[2024-01-24 13:09:49,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg39ac7125-3e7c-458d-9e18-78326d95d299/dqc_reference
[2024-01-24 13:09:50,846] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,847] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,847] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b6a22f4-65df-4282-be0f-645788df6351/GCF_009377175.1_ASM937717v1_genomic.fna.gz | prodigal -d GCF_009377175.1_ASM937717v1_genomic.fna/cds.fna -a GCF_009377175.1_ASM937717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:16,965] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:16,965] [INFO] Task started: HMMsearch
[2024-01-24 13:10:16,966] [INFO] Running command: hmmsearch --tblout GCF_009377175.1_ASM937717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39ac7125-3e7c-458d-9e18-78326d95d299/dqc_reference/reference_markers.hmm GCF_009377175.1_ASM937717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:17,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:17,346] [INFO] Found 6/6 markers.
[2024-01-24 13:10:17,429] [INFO] Query marker FASTA was written to GCF_009377175.1_ASM937717v1_genomic.fna/markers.fasta
[2024-01-24 13:10:17,429] [INFO] Task started: Blastn
[2024-01-24 13:10:17,429] [INFO] Running command: blastn -query GCF_009377175.1_ASM937717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39ac7125-3e7c-458d-9e18-78326d95d299/dqc_reference/reference_markers.fasta -out GCF_009377175.1_ASM937717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:18,736] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:18,739] [INFO] Selected 30 target genomes.
[2024-01-24 13:10:18,739] [INFO] Target genome list was writen to GCF_009377175.1_ASM937717v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:18,842] [INFO] Task started: fastANI
[2024-01-24 13:10:18,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6a22f4-65df-4282-be0f-645788df6351/GCF_009377175.1_ASM937717v1_genomic.fna.gz --refList GCF_009377175.1_ASM937717v1_genomic.fna/target_genomes.txt --output GCF_009377175.1_ASM937717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:11:21,973] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:21,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39ac7125-3e7c-458d-9e18-78326d95d299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:11:21,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39ac7125-3e7c-458d-9e18-78326d95d299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:11:22,006] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:11:22,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:11:22,007] [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 adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	100.0	3102	3117	95	conclusive
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	85.4982	1903	3117	95	below_threshold
Streptomyces mangrovisoli	strain=MUSC 149	GCA_000974985.2	1428628	1428628	type	True	85.1853	1824	3117	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	85.0672	1796	3117	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	85.0209	1817	3117	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	85.0071	1559	3117	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.9857	1734	3117	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.9643	1692	3117	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	84.9307	1739	3117	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.9233	1655	3117	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	84.8447	1754	3117	95	below_threshold
Streptomyces tuirus	strain=JCM 4255	GCA_014701095.1	68278	68278	type	True	84.8366	1596	3117	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.7968	1542	3117	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.7876	1825	3117	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	84.7424	1674	3117	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	84.6477	1371	3117	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	84.5761	1554	3117	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	84.5696	1616	3117	95	below_threshold
Streptomyces musisoli	strain=CH5-8	GCA_016741855.1	2802280	2802280	type	True	84.5674	1734	3117	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	84.5659	1766	3117	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	84.5595	1747	3117	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	84.556	1728	3117	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	84.5384	1556	3117	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.514	1702	3117	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.5085	1739	3117	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	84.4978	1690	3117	95	below_threshold
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	84.413	1862	3117	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.2476	1820	3117	95	below_threshold
Streptomyces alanosinicus	strain=JCM 4714	GCA_014650595.1	68171	68171	type	True	84.0807	1731	3117	95	below_threshold
Streptomyces roseirectus	strain=CRXT-G-22	GCA_014489635.1	2768066	2768066	type	True	82.8776	1574	3117	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:11:22,008] [INFO] DFAST Taxonomy check result was written to GCF_009377175.1_ASM937717v1_genomic.fna/tc_result.tsv
[2024-01-24 13:11:22,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:11:22,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:11:22,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39ac7125-3e7c-458d-9e18-78326d95d299/dqc_reference/checkm_data
[2024-01-24 13:11:22,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:11:22,105] [INFO] Task started: CheckM
[2024-01-24 13:11:22,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009377175.1_ASM937717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009377175.1_ASM937717v1_genomic.fna/checkm_input GCF_009377175.1_ASM937717v1_genomic.fna/checkm_result
[2024-01-24 13:12:55,437] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:55,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:12:55,467] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:55,468] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:55,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009377175.1_ASM937717v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:55,468] [INFO] Task started: Blastn
[2024-01-24 13:12:55,469] [INFO] Running command: blastn -query GCF_009377175.1_ASM937717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39ac7125-3e7c-458d-9e18-78326d95d299/dqc_reference/reference_markers_gtdb.fasta -out GCF_009377175.1_ASM937717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:57,510] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:57,515] [INFO] Selected 25 target genomes.
[2024-01-24 13:12:57,515] [INFO] Target genome list was writen to GCF_009377175.1_ASM937717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:00,787] [INFO] Task started: fastANI
[2024-01-24 13:13:00,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6a22f4-65df-4282-be0f-645788df6351/GCF_009377175.1_ASM937717v1_genomic.fna.gz --refList GCF_009377175.1_ASM937717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009377175.1_ASM937717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:59,303] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:59,325] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:59,326] [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_009377175.1	s__Streptomyces adustus	100.0	3102	3117	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_014648915.1	s__Streptomyces phaeofaciens	85.532	1897	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.2421	1792	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019855.1	s__Streptomyces antibioticus_B	85.2397	1742	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
GCF_000974985.2	s__Streptomyces mangrovisoli	85.1768	1826	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	85.093	1625	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384795.1	s__Streptomyces sp003384795	85.0754	1751	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016860545.1	s__Streptomyces asoensis	85.0539	1811	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.07	98.15	0.93	0.87	3	-
GCF_000718165.1	s__Streptomyces fulvoviolaceus	85.0402	1790	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001896135.2	s__Streptomyces phaeoluteigriseus	84.9926	1743	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514305.1	s__Streptomyces dysideae	84.9425	1695	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004028635.1	s__Streptomyces cyaneus	84.9341	1737	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105245.1	s__Streptomyces sp900105245	84.7805	1734	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.80	95.98	0.93	0.89	5	-
GCF_001514215.1	s__Streptomyces bungoensis	84.7318	1675	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280015.1	s__Streptomyces sp001280015	84.624	1686	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973465.1	s__Streptomyces sp008973465	84.5887	1623	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509795.1	s__Streptomyces sp001509795	84.5779	1598	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_016741855.1	s__Streptomyces musisoli	84.5646	1734	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009765.2	s__Streptomyces avermitilis	84.5267	1736	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.91	0.98	0.92	9	-
GCF_003634225.1	s__Streptomyces sp003634225	84.4698	1796	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.82	0.97	0.97	3	-
GCF_001866665.1	s__Streptomyces monashensis	84.4506	1699	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_009604455.1	s__Streptomyces sp009604455	84.4064	1803	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376565.1	s__Streptomyces hokutonensis	84.403	1864	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.37	96.37	0.82	0.82	2	-
GCF_014650595.1	s__Streptomyces alanosinicus	84.0938	1729	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373625.1	s__Streptomyces sp000373625	83.9781	1482	3117	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:59,328] [INFO] GTDB search result was written to GCF_009377175.1_ASM937717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:59,328] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:59,335] [INFO] DFAST_QC result json was written to GCF_009377175.1_ASM937717v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:59,335] [INFO] DFAST_QC completed!
[2024-01-24 13:13:59,335] [INFO] Total running time: 0h4m10s