[2024-01-24 14:55:51,314] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:51,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:51,316] [INFO] DQC Reference Directory: /var/lib/cwl/stgac4bd0f3-2d2b-41d1-8033-20d17ee53a2b/dqc_reference
[2024-01-24 14:55:52,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,555] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg2eb0bdac-7640-4b38-aa89-f42d38910b3c/GCF_900458965.1_43188_F01_genomic.fna.gz | prodigal -d GCF_900458965.1_43188_F01_genomic.fna/cds.fna -a GCF_900458965.1_43188_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:57,314] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:57,315] [INFO] Task started: HMMsearch
[2024-01-24 14:55:57,315] [INFO] Running command: hmmsearch --tblout GCF_900458965.1_43188_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac4bd0f3-2d2b-41d1-8033-20d17ee53a2b/dqc_reference/reference_markers.hmm GCF_900458965.1_43188_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:57,593] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:57,594] [INFO] Found 6/6 markers.
[2024-01-24 14:55:57,622] [INFO] Query marker FASTA was written to GCF_900458965.1_43188_F01_genomic.fna/markers.fasta
[2024-01-24 14:55:57,623] [INFO] Task started: Blastn
[2024-01-24 14:55:57,623] [INFO] Running command: blastn -query GCF_900458965.1_43188_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgac4bd0f3-2d2b-41d1-8033-20d17ee53a2b/dqc_reference/reference_markers.fasta -out GCF_900458965.1_43188_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:58,245] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:58,248] [INFO] Selected 20 target genomes.
[2024-01-24 14:55:58,248] [INFO] Target genome list was writen to GCF_900458965.1_43188_F01_genomic.fna/target_genomes.txt
[2024-01-24 14:55:58,283] [INFO] Task started: fastANI
[2024-01-24 14:55:58,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eb0bdac-7640-4b38-aa89-f42d38910b3c/GCF_900458965.1_43188_F01_genomic.fna.gz --refList GCF_900458965.1_43188_F01_genomic.fna/target_genomes.txt --output GCF_900458965.1_43188_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:06,930] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:06,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac4bd0f3-2d2b-41d1-8033-20d17ee53a2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:06,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac4bd0f3-2d2b-41d1-8033-20d17ee53a2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:06,944] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:06,944] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:06,944] [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 agalactiae	strain=NCTC8181	GCA_900458965.1	1311	1311	suspected-type	True	100.0	799	809	95	conclusive
Streptococcus agalactiae	strain=ATCC 13813	GCA_000186445.1	1311	1311	type	True	99.628	735	809	95	conclusive
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	82.2552	175	809	95	below_threshold
Streptococcus dysgalactiae subsp. dysgalactiae	strain=NCTC13731	GCA_900459225.1	99822	1334	type	True	82.0748	173	809	95	below_threshold
Streptococcus urinalis	strain=NCTC13766	GCA_900636885.1	149016	149016	type	True	81.3992	195	809	95	below_threshold
Streptococcus urinalis	strain=2285-97	GCA_000188055.3	149016	149016	type	True	81.3172	193	809	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	80.9711	160	809	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	80.6335	127	809	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	80.4266	86	809	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	80.2939	154	809	95	below_threshold
Lactococcus protaetiae	strain=KACC 19320	GCA_006965445.1	2592653	2592653	type	True	80.0629	52	809	95	below_threshold
Streptococcus saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	79.4426	139	809	95	below_threshold
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	79.4013	121	809	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	79.3653	96	809	95	below_threshold
Streptococcus caballi	strain=DSM 19004	GCA_000379985.1	439220	439220	type	True	79.1563	117	809	95	below_threshold
Streptococcus troglodytae	strain=TKU 31	GCA_002355215.1	1111760	1111760	type	True	78.6559	116	809	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	78.5592	154	809	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:06,946] [INFO] DFAST Taxonomy check result was written to GCF_900458965.1_43188_F01_genomic.fna/tc_result.tsv
[2024-01-24 14:56:06,946] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:06,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:06,947] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac4bd0f3-2d2b-41d1-8033-20d17ee53a2b/dqc_reference/checkm_data
[2024-01-24 14:56:06,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:06,973] [INFO] Task started: CheckM
[2024-01-24 14:56:06,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900458965.1_43188_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900458965.1_43188_F01_genomic.fna/checkm_input GCF_900458965.1_43188_F01_genomic.fna/checkm_result
[2024-01-24 14:56:28,437] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:28,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:28,461] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:28,461] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:28,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900458965.1_43188_F01_genomic.fna/markers.fasta)
[2024-01-24 14:56:28,462] [INFO] Task started: Blastn
[2024-01-24 14:56:28,462] [INFO] Running command: blastn -query GCF_900458965.1_43188_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgac4bd0f3-2d2b-41d1-8033-20d17ee53a2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900458965.1_43188_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:29,278] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:29,282] [INFO] Selected 23 target genomes.
[2024-01-24 14:56:29,282] [INFO] Target genome list was writen to GCF_900458965.1_43188_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:29,297] [INFO] Task started: fastANI
[2024-01-24 14:56:29,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eb0bdac-7640-4b38-aa89-f42d38910b3c/GCF_900458965.1_43188_F01_genomic.fna.gz --refList GCF_900458965.1_43188_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900458965.1_43188_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:39,440] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:39,459] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:39,460] [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_000186445.1	s__Streptococcus agalactiae	99.628	735	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	conclusive
GCA_000283635.1	s__Streptococcus macedonicus	82.3769	176	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	99.04	98.50	0.90	0.83	11	-
GCF_900459225.1	s__Streptococcus dysgalactiae	82.0039	174	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	-
GCF_900475415.1	s__Streptococcus porcinus	81.3364	157	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_000188055.2	s__Streptococcus urinalis	81.2839	194	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.98	99.96	0.98	0.97	3	-
GCF_900636575.1	s__Streptococcus canis	80.9241	156	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	80.6335	127	809	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	80.2939	154	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_000154985.1	s__Streptococcus infantarius	80.2127	149	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_001598035.1	s__Streptococcus halotolerans	80.0461	112	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101445.1	s__Streptococcus equinus_B	79.7229	132	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_015594605.1	s__Streptococcus sp015594605	79.5852	142	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010604095.1	s__Streptococcus sp000187445	79.5285	93	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_000187975.2	s__Streptococcus criceti	79.4509	73	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	79.4247	140	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380105.1	s__Streptococcus orisratti	79.4013	121	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188015.2	s__Streptococcus ictaluri	79.2621	163	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379985.1	s__Streptococcus caballi	79.1563	117	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337175.1	s__Streptococcus gallolyticus_B	79.1011	140	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_009870755.1	s__Streptococcus halichoeri	79.0101	94	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.35	98.15	0.92	0.87	20	-
GCF_900104225.1	s__Streptococcus equinus_D	78.8805	143	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461705.1	s__Streptococcus vicugnae	78.5592	154	809	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_002355215.1	s__Streptococcus troglodytae	78.2771	113	809	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 14:56:39,462] [INFO] GTDB search result was written to GCF_900458965.1_43188_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:39,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:39,466] [INFO] DFAST_QC result json was written to GCF_900458965.1_43188_F01_genomic.fna/dqc_result.json
[2024-01-24 14:56:39,467] [INFO] DFAST_QC completed!
[2024-01-24 14:56:39,467] [INFO] Total running time: 0h0m48s