__Streptococcus caballi	77.1698	94	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686605.1	s__Streptococcus sobrinus	76.9768	64	814	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.93	98.60	0.95	0.92	52	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:12,533] [INFO] GTDB search result was written to GCF_003086355.1_ASM308635v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:12,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:12,537] [INFO] DFAST_QC result json was written to GCF_003086355.1_ASM308635v2_genomic.fna/dqc_result.json
[2024-01-24 15:19:12,537] [INFO] DFAST_QC completed!
[2024-01-24 15:19:12,537] [INFO] Total running time: 0h0m53s