[2024-01-24 14:55:07,908] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:07,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:07,910] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4a8b4e1-167b-496c-bf40-55c430a6322e/dqc_reference
[2024-01-24 14:55:09,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,499] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg51ec1405-d675-4531-a673-980e0cb8967e/GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna.gz | prodigal -d GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/cds.fna -a GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:15,214] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:15,214] [INFO] Task started: HMMsearch
[2024-01-24 14:55:15,215] [INFO] Running command: hmmsearch --tblout GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4a8b4e1-167b-496c-bf40-55c430a6322e/dqc_reference/reference_markers.hmm GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:15,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:15,449] [INFO] Found 6/6 markers.
[2024-01-24 14:55:15,479] [INFO] Query marker FASTA was written to GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/markers.fasta
[2024-01-24 14:55:15,479] [INFO] Task started: Blastn
[2024-01-24 14:55:15,479] [INFO] Running command: blastn -query GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4a8b4e1-167b-496c-bf40-55c430a6322e/dqc_reference/reference_markers.fasta -out GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:16,092] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:16,096] [INFO] Selected 25 target genomes.
[2024-01-24 14:55:16,097] [INFO] Target genome list was writen to GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:16,235] [INFO] Task started: fastANI
[2024-01-24 14:55:16,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ec1405-d675-4531-a673-980e0cb8967e/GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna.gz --refList GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/target_genomes.txt --output GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:25,450] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:25,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4a8b4e1-167b-496c-bf40-55c430a6322e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:25,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4a8b4e1-167b-496c-bf40-55c430a6322e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:25,469] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:25,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:25,470] [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 varani	strain=FF10	GCA_001375655.1	1608583	1608583	type	True	100.0	812	813	95	conclusive
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	79.1017	144	813	95	below_threshold
Streptococcus suis	strain=S735	GCA_000294495.1	1307	1307	type	True	79.0792	149	813	95	below_threshold
Streptococcus ovis	strain=DSM 16829	GCA_000380125.1	82806	82806	type	True	79.0549	218	813	95	below_threshold
Streptococcus suis	strain=NCTC10234	GCA_900475585.1	1307	1307	type	True	78.9726	149	813	95	below_threshold
Streptococcus oriscaviae	strain=HKU75	GCA_018137985.1	2781599	2781599	type	True	78.9618	153	813	95	below_threshold
Streptococcus constellatus subsp. pharyngis	strain=CCUG 46377	GCA_000474135.1	184250	76860	type	True	78.9378	76	813	95	below_threshold
Streptococcus salivarius	strain=NCTC 8618	GCA_000785515.1	1304	1304	suspected-type	True	78.9219	86	813	95	below_threshold
Streptococcus respiraculi	strain=HTS25	GCA_003595525.1	2021971	2021971	type	True	78.7711	136	813	95	below_threshold
Streptococcus minor	strain=DSM 17118	GCA_000377005.1	229549	229549	type	True	78.7658	279	813	95	below_threshold
Streptococcus salivarius	strain=JCM 5707	GCA_019972895.1	1304	1304	suspected-type	True	78.6423	85	813	95	below_threshold
Streptococcus henryi	strain=DSM 19005	GCA_000376985.1	439219	439219	type	True	78.586	158	813	95	below_threshold
Streptococcus infantarius	strain=FDAARGOS_1019	GCA_016127275.1	102684	102684	type	True	78.5025	91	813	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.4751	104	813	95	below_threshold
Streptococcus orisratti	strain=DSM 15617	GCA_000380105.1	114652	114652	type	True	78.4671	105	813	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	78.4075	81	813	95	below_threshold
Streptococcus halitosis	strain=VT-4	GCA_003143695.2	2172545	2172545	type	True	78.4011	100	813	95	below_threshold
Streptococcus gallolyticus	strain=NCTC13773	GCA_900475715.1	315405	315405	suspected-type	True	78.3608	92	813	95	below_threshold
Streptococcus ruminantium	strain=GUT187T	GCA_003609975.1	1917441	1917441	type	True	78.3233	129	813	95	below_threshold
Streptococcus infantarius subsp. infantarius	strain=ATCC BAA-102	GCA_000154985.1	150054	102684	type	True	78.3007	91	813	95	below_threshold
Streptococcus infantarius	strain=NCTC13760	GCA_900459445.1	102684	102684	type	True	78.2986	89	813	95	below_threshold
Streptococcus gallolyticus subsp. gallolyticus	strain=DSM 16831	GCA_002000985.1	53354	315405	type	True	78.2734	92	813	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	78.1736	106	813	95	below_threshold
Streptococcus sobrinus	strain=SL1	GCA_003172995.1	1310	1310	type	True	77.7292	70	813	95	below_threshold
Streptococcus sobrinus	strain=DSM 20742	GCA_000686605.1	1310	1310	type	True	77.161	66	813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:25,471] [INFO] DFAST Taxonomy check result was written to GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:25,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:25,472] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:25,472] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4a8b4e1-167b-496c-bf40-55c430a6322e/dqc_reference/checkm_data
[2024-01-24 14:55:25,473] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:25,500] [INFO] Task started: CheckM
[2024-01-24 14:55:25,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/checkm_input GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/checkm_result
[2024-01-24 14:55:50,595] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:50,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:50,612] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:50,612] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:50,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/markers.fasta)
[2024-01-24 14:55:50,613] [INFO] Task started: Blastn
[2024-01-24 14:55:50,613] [INFO] Running command: blastn -query GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4a8b4e1-167b-496c-bf40-55c430a6322e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:51,473] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:51,477] [INFO] Selected 24 target genomes.
