[2024-01-25 17:45:20,296] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:20,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:20,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ea2e5dd-2750-4769-8163-84b76db5f992/dqc_reference
[2024-01-25 17:45:21,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:21,373] [INFO] Task started: Prodigal
[2024-01-25 17:45:21,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg780c702e-e06c-47b2-a0ea-3779b1ef090b/GCF_000188015.2_ASM18801v3_genomic.fna.gz | prodigal -d GCF_000188015.2_ASM18801v3_genomic.fna/cds.fna -a GCF_000188015.2_ASM18801v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:25,294] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:25,294] [INFO] Task started: HMMsearch
[2024-01-25 17:45:25,294] [INFO] Running command: hmmsearch --tblout GCF_000188015.2_ASM18801v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ea2e5dd-2750-4769-8163-84b76db5f992/dqc_reference/reference_markers.hmm GCF_000188015.2_ASM18801v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:25,531] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:25,532] [INFO] Found 6/6 markers.
[2024-01-25 17:45:25,559] [INFO] Query marker FASTA was written to GCF_000188015.2_ASM18801v3_genomic.fna/markers.fasta
[2024-01-25 17:45:25,559] [INFO] Task started: Blastn
[2024-01-25 17:45:25,559] [INFO] Running command: blastn -query GCF_000188015.2_ASM18801v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ea2e5dd-2750-4769-8163-84b76db5f992/dqc_reference/reference_markers.fasta -out GCF_000188015.2_ASM18801v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:26,126] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:26,129] [INFO] Selected 24 target genomes.
[2024-01-25 17:45:26,129] [INFO] Target genome list was writen to GCF_000188015.2_ASM18801v3_genomic.fna/target_genomes.txt
[2024-01-25 17:45:26,167] [INFO] Task started: fastANI
[2024-01-25 17:45:26,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg780c702e-e06c-47b2-a0ea-3779b1ef090b/GCF_000188015.2_ASM18801v3_genomic.fna.gz --refList GCF_000188015.2_ASM18801v3_genomic.fna/target_genomes.txt --output GCF_000188015.2_ASM18801v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:35,358] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:35,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ea2e5dd-2750-4769-8163-84b76db5f992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:35,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ea2e5dd-2750-4769-8163-84b76db5f992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:35,370] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:45:35,370] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:45:35,371] [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 pyogenes	strain=FDAARGOS_774	GCA_006364235.1	1314	1314	type	True	81.1604	280	741	95	below_threshold
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	81.0839	283	741	95	below_threshold
Streptococcus pyogenes	strain=CCUG 4207	GCA_004028355.1	1314	1314	type	True	81.0605	282	741	95	below_threshold
Streptococcus pyogenes	strain=NCTC8198	GCA_002055535.1	1314	1314	type	True	81.0343	282	741	95	below_threshold
Streptococcus dysgalactiae subsp. dysgalactiae	strain=NCTC13731	GCA_900459225.1	99822	1334	type	True	81.0322	288	741	95	below_threshold
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	80.9933	290	741	95	below_threshold
Streptococcus pyogenes	strain=CCUG 4207	GCA_001982785.1	1314	1314	type	True	80.8055	268	741	95	below_threshold
Streptococcus pyogenes	strain=DSM 20565	GCA_000421785.1	1314	1314	type	True	80.7071	272	741	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	80.486	276	741	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	80.0598	210	741	95	below_threshold
Streptococcus parauberis	strain=NCFD 2020	GCA_000187935.2	1348	1348	type	True	79.996	195	741	95	below_threshold
Streptococcus phocae	strain=ATCC 51973	GCA_001302265.1	119224	119224	type	True	79.9331	213	741	95	below_threshold
Streptococcus phocae subsp. salmonis	strain=C-4	GCA_000772915.1	1000562	119224	type	True	79.7946	197	741	95	below_threshold
Streptococcus australis	strain=NCTC13166	GCA_900476055.1	113107	113107	type	True	79.7754	75	741	95	below_threshold
Streptococcus pseudoporcinus	strain=LQ 940-04	GCA_000188035.3	361101	361101	type	True	79.582	173	741	95	below_threshold
Streptococcus pseudoporcinus	strain=NCTC13786	GCA_900637075.1	361101	361101	type	True	79.53	170	741	95	below_threshold
Streptococcus uberis	strain=NCTC3858	GCA_900475595.1	1349	1349	type	True	79.4716	192	741	95	below_threshold
Streptococcus bovimastitidis	strain=NZ1587	GCA_001885095.1	1856638	1856638	type	True	79.3899	186	741	95	below_threshold
Streptococcus didelphis	strain=DSM 15616	GCA_000380005.1	102886	102886	type	True	79.3607	187	741	95	below_threshold
