[2024-01-24 13:01:20,142] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:20,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:20,149] [INFO] DQC Reference Directory: /var/lib/cwl/stg618a5feb-e70c-475c-8966-eca75830d864/dqc_reference
[2024-01-24 13:01:21,445] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:21,446] [INFO] Task started: Prodigal
[2024-01-24 13:01:21,447] [INFO] Running command: gunzip -c /var/lib/cwl/stge5cb005b-4607-48da-b1a7-8ba44ef4dd78/GCF_024171785.1_ASM2417178v1_genomic.fna.gz | prodigal -d GCF_024171785.1_ASM2417178v1_genomic.fna/cds.fna -a GCF_024171785.1_ASM2417178v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:02,978] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:02,979] [INFO] Task started: HMMsearch
[2024-01-24 13:02:02,979] [INFO] Running command: hmmsearch --tblout GCF_024171785.1_ASM2417178v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg618a5feb-e70c-475c-8966-eca75830d864/dqc_reference/reference_markers.hmm GCF_024171785.1_ASM2417178v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:03,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:03,337] [INFO] Found 6/6 markers.
[2024-01-24 13:02:03,407] [INFO] Query marker FASTA was written to GCF_024171785.1_ASM2417178v1_genomic.fna/markers.fasta
[2024-01-24 13:02:03,408] [INFO] Task started: Blastn
[2024-01-24 13:02:03,408] [INFO] Running command: blastn -query GCF_024171785.1_ASM2417178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg618a5feb-e70c-475c-8966-eca75830d864/dqc_reference/reference_markers.fasta -out GCF_024171785.1_ASM2417178v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:04,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:04,848] [INFO] Selected 28 target genomes.
[2024-01-24 13:02:04,849] [INFO] Target genome list was writen to GCF_024171785.1_ASM2417178v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:04,861] [INFO] Task started: fastANI
[2024-01-24 13:02:04,861] [INFO] Running command: fastANI --query /var/lib/cwl/stge5cb005b-4607-48da-b1a7-8ba44ef4dd78/GCF_024171785.1_ASM2417178v1_genomic.fna.gz --refList GCF_024171785.1_ASM2417178v1_genomic.fna/target_genomes.txt --output GCF_024171785.1_ASM2417178v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:01,838] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:01,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg618a5feb-e70c-475c-8966-eca75830d864/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:01,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg618a5feb-e70c-475c-8966-eca75830d864/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:01,864] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:03:01,864] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:03:01,865] [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
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	80.1732	1263	2897	95	below_threshold
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	80.1223	1293	2897	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	79.3555	1456	2897	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	79.3502	1453	2897	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	79.2683	1126	2897	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	79.2206	1056	2897	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	79.1757	1186	2897	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	79.1343	1248	2897	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	79.0375	1304	2897	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	79.0266	1118	2897	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	78.9398	1291	2897	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	78.9381	1277	2897	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	78.8362	1169	2897	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	78.6897	1267	2897	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	78.6329	1285	2897	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	78.5561	992	2897	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.5501	1018	2897	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.4966	942	2897	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	78.387	933	2897	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	78.3626	910	2897	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	78.3271	971	2897	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.3085	935	2897	95	below_threshold
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	78.2091	1210	2897	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.1293	975	2897	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	78.072	1047	2897	95	below_threshold
Kibdelosporangium persicum	strain=4NS15	GCA_013280595.1	2698649	2698649	type	True	78.0606	1050	2897	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.7684	892	2897	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.6025	1127	2897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:01,867] [INFO] DFAST Taxonomy check result was written to GCF_024171785.1_ASM2417178v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:01,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:01,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:01,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg618a5feb-e70c-475c-8966-eca75830d864/dqc_reference/checkm_data
[2024-01-24 13:03:01,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:01,948] [INFO] Task started: CheckM
[2024-01-24 13:03:01,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024171785.1_ASM2417178v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024171785.1_ASM2417178v1_genomic.fna/checkm_input GCF_024171785.1_ASM2417178v1_genomic.fna/checkm_result
[2024-01-24 13:06:04,908] [INFO] Task succeeded: CheckM
[2024-01-24 13:06:04,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:06:04,933] [INFO] ===== Completeness check finished =====
[2024-01-24 13:06:04,934] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:06:04,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024171785.1_ASM2417178v1_genomic.fna/markers.fasta)
[2024-01-24 13:06:04,934] [INFO] Task started: Blastn
[2024-01-24 13:06:04,935] [INFO] Running command: blastn -query GCF_024171785.1_ASM2417178v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg618a5feb-e70c-475c-8966-eca75830d864/dqc_reference/reference_markers_gtdb.fasta -out GCF_024171785.1_ASM2417178v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:06:07,417] [INFO] Task succeeded: Blastn
[2024-01-24 13:06:07,423] [INFO] Selected 23 target genomes.
[2024-01-24 13:06:07,423] [INFO] Target genome list was writen to GCF_024171785.1_ASM2417178v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:06:07,460] [INFO] Task started: fastANI
[2024-01-24 13:06:07,461] [INFO] Running command: fastANI --query /var/lib/cwl/stge5cb005b-4607-48da-b1a7-8ba44ef4dd78/GCF_024171785.1_ASM2417178v1_genomic.fna.gz --refList GCF_024171785.1_ASM2417178v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024171785.1_ASM2417178v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:06:56,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:06:56,752] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:06:56,752] [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_000715825.1	s__Goodfellowiella coeruleoviolacea	99.569	2767	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014648515.1	s__Actinosynnema coeruleofuscum	80.2428	1251	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_005405885.1	s__Gandjariella thermophila	79.8486	1034	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	79.5993	1234	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	79.3411	1456	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	79.2594	1127	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	79.1665	837	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	79.1659	1190	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	79.1284	1251	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	79.0391	1115	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328705.1	s__Actinosynnema espanaense	78.993	1275	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263855.1	s__Kutzneria sp018263855	78.7768	1296	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354875.1	s__Actinosynnema auranticum	78.759	1223	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	100.00	100.00	1.00	1.00	2	-
GCF_014203355.1	s__Kutzneria kofuensis	78.677	1268	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204915.1	s__Crossiella cryophila	78.6343	1287	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	78.5285	997	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876755.1	s__Crossiella equi	78.5274	1244	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004214935.1	s__Amycolatopsis suaedae	78.3783	1070	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907695.1	s__Actinokineospora baliensis	78.3139	951	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875555.1	s__Amycolatopsis magusensis	78.2125	1204	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009429145.1	s__Amycolatopsis sp009429145	78.2068	1238	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921215.1	s__Actinophytocola xinjiangensis	78.1442	1235	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013280595.1	s__Kibdelosporangium persicum	78.0769	1038	2897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:06:56,754] [INFO] GTDB search result was written to GCF_024171785.1_ASM2417178v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:06:56,755] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:06:56,760] [INFO] DFAST_QC result json was written to GCF_024171785.1_ASM2417178v1_genomic.fna/dqc_result.json
[2024-01-24 13:06:56,760] [INFO] DFAST_QC completed!
[2024-01-24 13:06:56,760] [INFO] Total running time: 0h5m37s