[2024-01-24 13:28:13,238] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg836a87ee-54be-4bc1-a25d-41ae76bc0470/dqc_reference
[2024-01-24 13:28:14,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,595] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d0edd55-9fee-4483-8820-d2e0d15f31af/GCF_014649955.1_ASM1464995v1_genomic.fna.gz | prodigal -d GCF_014649955.1_ASM1464995v1_genomic.fna/cds.fna -a GCF_014649955.1_ASM1464995v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,965] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,966] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,966] [INFO] Running command: hmmsearch --tblout GCF_014649955.1_ASM1464995v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg836a87ee-54be-4bc1-a25d-41ae76bc0470/dqc_reference/reference_markers.hmm GCF_014649955.1_ASM1464995v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:42,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:42,407] [INFO] Found 6/6 markers.
[2024-01-24 13:28:42,486] [INFO] Query marker FASTA was written to GCF_014649955.1_ASM1464995v1_genomic.fna/markers.fasta
[2024-01-24 13:28:42,486] [INFO] Task started: Blastn
[2024-01-24 13:28:42,487] [INFO] Running command: blastn -query GCF_014649955.1_ASM1464995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg836a87ee-54be-4bc1-a25d-41ae76bc0470/dqc_reference/reference_markers.fasta -out GCF_014649955.1_ASM1464995v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:43,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:43,940] [INFO] Selected 21 target genomes.
[2024-01-24 13:28:43,941] [INFO] Target genome list was writen to GCF_014649955.1_ASM1464995v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:43,955] [INFO] Task started: fastANI
[2024-01-24 13:28:43,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d0edd55-9fee-4483-8820-d2e0d15f31af/GCF_014649955.1_ASM1464995v1_genomic.fna.gz --refList GCF_014649955.1_ASM1464995v1_genomic.fna/target_genomes.txt --output GCF_014649955.1_ASM1464995v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:28,415] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:28,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg836a87ee-54be-4bc1-a25d-41ae76bc0470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:28,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg836a87ee-54be-4bc1-a25d-41ae76bc0470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:28,439] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:28,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:28,439] [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 violascens	strain=JCM 4424	GCA_014649955.1	67381	67381	type	True	100.0	2987	2995	95	conclusive
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	99.8697	2622	2995	95	conclusive
Streptomyces xanthochromogenes	strain=JCM 4612	GCA_014650455.1	67384	67384	type	True	90.0287	2004	2995	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	85.2194	1732	2995	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	82.9992	1417	2995	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	82.9329	1423	2995	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	82.7869	1438	2995	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.7659	1429	2995	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.7546	1476	2995	95	below_threshold
Streptomyces anulatus	strain=JCM 4721	GCA_014650675.1	1892	1892	type	True	82.4653	1420	2995	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	82.0647	1231	2995	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	82.0427	1432	2995	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	82.0096	1453	2995	95	below_threshold
Streptomyces marianii	strain=ICN19	GCA_005795905.1	1817406	1817406	type	True	81.9721	1323	2995	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	81.9559	1504	2995	95	below_threshold
Streptomyces lushanensis	strain=NRRL B-24994	GCA_001700515.1	1434255	1434255	type	True	81.7871	1082	2995	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.5935	1422	2995	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	81.3419	1433	2995	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.1846	1302	2995	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	79.61	1165	2995	95	below_threshold
Kibdelosporangium phytohabitans	strain=KLBMP1111	GCA_001302585.1	860235	860235	type	True	76.1053	512	2995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:28,441] [INFO] DFAST Taxonomy check result was written to GCF_014649955.1_ASM1464995v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:28,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:28,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:28,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg836a87ee-54be-4bc1-a25d-41ae76bc0470/dqc_reference/checkm_data
[2024-01-24 13:29:28,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:28,532] [INFO] Task started: CheckM
[2024-01-24 13:29:28,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649955.1_ASM1464995v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649955.1_ASM1464995v1_genomic.fna/checkm_input GCF_014649955.1_ASM1464995v1_genomic.fna/checkm_result
[2024-01-24 13:30:50,026] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:50,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:50,048] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:50,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:50,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649955.1_ASM1464995v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:50,049] [INFO] Task started: Blastn
[2024-01-24 13:30:50,049] [INFO] Running command: blastn -query GCF_014649955.1_ASM1464995v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg836a87ee-54be-4bc1-a25d-41ae76bc0470/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649955.1_ASM1464995v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:52,122] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:52,126] [INFO] Selected 15 target genomes.
[2024-01-24 13:30:52,126] [INFO] Target genome list was writen to GCF_014649955.1_ASM1464995v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:52,145] [INFO] Task started: fastANI
[2024-01-24 13:30:52,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d0edd55-9fee-4483-8820-d2e0d15f31af/GCF_014649955.1_ASM1464995v1_genomic.fna.gz --refList GCF_014649955.1_ASM1464995v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649955.1_ASM1464995v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:21,559] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:21,576] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:21,576] [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_014649955.1	s__Streptomyces violascens	100.0	2987	2995	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_001279695.1	s__Streptomyces sp001279695	93.7109	2278	2995	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	90.8569	2137	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650455.1	s__Streptomyces xanthochromogenes	90.043	2002	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	97.90	0.92	0.90	3	-
GCF_002803085.1	s__Streptomyces sp002803085	89.8254	1975	2995	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	89.5914	1951	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	85.2178	1732	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_001653515.1	s__Streptomyces sp001653515	85.0168	1454	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005795905.1	s__Streptomyces marianii	81.9835	1321	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002155895.1	s__Streptomyces rochei	81.9225	1196	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.25	0.91	0.79	28	-
GCF_001700515.1	s__Streptomyces lushanensis	81.7959	1080	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013046785.1	s__Streptomyces sp013046785	81.6105	1402	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716535.1	s__Streptomyces flaveolus_A	81.6052	1450	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.84	0.94	0.91	9	-
GCF_013155375.1	s__Nocardioides sp013155375	76.6476	408	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001302585.1	s__Kibdelosporangium phytohabitans	76.099	516	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:21,578] [INFO] GTDB search result was written to GCF_014649955.1_ASM1464995v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:21,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:21,582] [INFO] DFAST_QC result json was written to GCF_014649955.1_ASM1464995v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:21,582] [INFO] DFAST_QC completed!
[2024-01-24 13:31:21,582] [INFO] Total running time: 0h3m8s