[2024-01-24 12:14:09,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,783] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbda704b-0aa3-40e5-91a8-834cf7c71f84/dqc_reference
[2024-01-24 12:14:11,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,073] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg78964dfe-9083-49bd-a251-dbce8e15e971/GCF_000423745.1_ASM42374v1_genomic.fna.gz | prodigal -d GCF_000423745.1_ASM42374v1_genomic.fna/cds.fna -a GCF_000423745.1_ASM42374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:15,842] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:15,842] [INFO] Task started: HMMsearch
[2024-01-24 12:14:15,842] [INFO] Running command: hmmsearch --tblout GCF_000423745.1_ASM42374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbda704b-0aa3-40e5-91a8-834cf7c71f84/dqc_reference/reference_markers.hmm GCF_000423745.1_ASM42374v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:16,144] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:16,145] [INFO] Found 6/6 markers.
[2024-01-24 12:14:16,174] [INFO] Query marker FASTA was written to GCF_000423745.1_ASM42374v1_genomic.fna/markers.fasta
[2024-01-24 12:14:16,175] [INFO] Task started: Blastn
[2024-01-24 12:14:16,175] [INFO] Running command: blastn -query GCF_000423745.1_ASM42374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbda704b-0aa3-40e5-91a8-834cf7c71f84/dqc_reference/reference_markers.fasta -out GCF_000423745.1_ASM42374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:16,812] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:16,817] [INFO] Selected 25 target genomes.
[2024-01-24 12:14:16,818] [INFO] Target genome list was writen to GCF_000423745.1_ASM42374v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:16,825] [INFO] Task started: fastANI
[2024-01-24 12:14:16,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg78964dfe-9083-49bd-a251-dbce8e15e971/GCF_000423745.1_ASM42374v1_genomic.fna.gz --refList GCF_000423745.1_ASM42374v1_genomic.fna/target_genomes.txt --output GCF_000423745.1_ASM42374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:25,409] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:25,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbda704b-0aa3-40e5-91a8-834cf7c71f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:25,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbda704b-0aa3-40e5-91a8-834cf7c71f84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:25,431] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:25,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:25,431] [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 plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	100.0	682	684	95	conclusive
Streptococcus suis	strain=NCTC10234	GCA_900475585.1	1307	1307	type	True	82.8334	175	684	95	below_threshold
Streptococcus suis	strain=S735	GCA_000294495.1	1307	1307	type	True	82.8219	176	684	95	below_threshold
Streptococcus porci	strain=DSM 23759	GCA_000423765.1	502567	502567	type	True	82.3263	242	684	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	82.1244	150	684	95	below_threshold
Streptococcus hyovaginalis	strain=DSM 12219	GCA_000420785.1	149015	149015	type	True	81.4777	115	684	95	below_threshold
Streptococcus pseudoporcinus	strain=LQ 940-04	GCA_000188035.3	361101	361101	type	True	80.9608	88	684	95	below_threshold
Streptococcus pseudoporcinus	strain=NCTC13786	GCA_900637075.1	361101	361101	type	True	80.8875	89	684	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	80.3995	132	684	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	80.1757	113	684	95	below_threshold
Streptococcus salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	79.1335	91	684	95	below_threshold
Streptococcus hillyeri	strain=28462	GCA_003686955.1	2282420	2282420	type	True	78.9401	206	684	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	78.8447	104	684	95	below_threshold
Streptococcus pyogenes	strain=CCUG 4207	GCA_004028355.1	1314	1314	type	True	78.8069	93	684	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.7742	117	684	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	78.747	107	684	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	78.7024	107	684	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.6803	96	684	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	78.6791	132	684	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.6161	85	684	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	78.377	96	684	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	78.3695	95	684	95	below_threshold
Streptococcus saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	78.3344	120	684	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	78.2932	135	684	95	below_threshold
Streptococcus troglodytae	strain=TKU 31	GCA_002355215.1	1111760	1111760	type	True	77.5008	76	684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:25,433] [INFO] DFAST Taxonomy check result was written to GCF_000423745.1_ASM42374v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:25,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:25,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:25,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbda704b-0aa3-40e5-91a8-834cf7c71f84/dqc_reference/checkm_data
[2024-01-24 12:14:25,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:25,459] [INFO] Task started: CheckM
[2024-01-24 12:14:25,459] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423745.1_ASM42374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423745.1_ASM42374v1_genomic.fna/checkm_input GCF_000423745.1_ASM42374v1_genomic.fna/checkm_result
[2024-01-24 12:14:48,143] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:48,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:48,176] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:48,177] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:48,178] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423745.1_ASM42374v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:48,178] [INFO] Task started: Blastn
[2024-01-24 12:14:48,178] [INFO] Running command: blastn -query GCF_000423745.1_ASM42374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbda704b-0aa3-40e5-91a8-834cf7c71f84/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423745.1_ASM42374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,147] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,152] [INFO] Selected 23 target genomes.
[2024-01-24 12:14:49,152] [INFO] Target genome list was writen to GCF_000423745.1_ASM42374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:49,184] [INFO] Task started: fastANI
[2024-01-24 12:14:49,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg78964dfe-9083-49bd-a251-dbce8e15e971/GCF_000423745.1_ASM42374v1_genomic.fna.gz --refList GCF_000423745.1_ASM42374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423745.1_ASM42374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:58,071] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:58,090] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:58,090] [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_000423745.1	s__Streptococcus plurextorum	100.0	682	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016743335.1	s__Streptococcus suis_Y	84.4338	197	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.53	95.45	0.79	0.78	5	-
GCF_902702775.1	s__Streptococcus suis_W	84.1457	184	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2533	96.52	95.78	0.85	0.77	106	-
GCF_002960445.1	s__Streptococcus suis_O	83.9892	189	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017601095.1	s__Streptococcus suis_Z	83.7863	178	684	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	83.7418	193	684	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	83.7134	175	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775005.1	s__Streptococcus suis_X	83.6343	174	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	97.65	0.91	0.90	4	-
GCA_000440235.1	s__Streptococcus suis_F	83.3581	202	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.62	95.22	0.78	0.75	8	-
GCF_000423765.1	s__Streptococcus porci	82.3209	242	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420785.1	s__Streptococcus hyovaginalis	81.5379	114	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.13	96.18	0.83	0.79	5	-
GCF_000188035.1	s__Streptococcus pseudoporcinus	81.1076	86	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.36	97.79	0.89	0.85	10	-
GCF_900636575.1	s__Streptococcus canis	80.3274	110	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_003686955.1	s__Streptococcus sp003686955	78.9401	206	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729355.1	s__Streptococcus sp902729355	78.9143	189	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_003609975.1	s__Streptococcus ruminantium	78.8844	114	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.78	98.55	0.91	0.88	24	-
GCF_002093545.1	s__Streptococcus oralis_C	78.8468	93	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.13	97.13	0.96	0.96	2	-
GCF_000154985.1	s__Streptococcus infantarius	78.6997	107	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_000376985.1	s__Streptococcus henryi	78.6791	132	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_016908655.1	s__Streptococcus saliviloxodontae	78.3989	118	684	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	78.3207	105	684	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	78.1214	97	684	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_002355215.1	s__Streptococcus troglodytae	77.5008	76	684	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 12:14:58,092] [INFO] GTDB search result was written to GCF_000423745.1_ASM42374v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:58,093] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:58,098] [INFO] DFAST_QC result json was written to GCF_000423745.1_ASM42374v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:58,098] [INFO] DFAST_QC completed!
[2024-01-24 12:14:58,098] [INFO] Total running time: 0h0m48s