[2024-01-25 19:11:51,046] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:51,047] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:51,047] [INFO] DQC Reference Directory: /var/lib/cwl/stg672112bf-72ae-4392-a533-f7f5669171cb/dqc_reference
[2024-01-25 19:11:52,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:52,225] [INFO] Task started: Prodigal
[2024-01-25 19:11:52,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg988c3eb1-2021-4102-a6d9-26bab4e6c5fd/GCF_000377005.1_ASM37700v1_genomic.fna.gz | prodigal -d GCF_000377005.1_ASM37700v1_genomic.fna/cds.fna -a GCF_000377005.1_ASM37700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:56,101] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:56,102] [INFO] Task started: HMMsearch
[2024-01-25 19:11:56,102] [INFO] Running command: hmmsearch --tblout GCF_000377005.1_ASM37700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg672112bf-72ae-4392-a533-f7f5669171cb/dqc_reference/reference_markers.hmm GCF_000377005.1_ASM37700v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:56,318] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:56,319] [INFO] Found 6/6 markers.
[2024-01-25 19:11:56,343] [INFO] Query marker FASTA was written to GCF_000377005.1_ASM37700v1_genomic.fna/markers.fasta
[2024-01-25 19:11:56,343] [INFO] Task started: Blastn
[2024-01-25 19:11:56,343] [INFO] Running command: blastn -query GCF_000377005.1_ASM37700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg672112bf-72ae-4392-a533-f7f5669171cb/dqc_reference/reference_markers.fasta -out GCF_000377005.1_ASM37700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:56,892] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:56,895] [INFO] Selected 28 target genomes.
[2024-01-25 19:11:56,895] [INFO] Target genome list was writen to GCF_000377005.1_ASM37700v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:56,917] [INFO] Task started: fastANI
[2024-01-25 19:11:56,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg988c3eb1-2021-4102-a6d9-26bab4e6c5fd/GCF_000377005.1_ASM37700v1_genomic.fna.gz --refList GCF_000377005.1_ASM37700v1_genomic.fna/target_genomes.txt --output GCF_000377005.1_ASM37700v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:06,807] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:06,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg672112bf-72ae-4392-a533-f7f5669171cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:06,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg672112bf-72ae-4392-a533-f7f5669171cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:06,822] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:06,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:06,822] [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 minor	strain=DSM 17118	GCA_000377005.1	229549	229549	type	True	100.0	625	626	95	conclusive
Streptococcus entericus	strain=DSM 14446	GCA_000380025.1	155680	155680	type	True	79.8061	74	626	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	79.4479	172	626	95	below_threshold
Streptococcus ferus	strain=NCTC12278	GCA_900475025.1	1345	1345	type	True	79.1549	86	626	95	below_threshold
Streptococcus varani	strain=FF10	GCA_001375655.1	1608583	1608583	type	True	78.9765	274	626	95	below_threshold
Streptococcus suis	strain=S735	GCA_000294495.1	1307	1307	type	True	78.8878	147	626	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	78.8703	176	626	95	below_threshold
Streptococcus suis	strain=NCTC10234	GCA_900475585.1	1307	1307	type	True	78.8437	148	626	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.8382	130	626	95	below_threshold
Streptococcus ferus	strain=DSM 20646	GCA_000372425.1	1345	1345	type	True	78.7158	85	626	95	below_threshold
Streptococcus hillyeri	strain=28462	GCA_003686955.1	2282420	2282420	type	True	78.6941	79	626	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	78.6907	97	626	95	below_threshold
Streptococcus bovimastitidis	strain=NZ1587	GCA_001885095.1	1856638	1856638	type	True	78.6446	65	626	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	78.5591	95	626	95	below_threshold
Streptococcus equi subsp. ruminatorum	strain=CECT 5772	GCA_000706805.1	254358	1336	type	True	78.5015	54	626	95	below_threshold
Streptococcus thoraltensis	strain=DSM 12221	GCA_000380145.1	55085	55085	type	True	78.3532	75	626	95	below_threshold
Streptococcus penaeicida	strain=CAIM 1838	GCA_002887775.1	1765960	1765960	type	True	78.23	63	626	95	below_threshold
Streptococcus koreensis	strain=JS71	GCA_003627135.1	2382163	2382163	type	True	78.2223	99	626	95	below_threshold
Streptococcus himalayensis	strain=HTS2	GCA_001708305.1	1888195	1888195	type	True	78.0304	90	626	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	78.0273	78	626	95	below_threshold
Streptococcus himalayensis	strain=CGMCC 1.15533	GCA_014643475.1	1888195	1888195	type	True	77.9808	88	626	95	below_threshold
Streptococcus ratti	strain=FA-1	GCA_000286075.1	1341	1341	suspected-type	True	77.9579	66	626	95	below_threshold
Streptococcus plurextorum	strain=DSM 22810	GCA_000423745.1	456876	456876	type	True	77.9089	106	626	95	below_threshold
Streptococcus ratti	strain=DSM 20564	GCA_000347915.1	1341	1341	suspected-type	True	77.7722	58	626	95	below_threshold
