[2023-06-08 08:34:50,990] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:34:50,992] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:34:50,993] [INFO] DQC Reference Directory: /var/lib/cwl/stgefef61ad-502f-4cb1-a0be-6e9f9e704787/dqc_reference
[2023-06-08 08:34:52,312] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:34:52,313] [INFO] Task started: Prodigal
[2023-06-08 08:34:52,313] [INFO] Running command: gunzip -c /var/lib/cwl/stgcda2add6-dfca-4776-baaa-61179b0b1fdf/GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:34:56,455] [INFO] Task succeeded: Prodigal
[2023-06-08 08:34:56,455] [INFO] Task started: HMMsearch
[2023-06-08 08:34:56,456] [INFO] Running command: hmmsearch --tblout GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefef61ad-502f-4cb1-a0be-6e9f9e704787/dqc_reference/reference_markers.hmm GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:34:56,707] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:34:56,709] [INFO] Found 6/6 markers.
[2023-06-08 08:34:56,730] [INFO] Query marker FASTA was written to GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 08:34:56,730] [INFO] Task started: Blastn
[2023-06-08 08:34:56,730] [INFO] Running command: blastn -query GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgefef61ad-502f-4cb1-a0be-6e9f9e704787/dqc_reference/reference_markers.fasta -out GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:34:57,346] [INFO] Task succeeded: Blastn
[2023-06-08 08:34:57,352] [INFO] Selected 24 target genomes.
[2023-06-08 08:34:57,352] [INFO] Target genome list was writen to GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 08:34:57,375] [INFO] Task started: fastANI
[2023-06-08 08:34:57,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgcda2add6-dfca-4776-baaa-61179b0b1fdf/GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:35:05,932] [INFO] Task succeeded: fastANI
[2023-06-08 08:35:05,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefef61ad-502f-4cb1-a0be-6e9f9e704787/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:35:05,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefef61ad-502f-4cb1-a0be-6e9f9e704787/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:35:05,950] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2023-06-08 08:35:05,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 08:35:05,951] [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	98.3327	533	615	95	conclusive
Streptococcus ferus	strain=DSM 20646	GCA_000372425.1	1345	1345	type	True	98.2875	537	615	95	conclusive
Streptococcus ratti	strain=DSM 20564	GCA_000347915.1	1341	1341	suspected-type	True	79.7158	157	615	95	below_threshold
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	79.6789	95	615	95	below_threshold
Streptococcus ratti	strain=FA-1	GCA_000286075.1	1341	1341	suspected-type	True	79.6138	174	615	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.5804	88	615	95	below_threshold
Streptococcus suis	strain=S735	GCA_000294495.1	1307	1307	type	True	78.3681	70	615	95	below_threshold
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	78.3639	67	615	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	77.9529	60	615	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	77.9096	53	615	95	below_threshold
Streptococcus sanguinis	strain=NCTC7863	GCA_900475505.1	1305	1305	suspected-type	True	77.5036	72	615	95	below_threshold
Streptococcus devriesei	strain=DSM 19639	GCA_000423725.1	231233	231233	type	True	77.364	141	615	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	77.3036	59	615	95	below_threshold
Streptococcus sanguinis	strain=NCTC 7863	GCA_001593525.1	1305	1305	suspected-type	True	77.2248	71	615	95	below_threshold
Streptococcus thoraltensis	strain=DSM 12221	GCA_000380145.1	55085	55085	type	True	77.1483	76	615	95	below_threshold
Streptococcus mutans	strain=DSM 20523	GCA_000375505.1	1309	1309	type	True	77.1268	141	615	95	below_threshold
Streptococcus peroris	strain=ATCC 700780	GCA_000187585.1	68891	68891	type	True	77.0855	56	615	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	77.0321	60	615	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	76.8939	60	615	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	76.8813	55	615	95	below_threshold
Streptococcus halichoeri	strain=CCUG48324	GCA_009870755.1	254785	254785	type	True	76.3939	58	615	95	below_threshold
Streptococcus chenjunshii	strain=Z15	GCA_003086355.2	2173853	2173853	type	True	76.3714	79	615	95	below_threshold
Streptococcus pantholopis	strain=TA 26	GCA_001642085.1	1811193	1811193	type	True	76.0448	66	615	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:35:05,953] [INFO] DFAST Taxonomy check result was written to GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 08:35:05,954] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:35:05,954] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:35:05,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefef61ad-502f-4cb1-a0be-6e9f9e704787/dqc_reference/checkm_data
