[2024-01-24 14:22:03,787] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:03,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:03,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg1641ab0f-8cbf-438f-bc76-e4807a1f05ac/dqc_reference
[2024-01-24 14:22:05,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,238] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,238] [INFO] Running command: gunzip -c /var/lib/cwl/stg8de7d054-d95e-46ee-b5a2-27f820fb6338/GCF_900475025.1_41906_G01_genomic.fna.gz | prodigal -d GCF_900475025.1_41906_G01_genomic.fna/cds.fna -a GCF_900475025.1_41906_G01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:09,833] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:09,834] [INFO] Task started: HMMsearch
[2024-01-24 14:22:09,834] [INFO] Running command: hmmsearch --tblout GCF_900475025.1_41906_G01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1641ab0f-8cbf-438f-bc76-e4807a1f05ac/dqc_reference/reference_markers.hmm GCF_900475025.1_41906_G01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:10,073] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:10,074] [INFO] Found 6/6 markers.
[2024-01-24 14:22:10,097] [INFO] Query marker FASTA was written to GCF_900475025.1_41906_G01_genomic.fna/markers.fasta
[2024-01-24 14:22:10,098] [INFO] Task started: Blastn
[2024-01-24 14:22:10,098] [INFO] Running command: blastn -query GCF_900475025.1_41906_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1641ab0f-8cbf-438f-bc76-e4807a1f05ac/dqc_reference/reference_markers.fasta -out GCF_900475025.1_41906_G01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:10,703] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:10,707] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:10,708] [INFO] Target genome list was writen to GCF_900475025.1_41906_G01_genomic.fna/target_genomes.txt
[2024-01-24 14:22:10,723] [INFO] Task started: fastANI
[2024-01-24 14:22:10,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg8de7d054-d95e-46ee-b5a2-27f820fb6338/GCF_900475025.1_41906_G01_genomic.fna.gz --refList GCF_900475025.1_41906_G01_genomic.fna/target_genomes.txt --output GCF_900475025.1_41906_G01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:17,813] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:17,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1641ab0f-8cbf-438f-bc76-e4807a1f05ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:17,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1641ab0f-8cbf-438f-bc76-e4807a1f05ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:17,829] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:17,829] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:17,829] [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 ferus	strain=NCTC12278	GCA_900475025.1	1345	1345	type	True	100.0	623	624	95	conclusive
Streptococcus ferus	strain=DSM 20646	GCA_000372425.1	1345	1345	type	True	99.9857	607	624	95	conclusive
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	81.4252	113	624	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	80.1845	67	624	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	80.0722	76	624	95	below_threshold
Streptococcus ratti	strain=FA-1	GCA_000286075.1	1341	1341	suspected-type	True	79.6596	187	624	95	below_threshold
Streptococcus thermophilus	strain=ATCC 19258	GCA_010120595.1	1308	1308	type	True	79.5795	85	624	95	below_threshold
Streptococcus ratti	strain=DSM 20564	GCA_000347915.1	1341	1341	suspected-type	True	79.5564	172	624	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.4189	71	624	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	79.2612	86	624	95	below_threshold
Streptococcus sanguinis	strain=NCTC7863	GCA_900475505.1	1305	1305	suspected-type	True	78.9961	88	624	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	78.8841	68	624	95	below_threshold
Streptococcus pantholopis	strain=TA 26	GCA_001642085.1	1811193	1811193	type	True	78.6372	95	624	95	below_threshold
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	78.6256	77	624	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.5417	64	624	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.4785	68	624	95	below_threshold
Streptococcus troglodytae	strain=TKU 31	GCA_002355215.1	1111760	1111760	type	True	78.3048	157	624	95	below_threshold
Streptococcus devriesei	strain=DSM 19639	GCA_000423725.1	231233	231233	type	True	78.2938	158	624	95	below_threshold
Streptococcus peroris	strain=ATCC 700780	GCA_000187585.1	68891	68891	type	True	78.2192	63	624	95	below_threshold
Streptococcus sanguinis	strain=NCTC 7863	GCA_001593525.1	1305	1305	suspected-type	True	78.005	78	624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:17,831] [INFO] DFAST Taxonomy check result was written to GCF_900475025.1_41906_G01_genomic.fna/tc_result.tsv
[2024-01-24 14:22:17,832] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:17,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:17,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1641ab0f-8cbf-438f-bc76-e4807a1f05ac/dqc_reference/checkm_data
[2024-01-24 14:22:17,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:17,854] [INFO] Task started: CheckM
[2024-01-24 14:22:17,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900475025.1_41906_G01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900475025.1_41906_G01_genomic.fna/checkm_input GCF_900475025.1_41906_G01_genomic.fna/checkm_result
[2024-01-24 14:22:38,737] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:38,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:38,757] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:38,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:38,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900475025.1_41906_G01_genomic.fna/markers.fasta)
[2024-01-24 14:22:38,758] [INFO] Task started: Blastn
[2024-01-24 14:22:38,758] [INFO] Running command: blastn -query GCF_900475025.1_41906_G01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1641ab0f-8cbf-438f-bc76-e4807a1f05ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_900475025.1_41906_G01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:39,597] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:39,600] [INFO] Selected 27 target genomes.
