[2024-01-24 13:49:15,527] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:15,530] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:15,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg41cdca3f-a275-4aaa-9e38-ea769102c13f/dqc_reference
[2024-01-24 13:49:16,799] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:16,799] [INFO] Task started: Prodigal
[2024-01-24 13:49:16,800] [INFO] Running command: gunzip -c /var/lib/cwl/stg786f49f1-7da5-45ed-b97b-bec8de465237/GCF_000372425.1_ASM37242v1_genomic.fna.gz | prodigal -d GCF_000372425.1_ASM37242v1_genomic.fna/cds.fna -a GCF_000372425.1_ASM37242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:21,121] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:21,122] [INFO] Task started: HMMsearch
[2024-01-24 13:49:21,122] [INFO] Running command: hmmsearch --tblout GCF_000372425.1_ASM37242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41cdca3f-a275-4aaa-9e38-ea769102c13f/dqc_reference/reference_markers.hmm GCF_000372425.1_ASM37242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:21,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:21,399] [INFO] Found 6/6 markers.
[2024-01-24 13:49:21,420] [INFO] Query marker FASTA was written to GCF_000372425.1_ASM37242v1_genomic.fna/markers.fasta
[2024-01-24 13:49:21,421] [INFO] Task started: Blastn
[2024-01-24 13:49:21,421] [INFO] Running command: blastn -query GCF_000372425.1_ASM37242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41cdca3f-a275-4aaa-9e38-ea769102c13f/dqc_reference/reference_markers.fasta -out GCF_000372425.1_ASM37242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:21,997] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:22,000] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:22,001] [INFO] Target genome list was writen to GCF_000372425.1_ASM37242v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:22,015] [INFO] Task started: fastANI
[2024-01-24 13:49:22,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg786f49f1-7da5-45ed-b97b-bec8de465237/GCF_000372425.1_ASM37242v1_genomic.fna.gz --refList GCF_000372425.1_ASM37242v1_genomic.fna/target_genomes.txt --output GCF_000372425.1_ASM37242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:28,774] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:28,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41cdca3f-a275-4aaa-9e38-ea769102c13f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:28,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41cdca3f-a275-4aaa-9e38-ea769102c13f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:28,790] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:28,791] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:28,791] [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 ferus	strain=DSM 20646	GCA_000372425.1	1345	1345	type	True	100.0	609	610	95	conclusive
Streptococcus ferus	strain=NCTC12278	GCA_900475025.1	1345	1345	type	True	99.9972	610	610	95	conclusive
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	80.2129	107	610	95	below_threshold
Streptococcus ratti	strain=DSM 20564	GCA_000347915.1	1341	1341	suspected-type	True	79.8316	158	610	95	below_threshold
Streptococcus ratti	strain=FA-1	GCA_000286075.1	1341	1341	suspected-type	True	79.769	176	610	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	79.7503	77	610	95	below_threshold
Streptococcus thermophilus	strain=ATCC 19258	GCA_010120595.1	1308	1308	type	True	78.8849	74	610	95	below_threshold
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	78.7656	73	610	95	below_threshold
Streptococcus thermophilus	strain=DSM 20617	GCA_019972875.1	1308	1308	type	True	78.6905	74	610	95	below_threshold
Streptococcus catagoni	strain=99-1/2017	GCA_011421425.1	2654874	2654874	type	True	78.4956	64	610	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.105	62	610	95	below_threshold
Streptococcus devriesei	strain=DSM 19639	GCA_000423725.1	231233	231233	type	True	78.0833	155	610	95	below_threshold
Streptococcus sanguinis	strain=NCTC7863	GCA_900475505.1	1305	1305	suspected-type	True	78.0106	86	610	95	below_threshold
Streptococcus peroris	strain=ATCC 700780	GCA_000187585.1	68891	68891	type	True	77.9041	61	610	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	77.9035	65	610	95	below_threshold
Streptococcus troglodytae	strain=TKU 31	GCA_002355215.1	1111760	1111760	type	True	77.851	143	610	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	77.7785	71	610	95	below_threshold
Streptococcus sanguinis	strain=NCTC 7863	GCA_001593525.1	1305	1305	suspected-type	True	77.7754	79	610	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	77.658	75	610	95	below_threshold
Streptococcus pantholopis	strain=TA 26	GCA_001642085.1	1811193	1811193	type	True	77.4685	71	610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:28,793] [INFO] DFAST Taxonomy check result was written to GCF_000372425.1_ASM37242v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:28,793] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:28,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:28,794] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41cdca3f-a275-4aaa-9e38-ea769102c13f/dqc_reference/checkm_data