[2023-06-08 08:35:05,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:35:05,980] [INFO] Task started: CheckM
[2023-06-08 08:35:05,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 08:35:26,892] [INFO] Task succeeded: CheckM
[2023-06-08 08:35:26,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 08:35:26,913] [INFO] ===== Completeness check finished =====
[2023-06-08 08:35:26,914] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:35:26,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 08:35:26,915] [INFO] Task started: Blastn
[2023-06-08 08:35:26,915] [INFO] Running command: blastn -query GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgefef61ad-502f-4cb1-a0be-6e9f9e704787/dqc_reference/reference_markers_gtdb.fasta -out GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:35:27,715] [INFO] Task succeeded: Blastn
[2023-06-08 08:35:27,725] [INFO] Selected 27 target genomes.
[2023-06-08 08:35:27,725] [INFO] Target genome list was writen to GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:35:27,823] [INFO] Task started: fastANI
[2023-06-08 08:35:27,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgcda2add6-dfca-4776-baaa-61179b0b1fdf/GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:35:37,047] [INFO] Task succeeded: fastANI
[2023-06-08 08:35:37,071] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:35:37,071] [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	98.2875	537	615	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_000286075.1	s__Streptococcus ratti	79.6435	173	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_018137985.1	s__Streptococcus sp018137985	79.5804	88	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964575.1	s__Streptococcus suis_R	79.2858	78	615	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	79.2603	72	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.50	95.50	0.81	0.81	2	-
GCF_000440115.1	s__Streptococcus suis_L	79.0635	77	615	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	78.5551	62	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_010120595.1	s__Streptococcus thermophilus	78.4581	65	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.46	97.47	0.91	0.81	130	-
GCF_001937065.1	s__Streptococcus sp001937065	77.7514	156	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194945.1	s__Streptococcus sanguinis	77.5007	72	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.01	0.93	0.89	47	-
GCF_000423725.1	s__Streptococcus devriesei	77.3847	140	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963275.1	s__Streptococcus parasanguinis_B	77.3763	58	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.64	95.37	0.88	0.85	11	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	77.3203	77	615	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	77.2399	69	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.75	95.06	0.92	0.88	13	-
GCF_003337175.1	s__Streptococcus gallolyticus_B	77.1527	84	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_001078705.1	s__Streptococcus sanguinis_D	77.1486	59	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380145.1	s__Streptococcus thoraltensis	77.1483	76	615	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	77.1349	55	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.03	96.03	0.87	0.87	2	-
GCF_001579665.1	s__Streptococcus mitis_S	77.1013	61	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.64	95.33	0.87	0.85	4	-
GCF_000187585.1	s__Streptococcus peroris	77.0855	56	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.68	96.68	0.90	0.90	2	-
GCF_003686955.1	s__Streptococcus sp003686955	77.0676	69	615	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	76.9567	87	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905221295.1	s__Streptococcus sp905221295	76.8881	56	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038795.1	s__Streptococcus sp011038795	76.4351	73	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	99.03	0.90	0.90	2	-
GCF_001642085.1	s__Streptococcus pantholopis	76.0448	66	615	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:35:37,073] [INFO] GTDB search result was written to GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 08:35:37,074] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:35:37,079] [INFO] DFAST_QC result json was written to GCA_945873255.1_SRR15732358_bin.4_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 08:35:37,079] [INFO] DFAST_QC completed!
[2023-06-08 08:35:37,079] [INFO] Total running time: 0h0m46s