[2024-01-24 14:22:39,600] [INFO] Target genome list was writen to GCF_900475025.1_41906_G01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:39,628] [INFO] Task started: fastANI
[2024-01-24 14:22:39,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg8de7d054-d95e-46ee-b5a2-27f820fb6338/GCF_900475025.1_41906_G01_genomic.fna.gz --refList GCF_900475025.1_41906_G01_genomic.fna/target_genomes_gtdb.txt --output GCF_900475025.1_41906_G01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:49,013] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:49,037] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:49,037] [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_000372425.1	s__Streptococcus ferus	99.9857	607	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018137985.1	s__Streptococcus sp018137985	81.3929	112	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002960625.1	s__Streptococcus suis_T	80.0082	88	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286075.1	s__Streptococcus ratti	79.6725	187	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_002964575.1	s__Streptococcus suis_R	79.5512	79	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598035.1	s__Streptococcus halotolerans	79.3125	82	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964045.1	s__Streptococcus suis_U	79.2376	83	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.50	95.50	0.81	0.81	2	-
GCF_001074155.1	s__Streptococcus pseudopneumoniae_A	79.1595	67	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078705.1	s__Streptococcus sanguinis_D	78.8093	79	624	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	78.7869	94	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.75	95.06	0.92	0.88	13	-
GCF_000963275.1	s__Streptococcus parasanguinis_B	78.7649	72	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.64	95.37	0.88	0.85	11	-
GCF_001650315.1	s__Streptococcus sp001650315	78.7569	63	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.60	97.60	0.91	0.91	2	-
GCF_000186445.1	s__Streptococcus agalactiae	78.5373	71	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_002355215.1	s__Streptococcus troglodytae	78.365	158	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423725.1	s__Streptococcus devriesei	78.2938	158	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642085.1	s__Streptococcus pantholopis	78.2917	91	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015594605.1	s__Streptococcus sp015594605	78.2764	89	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901875555.1	s__Streptococcus parasanguinis_H	78.2559	75	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096855.1	s__Streptococcus mitis_Y	78.2437	65	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.03	96.03	0.87	0.87	2	-
GCF_000187585.1	s__Streptococcus peroris	78.2192	63	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.68	96.68	0.90	0.90	2	-
GCF_001937065.1	s__Streptococcus sp001937065	78.177	165	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001579665.1	s__Streptococcus mitis_S	78.0364	65	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.64	95.33	0.87	0.85	4	-
GCF_011038795.1	s__Streptococcus sp011038795	78.0307	74	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	99.03	0.90	0.90	2	-
GCF_000194945.1	s__Streptococcus sanguinis	77.9792	81	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.01	0.93	0.89	47	-
GCF_009496285.1	s__Streptococcus mitis_BP	77.5668	68	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001811505.1	s__Streptococcus sp001811505	77.5155	69	624	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:49,039] [INFO] GTDB search result was written to GCF_900475025.1_41906_G01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:49,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:49,048] [INFO] DFAST_QC result json was written to GCF_900475025.1_41906_G01_genomic.fna/dqc_result.json
[2024-01-24 14:22:49,049] [INFO] DFAST_QC completed!
[2024-01-24 14:22:49,049] [INFO] Total running time: 0h0m45s