[2024-01-24 13:49:28,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:28,820] [INFO] Task started: CheckM
[2024-01-24 13:49:28,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000372425.1_ASM37242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000372425.1_ASM37242v1_genomic.fna/checkm_input GCF_000372425.1_ASM37242v1_genomic.fna/checkm_result
[2024-01-24 13:49:49,165] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:49,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:49,196] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:49,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:49,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000372425.1_ASM37242v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:49,197] [INFO] Task started: Blastn
[2024-01-24 13:49:49,198] [INFO] Running command: blastn -query GCF_000372425.1_ASM37242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41cdca3f-a275-4aaa-9e38-ea769102c13f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000372425.1_ASM37242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:49,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:49,975] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:49,975] [INFO] Target genome list was writen to GCF_000372425.1_ASM37242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:49,994] [INFO] Task started: fastANI
[2024-01-24 13:49:49,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg786f49f1-7da5-45ed-b97b-bec8de465237/GCF_000372425.1_ASM37242v1_genomic.fna.gz --refList GCF_000372425.1_ASM37242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000372425.1_ASM37242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:59,345] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:59,372] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:59,372] [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_000372425.1	s__Streptococcus ferus	100.0	609	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_018137985.1	s__Streptococcus sp018137985	80.1606	109	610	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	79.7988	175	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_002964045.1	s__Streptococcus suis_U	79.3979	73	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.50	95.50	0.81	0.81	2	-
GCF_002964575.1	s__Streptococcus suis_R	79.3029	79	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002960625.1	s__Streptococcus suis_T	79.2755	88	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186445.1	s__Streptococcus agalactiae	78.7614	72	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.63	98.18	0.88	0.63	1516	-
GCF_001074155.1	s__Streptococcus pseudopneumoniae_A	78.1665	62	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423725.1	s__Streptococcus devriesei	78.0833	155	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001937065.1	s__Streptococcus sp001937065	78.0598	161	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901875555.1	s__Streptococcus parasanguinis_H	78.0515	74	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000963275.1	s__Streptococcus parasanguinis_B	78.0362	69	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2991	95.64	95.37	0.88	0.85	11	-
GCF_002096855.1	s__Streptococcus mitis_Y	78.0041	64	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.03	96.03	0.87	0.87	2	-
GCF_001078705.1	s__Streptococcus sanguinis_D	77.995	77	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650315.1	s__Streptococcus sp001650315	77.9404	69	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.60	97.60	0.91	0.91	2	-
GCF_000194945.1	s__Streptococcus sanguinis	77.9166	83	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.01	0.93	0.89	47	-
GCF_000187585.1	s__Streptococcus peroris	77.9041	61	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.68	96.68	0.90	0.90	2	-
GCF_002355215.1	s__Streptococcus troglodytae	77.851	143	610	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	77.7719	89	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598035.1	s__Streptococcus halotolerans	77.7048	83	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038795.1	s__Streptococcus sp011038795	77.6689	84	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.03	99.03	0.90	0.90	2	-
GCF_001579665.1	s__Streptococcus mitis_S	77.6567	70	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.64	95.33	0.87	0.85	4	-
GCF_001811505.1	s__Streptococcus sp001811505	77.6172	71	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496285.1	s__Streptococcus mitis_BP	77.6036	71	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013343115.1	s__Streptococcus sanguinis_H	77.4886	91	610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.75	95.06	0.92	0.88	13	-
GCF_001642085.1	s__Streptococcus pantholopis	77.4685	71	610	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 13:49:59,374] [INFO] GTDB search result was written to GCF_000372425.1_ASM37242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:59,374] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:59,379] [INFO] DFAST_QC result json was written to GCF_000372425.1_ASM37242v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:59,379] [INFO] DFAST_QC completed!
[2024-01-24 13:49:59,379] [INFO] Total running time: 0h0m44s