[2024-01-24 13:56:27,361] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,363] [INFO] DQC Reference Directory: /var/lib/cwl/stg5001d8a6-06c1-489a-98b7-fa075dda09a8/dqc_reference
[2024-01-24 13:56:28,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,627] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg51ed50b1-564d-4df8-ac5e-4dce9b47ab5d/GCF_008974245.1_ASM897424v1_genomic.fna.gz | prodigal -d GCF_008974245.1_ASM897424v1_genomic.fna/cds.fna -a GCF_008974245.1_ASM897424v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:50,432] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:50,432] [INFO] Task started: HMMsearch
[2024-01-24 13:56:50,433] [INFO] Running command: hmmsearch --tblout GCF_008974245.1_ASM897424v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5001d8a6-06c1-489a-98b7-fa075dda09a8/dqc_reference/reference_markers.hmm GCF_008974245.1_ASM897424v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:50,786] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:50,788] [INFO] Found 6/6 markers.
[2024-01-24 13:56:50,845] [INFO] Query marker FASTA was written to GCF_008974245.1_ASM897424v1_genomic.fna/markers.fasta
[2024-01-24 13:56:50,845] [INFO] Task started: Blastn
[2024-01-24 13:56:50,846] [INFO] Running command: blastn -query GCF_008974245.1_ASM897424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5001d8a6-06c1-489a-98b7-fa075dda09a8/dqc_reference/reference_markers.fasta -out GCF_008974245.1_ASM897424v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:52,236] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:52,240] [INFO] Selected 33 target genomes.
[2024-01-24 13:56:52,241] [INFO] Target genome list was writen to GCF_008974245.1_ASM897424v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:52,259] [INFO] Task started: fastANI
[2024-01-24 13:56:52,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ed50b1-564d-4df8-ac5e-4dce9b47ab5d/GCF_008974245.1_ASM897424v1_genomic.fna.gz --refList GCF_008974245.1_ASM897424v1_genomic.fna/target_genomes.txt --output GCF_008974245.1_ASM897424v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:56,926] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:56,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5001d8a6-06c1-489a-98b7-fa075dda09a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:56,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5001d8a6-06c1-489a-98b7-fa075dda09a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:56,950] [INFO] Found 33 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:56,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:56,951] [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
Streptomyces abyssomicinicus	strain=CHI39	GCA_008974245.1	574929	574929	type	True	100.0	2631	2631	95	conclusive
Streptomyces chilikensis	strain=RC 1830	GCA_001642695.2	1194079	1194079	type	True	92.2185	1819	2631	95	below_threshold
Streptomyces fragilis	strain=NBRC 12862	GCA_003112515.1	67301	67301	type	True	88.9753	1794	2631	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	82.4473	1298	2631	95	below_threshold
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	82.4	1450	2631	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	82.3665	1273	2631	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	82.3028	1409	2631	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	82.2755	1432	2631	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	82.2535	1422	2631	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	82.2109	1401	2631	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	82.1925	1381	2631	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	82.1888	1413	2631	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	82.1701	1414	2631	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	82.1073	1362	2631	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.8579	1390	2631	95	below_threshold
Streptomyces poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	81.8327	1344	2631	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	81.8094	1452	2631	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	81.7641	1339	2631	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	81.7261	1269	2631	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.66	1333	2631	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	81.3146	1354	2631	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	81.169	1311	2631	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	80.4079	1108	2631	95	below_threshold
Streptomyces montanisoli	strain=MMS17-BM035	GCA_017813245.1	2798581	2798581	type	True	79.7861	987	2631	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	79.5589	989	2631	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.5519	1091	2631	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	79.5178	1113	2631	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	79.4597	1082	2631	95	below_threshold
Streptomyces qinglanensis	strain=CGMCC 4.6825	GCA_900111245.1	943816	943816	type	True	79.35	1070	2631	95	below_threshold
Streptomyces qinglanensis	strain=172205	GCA_003265665.1	943816	943816	type	True	79.3297	1068	2631	95	below_threshold
Streptomyces cacaoi	strain=NRRL B-1220	GCA_002154495.1	1898	1898	type	True	79.2067	979	2631	95	below_threshold
Streptomyces cacaoi	strain=DSM 40057	GCA_013004455.1	1898	1898	type	True	79.1775	1074	2631	95	below_threshold