Streptococcus troglodytae	strain=TKU 31	GCA_002355215.1	1111760	1111760	type	True	77.6306	72	626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:06,823] [INFO] DFAST Taxonomy check result was written to GCF_000377005.1_ASM37700v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:06,824] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:06,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:06,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg672112bf-72ae-4392-a533-f7f5669171cb/dqc_reference/checkm_data
[2024-01-25 19:12:06,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:06,846] [INFO] Task started: CheckM
[2024-01-25 19:12:06,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000377005.1_ASM37700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000377005.1_ASM37700v1_genomic.fna/checkm_input GCF_000377005.1_ASM37700v1_genomic.fna/checkm_result
[2024-01-25 19:12:24,460] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:24,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:24,481] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:24,481] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:24,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000377005.1_ASM37700v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:24,482] [INFO] Task started: Blastn
[2024-01-25 19:12:24,482] [INFO] Running command: blastn -query GCF_000377005.1_ASM37700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg672112bf-72ae-4392-a533-f7f5669171cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000377005.1_ASM37700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:25,230] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:25,233] [INFO] Selected 25 target genomes.
[2024-01-25 19:12:25,233] [INFO] Target genome list was writen to GCF_000377005.1_ASM37700v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:25,251] [INFO] Task started: fastANI
[2024-01-25 19:12:25,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg988c3eb1-2021-4102-a6d9-26bab4e6c5fd/GCF_000377005.1_ASM37700v1_genomic.fna.gz --refList GCF_000377005.1_ASM37700v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000377005.1_ASM37700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:33,688] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:33,703] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:33,703] [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_000377005.1	s__Streptococcus minor	100.0	625	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.19	98.19	0.90	0.90	2	conclusive
GCF_018137985.1	s__Streptococcus sp018137985	79.4327	173	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004283785.1	s__Streptococcus parasuis	79.2162	104	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.19	96.80	0.84	0.77	20	-
GCF_001375655.1	s__Streptococcus varani	78.9765	274	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964575.1	s__Streptococcus suis_R	78.8772	166	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609975.1	s__Streptococcus ruminantium	78.8382	130	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.78	98.55	0.91	0.88	24	-
GCF_902702775.1	s__Streptococcus suis_W	78.8081	147	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2533	96.52	95.78	0.85	0.77	106	-
GCF_000376985.1	s__Streptococcus henryi	78.6946	97	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_000372425.1	s__Streptococcus ferus	78.6928	86	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002960445.1	s__Streptococcus suis_O	78.6652	153	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885095.1	s__Streptococcus bovimastitidis	78.5853	66	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004569635.1	s__Streptococcus sp004569635	78.5775	103	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016743335.1	s__Streptococcus suis_Y	78.5359	160	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.53	95.45	0.79	0.78	5	-
GCF_002960425.1	s__Streptococcus suis_S	78.4951	156	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.81	98.81	0.93	0.93	2	-
GCF_001937065.1	s__Streptococcus sp001937065	78.3015	61	626	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	78.23	63	626	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	78.2058	66	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369405.1	s__Streptococcus cristatus_G	78.1039	91	626	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	78.0593	63	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_000286075.1	s__Streptococcus ratti	77.9579	66	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.59	98.38	0.97	0.87	5	-
GCF_009496165.1	s__Streptococcus mitis_BM	77.957	98	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.49	95.44	0.98	0.88	26	-
GCA_905221375.1	s__Streptococcus sp905221375	77.8809	93	626	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	77.6306	72	626	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	77.3835	78	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_001431045.1	s__Streptococcus orisasini	77.1331	78	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:33,714] [INFO] GTDB search result was written to GCF_000377005.1_ASM37700v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:33,715] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:33,720] [INFO] DFAST_QC result json was written to GCF_000377005.1_ASM37700v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:33,720] [INFO] DFAST_QC completed!
[2024-01-25 19:12:33,721] [INFO] Total running time: 0h0m43s