[2024-01-24 14:55:51,477] [INFO] Target genome list was writen to GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:51,513] [INFO] Task started: fastANI
[2024-01-24 14:55:51,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ec1405-d675-4531-a673-980e0cb8967e/GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna.gz --refList GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:01,220] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:01,241] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:01,242] [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_001375655.1	s__Streptococcus varani	100.0	812	813	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_004283785.1	s__Streptococcus parasuis	79.1722	116	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.19	96.80	0.84	0.77	20	-
GCF_000294495.1	s__Streptococcus suis	79.1095	148	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.2533	98.55	95.80	0.92	0.80	1267	-
GCF_000380125.1	s__Streptococcus ovis	79.0443	219	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627135.1	s__Streptococcus koreensis	78.9973	91	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.43	95.11	0.91	0.89	8	-
GCF_018137985.1	s__Streptococcus sp018137985	78.9618	153	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000785515.1	s__Streptococcus salivarius	78.9219	86	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.08	95.32	0.88	0.82	131	-
GCF_000440555.1	s__Streptococcus suis_N	78.9158	130	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.61	95.42	0.83	0.79	5	-
GCF_002960445.1	s__Streptococcus suis_O	78.8024	153	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377005.1	s__Streptococcus minor	78.7884	277	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.19	98.19	0.90	0.90	2	-
GCF_900101445.1	s__Streptococcus equinus_B	78.7269	78	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.02	95.22	0.90	0.87	9	-
GCF_900475675.1	s__Streptococcus lutetiensis	78.7078	84	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.21	95.22	0.92	0.85	50	-
GCF_004785935.1	s__Streptococcus rubneri	78.693	106	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.13	96.92	0.96	0.90	4	-
GCF_017639855.1	s__Streptococcus sp013623465	78.6927	116	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.97	99.93	0.99	0.98	7	-
GCF_001579525.1	s__Streptococcus oralis_M	78.6389	86	813	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	78.5953	155	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.14	98.14	0.85	0.85	2	-
GCF_001182825.2	s__Streptococcus sp001182825	78.5752	143	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.88	99.88	1.00	1.00	2	-
GCF_000380105.1	s__Streptococcus orisratti	78.4556	106	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000187265.1	s__Streptococcus equinus	78.4075	81	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.03	95.86	0.90	0.87	42	-
GCF_000154985.1	s__Streptococcus infantarius	78.3007	91	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.67	95.30	0.89	0.82	24	-
GCF_002000985.1	s__Streptococcus gallolyticus	78.2734	92	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	96.3165	98.04	96.86	0.89	0.79	22	-
GCF_900459175.1	s__Streptococcus downei	77.323	83	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.20	97.65	0.95	0.94	6	-
GCF_000686605.1	s__Streptococcus sobrinus	77.161	66	813	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.93	98.60	0.95	0.92	52	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:01,243] [INFO] GTDB search result was written to GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:01,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:01,250] [INFO] DFAST_QC result json was written to GCF_001375655.1_PRJEB8936_assembly_1_genomic.fna/dqc_result.json
[2024-01-24 14:56:01,250] [INFO] DFAST_QC completed!
[2024-01-24 14:56:01,250] [INFO] Total running time: 0h0m53s