Streptomyces cacaoi	strain=NBRC 12748	GCA_006539165.1	1898	1898	type	True	79.107	1118	2631	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:56,953] [INFO] DFAST Taxonomy check result was written to GCF_008974245.1_ASM897424v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:56,954] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:56,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:56,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5001d8a6-06c1-489a-98b7-fa075dda09a8/dqc_reference/checkm_data
[2024-01-24 13:57:56,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:57,033] [INFO] Task started: CheckM
[2024-01-24 13:57:57,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008974245.1_ASM897424v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008974245.1_ASM897424v1_genomic.fna/checkm_input GCF_008974245.1_ASM897424v1_genomic.fna/checkm_result
[2024-01-24 13:59:51,243] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:51,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:51,270] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:51,270] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:51,271] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008974245.1_ASM897424v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:51,271] [INFO] Task started: Blastn
[2024-01-24 13:59:51,271] [INFO] Running command: blastn -query GCF_008974245.1_ASM897424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5001d8a6-06c1-489a-98b7-fa075dda09a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_008974245.1_ASM897424v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:53,554] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:53,562] [INFO] Selected 27 target genomes.
[2024-01-24 13:59:53,562] [INFO] Target genome list was writen to GCF_008974245.1_ASM897424v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:53,644] [INFO] Task started: fastANI
[2024-01-24 13:59:53,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg51ed50b1-564d-4df8-ac5e-4dce9b47ab5d/GCF_008974245.1_ASM897424v1_genomic.fna.gz --refList GCF_008974245.1_ASM897424v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008974245.1_ASM897424v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:50,312] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:50,335] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:50,336] [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_008974245.1	s__Streptomyces abyssomicinicus	100.0	2631	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001642695.1	s__Streptomyces chilikensis	92.1635	1825	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112515.1	s__Streptomyces fragilis	88.984	1793	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	82.4979	1387	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	82.3708	1410	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	82.3053	1374	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006782915.1	s__Streptomyces calvus	82.2662	1425	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_005280195.1	s__Streptomyces galbus	82.2134	1409	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_014648855.1	s__Streptomyces parvulus	82.1685	1386	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_001514125.1	s__Streptomyces longwoodensis	82.1518	1411	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_001514215.1	s__Streptomyces bungoensis	82.1007	1363	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	82.037	1357	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_000373625.1	s__Streptomyces sp000373625	82.0048	1259	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155905.1	s__Streptomyces tricolor	81.93	1192	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	98.00	0.86	0.72	5	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	81.7625	1462	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_001280015.1	s__Streptomyces sp001280015	81.6961	1326	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675325.1	s__Streptomyces sp003675325	81.6538	1317	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317595.1	s__Streptomyces ipomoeae	80.9046	1254	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_017813245.1	s__Streptomyces bomunensis	79.7629	992	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013302895.1	s__Streptomyces chlorinus	79.6437	1035	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	79.5388	1094	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	79.4609	1073	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424785.1	s__Streptomyces sp000424785	79.399	1067	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111245.1	s__Streptomyces qinglanensis	79.3415	1073	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	0.99	0.99	2	-
GCF_006539165.1	s__Streptomyces cacaoi	79.0717	1126	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.44	99.09	0.96	0.94	7	-
GCF_001625365.1	s__Kitasatospora sp001625365	78.9078	1118	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014284505.1	s__Streptacidiphilus sp014284505	78.5032	965	2631	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:50,338] [INFO] GTDB search result was written to GCF_008974245.1_ASM897424v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:50,338] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:50,344] [INFO] DFAST_QC result json was written to GCF_008974245.1_ASM897424v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:50,344] [INFO] DFAST_QC completed!
[2024-01-24 14:00:50,345] [INFO] Total running time: 0h4m23s