[2024-01-24 13:28:28,810] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:28,812] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:28,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e237779-f7a5-4926-b4f8-3f7e84654988/dqc_reference
[2024-01-24 13:28:30,067] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,068] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,068] [INFO] Running command: gunzip -c /var/lib/cwl/stgac3daf06-9121-4fc9-90fb-7f33f209968a/GCF_000423765.1_ASM42376v1_genomic.fna.gz | prodigal -d GCF_000423765.1_ASM42376v1_genomic.fna/cds.fna -a GCF_000423765.1_ASM42376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:35,160] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:35,161] [INFO] Task started: HMMsearch
[2024-01-24 13:28:35,161] [INFO] Running command: hmmsearch --tblout GCF_000423765.1_ASM42376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e237779-f7a5-4926-b4f8-3f7e84654988/dqc_reference/reference_markers.hmm GCF_000423765.1_ASM42376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:35,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:35,435] [INFO] Found 6/6 markers.
[2024-01-24 13:28:35,458] [INFO] Query marker FASTA was written to GCF_000423765.1_ASM42376v1_genomic.fna/markers.fasta
[2024-01-24 13:28:35,458] [INFO] Task started: Blastn
[2024-01-24 13:28:35,459] [INFO] Running command: blastn -query GCF_000423765.1_ASM42376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e237779-f7a5-4926-b4f8-3f7e84654988/dqc_reference/reference_markers.fasta -out GCF_000423765.1_ASM42376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:36,055] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:36,058] [INFO] Selected 22 target genomes.
[2024-01-24 13:28:36,059] [INFO] Target genome list was writen to GCF_000423765.1_ASM42376v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:36,121] [INFO] Task started: fastANI
[2024-01-24 13:28:36,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgac3daf06-9121-4fc9-90fb-7f33f209968a/GCF_000423765.1_ASM42376v1_genomic.fna.gz --refList GCF_000423765.1_ASM42376v1_genomic.fna/target_genomes.txt --output GCF_000423765.1_ASM42376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:43,979] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:43,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e237779-f7a5-4926-b4f8-3f7e84654988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:43,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e237779-f7a5-4926-b4f8-3f7e84654988/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:43,995] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:43,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:43,995] [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 porci	strain=DSM 23759	GCA_000423765.1	502567	502567	type	True	100.0	744	746	95	conclusive
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	82.2057	146	746	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	82.1086	252	746	95	below_threshold
Streptococcus suis	strain=NCTC10234	GCA_900475585.1	1307	1307	type	True	82.0073	150	746	95	below_threshold
Streptococcus suis	strain=S735	GCA_000294495.1	1307	1307	type	True	81.9729	150	746	95	below_threshold
Streptococcus hillyeri	strain=28462	GCA_003686955.1	2282420	2282420	type	True	79.8789	285	746	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	79.8382	129	746	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	79.3886	189	746	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	79.0183	104	746	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.9857	99	746	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.9573	101	746	95	below_threshold
Streptococcus caballi	strain=DSM 19004	GCA_000379985.1	439220	439220	type	True	78.8884	168	746	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.8476	102	746	95	below_threshold
Streptococcus saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	78.8364	131	746	95	below_threshold
Streptococcus lutetiensis	strain=FDAARGOS_1158	GCA_016725165.1	150055	150055	type	True	78.8208	122	746	95	below_threshold
Streptococcus lutetiensis	strain=NCTC13774	GCA_900475675.1	150055	150055	type	True	78.8033	120	746	95	below_threshold
Streptococcus vestibularis	strain=ATCC 49124	GCA_000188295.1	1343	1343	type	True	78.5937	114	746	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	78.4971	165	746	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	78.1337	132	746	95	below_threshold
Streptococcus mutans	strain=DSM 20523	GCA_000375505.1	1309	1309	type	True	77.5949	97	746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:43,997] [INFO] DFAST Taxonomy check result was written to GCF_000423765.1_ASM42376v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:43,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:43,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:43,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e237779-f7a5-4926-b4f8-3f7e84654988/dqc_reference/checkm_data
[2024-01-24 13:28:43,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:44,022] [INFO] Task started: CheckM
[2024-01-24 13:28:44,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423765.1_ASM42376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423765.1_ASM42376v1_genomic.fna/checkm_input GCF_000423765.1_ASM42376v1_genomic.fna/checkm_result
[2024-01-24 13:29:06,346] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:06,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:06,365] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:06,365] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:06,366] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423765.1_ASM42376v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:06,366] [INFO] Task started: Blastn
[2024-01-24 13:29:06,366] [INFO] Running command: blastn -query GCF_000423765.1_ASM42376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e237779-f7a5-4926-b4f8-3f7e84654988/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423765.1_ASM42376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:07,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:07,255] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:07,256] [INFO] Target genome list was writen to GCF_000423765.1_ASM42376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:07,280] [INFO] Task started: fastANI
[2024-01-24 13:29:07,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgac3daf06-9121-4fc9-90fb-7f33f209968a/GCF_000423765.1_ASM42376v1_genomic.fna.gz --refList GCF_000423765.1_ASM42376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423765.1_ASM42376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:14,160] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:14,181] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:14,182] [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_000423765.1	s__Streptococcus porci	100.0	744	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000440235.1	s__Streptococcus suis_F	84.5035	176	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.62	95.22	0.78	0.75	8	-
GCA_002831545.1	s__Streptococcus suis_P	83.0929	179	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.04	0.87	0.78	133	-
GCF_002960425.1	s__Streptococcus suis_S	82.6364	148	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.81	98.81	0.93	0.93	2	-
GCF_000440555.1	s__Streptococcus suis_N	82.5953	134	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.61	95.42	0.83	0.79	5	-
GCF_000423745.1	s__Streptococcus plurextorum	82.1593	250	746	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	79.9628	312	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_003686955.1	s__Streptococcus sp003686955	79.8503	287	746	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	79.4291	186	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_900101445.1	s__Streptococcus equinus_B	79.0198	107	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_000379985.1	s__Streptococcus caballi	78.9147	167	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002096615.1	s__Streptococcus oralis_U	78.8136	99	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900475675.1	s__Streptococcus lutetiensis	78.8033	120	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_000188295.1	s__Streptococcus vestibularis	78.6175	114	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.03	95.83	0.91	0.87	14	-
GCF_000188015.2	s__Streptococcus ictaluri	78.5487	103	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908645.1	s__Streptococcus loxodontisalivarius	78.4971	165	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009738225.1	s__Streptococcus sp001556435	78.4591	130	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.11	95.45	0.91	0.84	79	-
GCF_010604095.1	s__Streptococcus sp000187445	78.1543	124	746	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:14,183] [INFO] GTDB search result was written to GCF_000423765.1_ASM42376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:14,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:14,191] [INFO] DFAST_QC result json was written to GCF_000423765.1_ASM42376v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:14,191] [INFO] DFAST_QC completed!
[2024-01-24 13:29:14,191] [INFO] Total running time: 0h0m45s