Streptococcus penaeicida	strain=CAIM 1838	GCA_002887775.1	1765960	1765960	type	True	79.2863	181	741	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:35,372] [INFO] DFAST Taxonomy check result was written to GCF_000188015.2_ASM18801v3_genomic.fna/tc_result.tsv
[2024-01-25 17:45:35,372] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:35,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:35,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ea2e5dd-2750-4769-8163-84b76db5f992/dqc_reference/checkm_data
[2024-01-25 17:45:35,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:35,398] [INFO] Task started: CheckM
[2024-01-25 17:45:35,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000188015.2_ASM18801v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000188015.2_ASM18801v3_genomic.fna/checkm_input GCF_000188015.2_ASM18801v3_genomic.fna/checkm_result
[2024-01-25 17:45:53,338] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:53,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:53,354] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:53,354] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:53,354] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000188015.2_ASM18801v3_genomic.fna/markers.fasta)
[2024-01-25 17:45:53,355] [INFO] Task started: Blastn
[2024-01-25 17:45:53,355] [INFO] Running command: blastn -query GCF_000188015.2_ASM18801v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ea2e5dd-2750-4769-8163-84b76db5f992/dqc_reference/reference_markers_gtdb.fasta -out GCF_000188015.2_ASM18801v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:54,203] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:54,206] [INFO] Selected 18 target genomes.
[2024-01-25 17:45:54,206] [INFO] Target genome list was writen to GCF_000188015.2_ASM18801v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:54,253] [INFO] Task started: fastANI
[2024-01-25 17:45:54,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg780c702e-e06c-47b2-a0ea-3779b1ef090b/GCF_000188015.2_ASM18801v3_genomic.fna.gz --refList GCF_000188015.2_ASM18801v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000188015.2_ASM18801v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:03,149] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:03,160] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:03,160] [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_000188015.2	s__Streptococcus ictaluri	100.0	740	741	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_002055535.1	s__Streptococcus pyogenes	81.0887	283	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.85	98.36	0.95	0.87	2144	-
GCF_900459225.1	s__Streptococcus dysgalactiae	80.976	289	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	-
GCF_900636575.1	s__Streptococcus canis	80.5558	277	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_000785785.1	s__Streptococcus uberis_A	80.4221	197	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425025.1	s__Streptococcus castoreus	80.0732	256	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000187935.1	s__Streptococcus parauberis	80.0099	195	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.87	98.45	0.89	0.84	24	-
GCF_001302265.1	s__Streptococcus phocae	79.9331	213	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.05	97.05	0.87	0.87	2	-
GCF_000188035.1	s__Streptococcus pseudoporcinus	79.683	174	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.36	97.79	0.89	0.85	10	-
GCF_900475415.1	s__Streptococcus porcinus	79.4613	171	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_003674745.1	s__Streptococcus iniae	79.4101	184	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.92	98.80	0.96	0.87	94	-
GCF_001885095.1	s__Streptococcus bovimastitidis	79.3646	187	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887775.1	s__Streptococcus penaeicida	79.2863	181	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901542335.1	s__Streptococcus porcinus_A	79.1643	179	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_016461705.1	s__Streptococcus vicugnae	79.1355	124	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCF_010604095.1	s__Streptococcus sp000187445	78.9429	99	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_900101445.1	s__Streptococcus equinus_B	78.7791	131	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_012277075.1	s__Streptococcus alactolyticus	78.6311	115	741	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.29	98.88	0.94	0.83	11	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:03,162] [INFO] GTDB search result was written to GCF_000188015.2_ASM18801v3_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:03,162] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:03,166] [INFO] DFAST_QC result json was written to GCF_000188015.2_ASM18801v3_genomic.fna/dqc_result.json
[2024-01-25 17:46:03,166] [INFO] DFAST_QC completed!
[2024-01-25 17:46:03,167] [INFO] Total running time: 0h0m43s