[2024-01-24 14:06:14,847] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,849] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,850] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b2fab51-5f41-442e-9b75-3f989a2ee1ae/dqc_reference
[2024-01-24 14:06:16,190] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:16,191] [INFO] Task started: Prodigal
[2024-01-24 14:06:16,191] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f6b6625-2d52-4be3-93a5-db2cac8879e6/GCF_900460185.1_41906_F01_genomic.fna.gz | prodigal -d GCF_900460185.1_41906_F01_genomic.fna/cds.fna -a GCF_900460185.1_41906_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:21,092] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:21,093] [INFO] Task started: HMMsearch
[2024-01-24 14:06:21,093] [INFO] Running command: hmmsearch --tblout GCF_900460185.1_41906_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b2fab51-5f41-442e-9b75-3f989a2ee1ae/dqc_reference/reference_markers.hmm GCF_900460185.1_41906_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:21,360] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:21,361] [INFO] Found 6/6 markers.
[2024-01-24 14:06:21,386] [INFO] Query marker FASTA was written to GCF_900460185.1_41906_F01_genomic.fna/markers.fasta
[2024-01-24 14:06:21,386] [INFO] Task started: Blastn
[2024-01-24 14:06:21,386] [INFO] Running command: blastn -query GCF_900460185.1_41906_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2fab51-5f41-442e-9b75-3f989a2ee1ae/dqc_reference/reference_markers.fasta -out GCF_900460185.1_41906_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:22,061] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:22,065] [INFO] Selected 7 target genomes.
[2024-01-24 14:06:22,066] [INFO] Target genome list was writen to GCF_900460185.1_41906_F01_genomic.fna/target_genomes.txt
[2024-01-24 14:06:22,080] [INFO] Task started: fastANI
[2024-01-24 14:06:22,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f6b6625-2d52-4be3-93a5-db2cac8879e6/GCF_900460185.1_41906_F01_genomic.fna.gz --refList GCF_900460185.1_41906_F01_genomic.fna/target_genomes.txt --output GCF_900460185.1_41906_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:26,103] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:26,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b2fab51-5f41-442e-9b75-3f989a2ee1ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:26,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b2fab51-5f41-442e-9b75-3f989a2ee1ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:26,113] [INFO] Found 7 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:06:26,113] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:26,113] [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 equi subsp. zooepidemicus	strain=NCTC7023	GCA_900460185.1	40041	1336	type	True	100.0	727	729	95	conclusive
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	96.6786	599	729	95	conclusive
Streptococcus equi subsp. zooepidemicus	strain=NCTC4676	GCA_900459475.1	40041	1336	type	True	96.6423	638	729	95	conclusive
Streptococcus equi	strain=ATCC 33398	GCA_900156215.1	1336	1336	type	True	96.2746	583	729	95	conclusive
Streptococcus equi	strain=DSM 20561	GCA_900110405.1	1336	1336	type	True	96.2304	578	729	95	conclusive
Streptococcus dysgalactiae	strain=FDAARGOS_1157	GCA_016724885.1	1334	1334	type	True	81.0677	250	729	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	80.6063	66	729	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:26,115] [INFO] DFAST Taxonomy check result was written to GCF_900460185.1_41906_F01_genomic.fna/tc_result.tsv
[2024-01-24 14:06:26,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:26,115] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:26,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b2fab51-5f41-442e-9b75-3f989a2ee1ae/dqc_reference/checkm_data
[2024-01-24 14:06:26,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:26,143] [INFO] Task started: CheckM
[2024-01-24 14:06:26,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460185.1_41906_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460185.1_41906_F01_genomic.fna/checkm_input GCF_900460185.1_41906_F01_genomic.fna/checkm_result
[2024-01-24 14:06:49,438] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:49,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:49,461] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:49,461] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:49,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460185.1_41906_F01_genomic.fna/markers.fasta)
[2024-01-24 14:06:49,462] [INFO] Task started: Blastn
[2024-01-24 14:06:49,462] [INFO] Running command: blastn -query GCF_900460185.1_41906_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b2fab51-5f41-442e-9b75-3f989a2ee1ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460185.1_41906_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:50,267] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:50,271] [INFO] Selected 21 target genomes.
[2024-01-24 14:06:50,272] [INFO] Target genome list was writen to GCF_900460185.1_41906_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:50,290] [INFO] Task started: fastANI
[2024-01-24 14:06:50,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f6b6625-2d52-4be3-93a5-db2cac8879e6/GCF_900460185.1_41906_F01_genomic.fna.gz --refList GCF_900460185.1_41906_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460185.1_41906_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:58,562] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:58,583] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:58,583] [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
GCA_900637675.1	s__Streptococcus equi	96.241	621	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.36	95.16	0.97	0.81	392	conclusive
GCF_000186445.1	s__Streptococcus agalactiae	81.1485	106	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_900459225.1	s__Streptococcus dysgalactiae	81.0023	245	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.49	0.83	0.78	121	-
GCF_003595525.1	s__Streptococcus respiraculi	80.8594	93	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900475415.1	s__Streptococcus porcinus	80.6575	139	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.32	99.10	0.96	0.93	7	-
GCF_901542335.1	s__Streptococcus porcinus_A	80.3528	144	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.24	98.24	0.90	0.90	2	-
GCF_000188035.1	s__Streptococcus pseudoporcinus	80.3396	148	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.36	97.79	0.89	0.85	10	-
GCF_900635155.1	s__Streptococcus sanguinis_G	80.2873	66	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.44	97.44	0.92	0.92	2	-
GCF_002000985.1	s__Streptococcus gallolyticus	80.0007	100	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	-
GCF_900636575.1	s__Streptococcus canis	79.9176	248	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_000188015.2	s__Streptococcus ictaluri	79.8449	220	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002055535.1	s__Streptococcus pyogenes	79.4429	223	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.85	98.36	0.95	0.87	2144	-
GCF_000425025.1	s__Streptococcus castoreus	79.2202	217	729	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	79.1548	87	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.29	98.88	0.94	0.83	11	-
GCF_000188295.1	s__Streptococcus vestibularis	79.0567	69	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.03	95.83	0.91	0.87	14	-
GCF_902729355.1	s__Streptococcus sp902729355	78.8383	95	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.77	98.74	0.88	0.87	5	-
GCF_010604095.1	s__Streptococcus sp000187445	78.765	80	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.94	96.18	0.90	0.80	19	-
GCF_003674745.1	s__Streptococcus iniae	78.5869	129	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.92	98.80	0.96	0.87	94	-
GCF_001302265.1	s__Streptococcus phocae	78.5691	179	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.05	97.05	0.87	0.87	2	-
GCF_003686955.1	s__Streptococcus sp003686955	78.5561	99	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000286075.1	s__Streptococcus ratti	78.0041	89	729	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:58,585] [INFO] GTDB search result was written to GCF_900460185.1_41906_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:58,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:58,588] [INFO] DFAST_QC result json was written to GCF_900460185.1_41906_F01_genomic.fna/dqc_result.json
[2024-01-24 14:06:58,589] [INFO] DFAST_QC completed!
[2024-01-24 14:06:58,589] [INFO] Total running time: 0h0m44s