[2024-01-24 11:35:22,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d0091c7-4f14-4397-b1e5-7488fe70d875/dqc_reference
[2024-01-24 11:35:26,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,249] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d942f5b-b245-41e5-a78f-1b19728f46ec/GCF_003686955.1_ASM368695v1_genomic.fna.gz | prodigal -d GCF_003686955.1_ASM368695v1_genomic.fna/cds.fna -a GCF_003686955.1_ASM368695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:30,934] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:30,935] [INFO] Task started: HMMsearch
[2024-01-24 11:35:30,935] [INFO] Running command: hmmsearch --tblout GCF_003686955.1_ASM368695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d0091c7-4f14-4397-b1e5-7488fe70d875/dqc_reference/reference_markers.hmm GCF_003686955.1_ASM368695v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:31,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:31,260] [INFO] Found 6/6 markers.
[2024-01-24 11:35:31,287] [INFO] Query marker FASTA was written to GCF_003686955.1_ASM368695v1_genomic.fna/markers.fasta
[2024-01-24 11:35:31,287] [INFO] Task started: Blastn
[2024-01-24 11:35:31,287] [INFO] Running command: blastn -query GCF_003686955.1_ASM368695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d0091c7-4f14-4397-b1e5-7488fe70d875/dqc_reference/reference_markers.fasta -out GCF_003686955.1_ASM368695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:32,956] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:32,960] [INFO] Selected 25 target genomes.
[2024-01-24 11:35:32,961] [INFO] Target genome list was writen to GCF_003686955.1_ASM368695v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,023] [INFO] Task started: fastANI
[2024-01-24 11:35:33,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d942f5b-b245-41e5-a78f-1b19728f46ec/GCF_003686955.1_ASM368695v1_genomic.fna.gz --refList GCF_003686955.1_ASM368695v1_genomic.fna/target_genomes.txt --output GCF_003686955.1_ASM368695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:42,466] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:42,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d0091c7-4f14-4397-b1e5-7488fe70d875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:42,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d0091c7-4f14-4397-b1e5-7488fe70d875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:42,486] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:42,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:42,487] [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 hillyeri	strain=28462	GCA_003686955.1	2282420	2282420	type	True	100.0	684	685	95	conclusive
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	81.4783	152	685	95	below_threshold
Streptococcus porci	strain=DSM 23759	GCA_000423765.1	502567	502567	type	True	79.882	297	685	95	below_threshold
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	79.6762	96	685	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	79.4997	171	685	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.27	115	685	95	below_threshold
Streptococcus saliviloxodontae	strain=DSM 27513	GCA_016908655.1	1349416	1349416	type	True	79.2313	162	685	95	below_threshold
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	79.1875	120	685	95	below_threshold
Streptococcus salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	79.1491	125	685	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	79.1395	209	685	95	below_threshold
Streptococcus vestibularis	strain=ATCC 49124	GCA_000188295.1	1343	1343	type	True	79.0917	124	685	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	79.071	147	685	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.0604	111	685	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	78.974	171	685	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.9458	103	685	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	78.9013	141	685	95	below_threshold
Streptococcus oralis	strain=CCUG 24891	GCA_001639375.1	1303	1303	type	True	78.8699	104	685	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	78.8074	141	685	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.7915	97	685	95	below_threshold
Streptococcus oralis	strain=ATCC 35037	GCA_000148565.2	1303	1303	type	True	78.7034	104	685	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.6285	92	685	95	below_threshold
Streptococcus devriesei	strain=DSM 19639	GCA_000423725.1	231233	231233	type	True	78.3054	86	685	95	below_threshold
Streptococcus criceti	strain=NCTC12277	GCA_900459215.1	1333	1333	type	True	78.0239	103	685	95	below_threshold
Streptococcus criceti	strain=HS-6	GCA_000187975.3	1333	1333	type	True	77.9331	102	685	95	below_threshold
Streptococcus troglodytae	strain=TKU 31	GCA_002355215.1	1111760	1111760	type	True	77.4636	103	685	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:42,488] [INFO] DFAST Taxonomy check result was written to GCF_003686955.1_ASM368695v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:42,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:42,489] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:42,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d0091c7-4f14-4397-b1e5-7488fe70d875/dqc_reference/checkm_data
[2024-01-24 11:35:42,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:42,515] [INFO] Task started: CheckM
[2024-01-24 11:35:42,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003686955.1_ASM368695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003686955.1_ASM368695v1_genomic.fna/checkm_input GCF_003686955.1_ASM368695v1_genomic.fna/checkm_result
[2024-01-24 11:36:04,256] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:04,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:04,276] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:04,276] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:04,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003686955.1_ASM368695v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:04,277] [INFO] Task started: Blastn
[2024-01-24 11:36:04,277] [INFO] Running command: blastn -query GCF_003686955.1_ASM368695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d0091c7-4f14-4397-b1e5-7488fe70d875/dqc_reference/reference_markers_gtdb.fasta -out GCF_003686955.1_ASM368695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:05,116] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:05,120] [INFO] Selected 15 target genomes.
[2024-01-24 11:36:05,121] [INFO] Target genome list was writen to GCF_003686955.1_ASM368695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:05,132] [INFO] Task started: fastANI
[2024-01-24 11:36:05,132] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d942f5b-b245-41e5-a78f-1b19728f46ec/GCF_003686955.1_ASM368695v1_genomic.fna.gz --refList GCF_003686955.1_ASM368695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003686955.1_ASM368695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:11,949] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:11,968] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:11,968] [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_003686955.1	s__Streptococcus sp003686955	100.0	684	685	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_902729355.1	s__Streptococcus sp902729355	87.765	495	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_000380125.1	s__Streptococcus ovis	81.4108	153	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423765.1	s__Streptococcus porci	79.8635	298	685	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	79.4995	171	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_010604095.1	s__Streptococcus sp000187445	79.4645	112	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_009738225.1	s__Streptococcus sp001556435	79.2058	125	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.11	95.45	0.91	0.84	79	-
GCF_000423745.1	s__Streptococcus plurextorum	79.1395	209	685	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	78.974	171	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104225.1	s__Streptococcus equinus_D	78.9095	136	685	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	78.7954	141	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_001431045.1	s__Streptococcus orisasini	78.6951	114	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012277075.1	s__Streptococcus alactolyticus	78.6424	117	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.29	98.88	0.94	0.83	11	-
GCF_000423725.1	s__Streptococcus devriesei	78.3054	86	685	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355215.1	s__Streptococcus troglodytae	77.4355	104	685	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 11:36:11,970] [INFO] GTDB search result was written to GCF_003686955.1_ASM368695v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:11,971] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:11,975] [INFO] DFAST_QC result json was written to GCF_003686955.1_ASM368695v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:11,976] [INFO] DFAST_QC completed!
[2024-01-24 11:36:11,976] [INFO] Total running time: 0h0m49s