[2024-01-24 10:58:06,467] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ccc5728-0d94-4970-8640-702111a2bb9b/dqc_reference
[2024-01-24 10:58:09,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,643] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a171119-9140-415d-8831-6b5fc55218b7/GCF_014650455.1_ASM1465045v1_genomic.fna.gz | prodigal -d GCF_014650455.1_ASM1465045v1_genomic.fna/cds.fna -a GCF_014650455.1_ASM1465045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:36,531] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:36,531] [INFO] Task started: HMMsearch
[2024-01-24 10:58:36,531] [INFO] Running command: hmmsearch --tblout GCF_014650455.1_ASM1465045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ccc5728-0d94-4970-8640-702111a2bb9b/dqc_reference/reference_markers.hmm GCF_014650455.1_ASM1465045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:36,982] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:36,983] [INFO] Found 6/6 markers.
[2024-01-24 10:58:37,048] [INFO] Query marker FASTA was written to GCF_014650455.1_ASM1465045v1_genomic.fna/markers.fasta
[2024-01-24 10:58:37,048] [INFO] Task started: Blastn
[2024-01-24 10:58:37,048] [INFO] Running command: blastn -query GCF_014650455.1_ASM1465045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ccc5728-0d94-4970-8640-702111a2bb9b/dqc_reference/reference_markers.fasta -out GCF_014650455.1_ASM1465045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:38,584] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:38,589] [INFO] Selected 24 target genomes.
[2024-01-24 10:58:38,594] [INFO] Target genome list was writen to GCF_014650455.1_ASM1465045v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:38,624] [INFO] Task started: fastANI
[2024-01-24 10:58:38,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a171119-9140-415d-8831-6b5fc55218b7/GCF_014650455.1_ASM1465045v1_genomic.fna.gz --refList GCF_014650455.1_ASM1465045v1_genomic.fna/target_genomes.txt --output GCF_014650455.1_ASM1465045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:59:25,171] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:25,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ccc5728-0d94-4970-8640-702111a2bb9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:59:25,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ccc5728-0d94-4970-8640-702111a2bb9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:59:25,198] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:59:25,198] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:59:25,198] [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 xanthochromogenes	strain=JCM 4612	GCA_014650455.1	67384	67384	type	True	100.0	2895	2899	95	conclusive
Streptomyces violascens	strain=JCM 4424	GCA_014649955.1	67381	67381	type	True	90.0576	1997	2899	95	below_threshold
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	89.9528	2009	2899	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	84.6909	1720	2899	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	82.8655	1412	2899	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.5494	1511	2899	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.4898	1366	2899	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	82.3587	1472	2899	95	below_threshold
Streptomyces californicus	strain=FDAARGOS_1209	GCA_016906185.1	67351	67351	type	True	82.2625	1441	2899	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	82.0547	1458	2899	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.0505	1551	2899	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	82.0374	1539	2899	95	below_threshold
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	82.0223	1408	2899	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	81.9256	1027	2899	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.6577	1205	2899	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.6231	1399	2899	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	81.4928	1246	2899	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.443	1265	2899	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.3847	1391	2899	95	below_threshold
Streptomyces thermodiastaticus	strain=JCM 4840	GCA_014656135.1	44061	44061	type	True	81.3186	1159	2899	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	81.2458	1165	2899	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.9484	1152	2899	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.6309	1055	2899	95	below_threshold
Actinacidiphila yeochonensis	strain=CN732	GCA_000745345.1	89050	89050	type	True	79.5014	1093	2899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:59:25,200] [INFO] DFAST Taxonomy check result was written to GCF_014650455.1_ASM1465045v1_genomic.fna/tc_result.tsv
[2024-01-24 10:59:25,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:59:25,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:59:25,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ccc5728-0d94-4970-8640-702111a2bb9b/dqc_reference/checkm_data
[2024-01-24 10:59:25,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:59:25,280] [INFO] Task started: CheckM
[2024-01-24 10:59:25,280] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650455.1_ASM1465045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650455.1_ASM1465045v1_genomic.fna/checkm_input GCF_014650455.1_ASM1465045v1_genomic.fna/checkm_result
[2024-01-24 11:00:55,390] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:55,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:00:55,420] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:55,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:55,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650455.1_ASM1465045v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:55,421] [INFO] Task started: Blastn
[2024-01-24 11:00:55,421] [INFO] Running command: blastn -query GCF_014650455.1_ASM1465045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ccc5728-0d94-4970-8640-702111a2bb9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650455.1_ASM1465045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:57,875] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:57,880] [INFO] Selected 12 target genomes.
[2024-01-24 11:00:57,880] [INFO] Target genome list was writen to GCF_014650455.1_ASM1465045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:57,891] [INFO] Task started: fastANI
[2024-01-24 11:00:57,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a171119-9140-415d-8831-6b5fc55218b7/GCF_014650455.1_ASM1465045v1_genomic.fna.gz --refList GCF_014650455.1_ASM1465045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650455.1_ASM1465045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:01:24,331] [INFO] Task succeeded: fastANI
[2024-01-24 11:01:24,342] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:01:24,342] [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_014650455.1	s__Streptomyces xanthochromogenes	100.0	2895	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	97.90	0.92	0.90	3	conclusive
GCF_002803085.1	s__Streptomyces sp002803085	93.1434	2349	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279695.1	s__Streptomyces sp001279695	90.0839	2008	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649955.1	s__Streptomyces violascens	90.0712	1995	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627815.1	s__Streptomyces hundungensis	89.5878	2021	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324565.1	s__Streptomyces sp003324565	89.5479	2056	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008345.1	s__Streptomyces showdoensis	82.8076	1464	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	82.3882	1331	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103455.1	s__Streptomyces wuyuanensis	82.0402	1405	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	81.5694	1494	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418335.1	s__Streptomyces aurantiacus	81.4589	1252	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_014203845.1	s__Streptomyces scabiei_E	81.3799	1338	2899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:01:24,344] [INFO] GTDB search result was written to GCF_014650455.1_ASM1465045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:01:24,345] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:01:24,349] [INFO] DFAST_QC result json was written to GCF_014650455.1_ASM1465045v1_genomic.fna/dqc_result.json
[2024-01-24 11:01:24,349] [INFO] DFAST_QC completed!
[2024-01-24 11:01:24,350] [INFO] Total running time: 0h3m18s