[2024-01-24 13:26:26,216] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:26,218] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:26,219] [INFO] DQC Reference Directory: /var/lib/cwl/stg762df252-66ab-478f-a87b-ef4f9c2ed637/dqc_reference
[2024-01-24 13:26:27,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:27,421] [INFO] Task started: Prodigal
[2024-01-24 13:26:27,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a5eaa98-db44-45e8-b6a4-7b98236eb22f/GCF_000186445.1_ASM18644v1_genomic.fna.gz | prodigal -d GCF_000186445.1_ASM18644v1_genomic.fna/cds.fna -a GCF_000186445.1_ASM18644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:31,549] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:31,550] [INFO] Task started: HMMsearch
[2024-01-24 13:26:31,550] [INFO] Running command: hmmsearch --tblout GCF_000186445.1_ASM18644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg762df252-66ab-478f-a87b-ef4f9c2ed637/dqc_reference/reference_markers.hmm GCF_000186445.1_ASM18644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:31,800] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:31,801] [INFO] Found 6/6 markers.
[2024-01-24 13:26:31,826] [INFO] Query marker FASTA was written to GCF_000186445.1_ASM18644v1_genomic.fna/markers.fasta
[2024-01-24 13:26:31,827] [INFO] Task started: Blastn
[2024-01-24 13:26:31,827] [INFO] Running command: blastn -query GCF_000186445.1_ASM18644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg762df252-66ab-478f-a87b-ef4f9c2ed637/dqc_reference/reference_markers.fasta -out GCF_000186445.1_ASM18644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:32,413] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:32,417] [INFO] Selected 20 target genomes.
[2024-01-24 13:26:32,418] [INFO] Target genome list was writen to GCF_000186445.1_ASM18644v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:32,522] [INFO] Task started: fastANI
[2024-01-24 13:26:32,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a5eaa98-db44-45e8-b6a4-7b98236eb22f/GCF_000186445.1_ASM18644v1_genomic.fna.gz --refList GCF_000186445.1_ASM18644v1_genomic.fna/target_genomes.txt --output GCF_000186445.1_ASM18644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:40,198] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:40,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg762df252-66ab-478f-a87b-ef4f9c2ed637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:40,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg762df252-66ab-478f-a87b-ef4f9c2ed637/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:40,213] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:26:40,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:40,213] [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=ATCC 13813	GCA_000186445.1	1311	1311	type	True	99.9501	732	751	95	conclusive
Streptococcus agalactiae	strain=NCTC8181	GCA_900458965.1	1311	1311	suspected-type	True	99.6692	724	751	95	conclusive
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	81.062	184	751	95	below_threshold
Streptococcus dysgalactiae subsp. dysgalactiae	strain=NCTC13731	GCA_900459225.1	99822	1334	type	True	80.7934	189	751	95	below_threshold
Streptococcus urinalis	strain=NCTC13766	GCA_900636885.1	149016	149016	type	True	80.7071	192	751	95	below_threshold
Streptococcus urinalis	strain=2285-97	GCA_000188055.3	149016	149016	type	True	80.524	200	751	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	80.3863	135	751	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	80.0536	167	751	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	79.5054	163	751	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	79.3639	104	751	95	below_threshold
Streptococcus saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	79.1486	143	751	95	below_threshold
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	78.9802	128	751	95	below_threshold
Streptococcus caballi	strain=DSM 19004	GCA_000379985.1	439220	439220	type	True	78.616	133	751	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	78.4992	166	751	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	77.7445	101	751	95	below_threshold
Streptococcus troglodytae	strain=TKU 31	GCA_002355215.1	1111760	1111760	type	True	77.3691	122	751	95	below_threshold
Lactococcus protaetiae	strain=KACC 19320	GCA_006965445.1	2592653	2592653	type	True	76.5882	58	751	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:40,215] [INFO] DFAST Taxonomy check result was written to GCF_000186445.1_ASM18644v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:40,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:40,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:40,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg762df252-66ab-478f-a87b-ef4f9c2ed637/dqc_reference/checkm_data
[2024-01-24 13:26:40,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:40,246] [INFO] Task started: CheckM
[2024-01-24 13:26:40,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000186445.1_ASM18644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000186445.1_ASM18644v1_genomic.fna/checkm_input GCF_000186445.1_ASM18644v1_genomic.fna/checkm_result
[2024-01-24 13:27:00,472] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:00,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:00,496] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:00,496] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:00,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000186445.1_ASM18644v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:00,497] [INFO] Task started: Blastn
[2024-01-24 13:27:00,498] [INFO] Running command: blastn -query GCF_000186445.1_ASM18644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg762df252-66ab-478f-a87b-ef4f9c2ed637/dqc_reference/reference_markers_gtdb.fasta -out GCF_000186445.1_ASM18644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:01,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:01,308] [INFO] Selected 23 target genomes.
[2024-01-24 13:27:01,309] [INFO] Target genome list was writen to GCF_000186445.1_ASM18644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:01,398] [INFO] Task started: fastANI
[2024-01-24 13:27:01,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a5eaa98-db44-45e8-b6a4-7b98236eb22f/GCF_000186445.1_ASM18644v1_genomic.fna.gz --refList GCF_000186445.1_ASM18644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000186445.1_ASM18644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:11,030] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:11,053] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:11,053] [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	99.9701	731	751	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	81.0746	178	751	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	80.8198	188	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	-
GCF_000188055.2	s__Streptococcus urinalis	80.5957	198	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.98	99.96	0.98	0.97	3	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	80.3264	136	751	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	80.0493	168	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_900475415.1	s__Streptococcus porcinus	79.7972	170	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_000154985.1	s__Streptococcus infantarius	79.6915	154	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_900636575.1	s__Streptococcus canis	79.5901	163	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_900101445.1	s__Streptococcus equinus_B	79.2058	152	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	79.1486	143	751	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	79.0334	162	751	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	79.0156	127	751	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	78.7023	147	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.6693	N/A	N/A	N/A	N/A	1	-
GCF_900104225.1	s__Streptococcus equinus_D	78.6655	158	751	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	78.6176	134	751	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	78.593	112	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_001598035.1	s__Streptococcus halotolerans	78.5929	109	751	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	78.4676	167	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_009870755.1	s__Streptococcus halichoeri	78.2461	112	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.35	98.15	0.92	0.87	20	-
GCF_000188015.2	s__Streptococcus ictaluri	78.1539	169	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000187975.2	s__Streptococcus criceti	77.5477	85	751	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002355215.1	s__Streptococcus troglodytae	77.343	123	751	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 13:27:11,055] [INFO] GTDB search result was written to GCF_000186445.1_ASM18644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:11,055] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:11,059] [INFO] DFAST_QC result json was written to GCF_000186445.1_ASM18644v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:11,059] [INFO] DFAST_QC completed!
[2024-01-24 13:27:11,060] [INFO] Total running time: 0h0m45s