[2024-01-24 12:54:05,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg68824b2e-1631-4216-8f51-120fc52bfa0b/dqc_reference
[2024-01-24 12:54:07,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,723] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ed84a7f-3e4f-4071-b51f-de3711eab365/GCF_022698145.1_ASM2269814v1_genomic.fna.gz | prodigal -d GCF_022698145.1_ASM2269814v1_genomic.fna/cds.fna -a GCF_022698145.1_ASM2269814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:35,768] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:35,769] [INFO] Task started: HMMsearch
[2024-01-24 12:54:35,769] [INFO] Running command: hmmsearch --tblout GCF_022698145.1_ASM2269814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68824b2e-1631-4216-8f51-120fc52bfa0b/dqc_reference/reference_markers.hmm GCF_022698145.1_ASM2269814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:36,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:36,299] [INFO] Found 6/6 markers.
[2024-01-24 12:54:36,378] [INFO] Query marker FASTA was written to GCF_022698145.1_ASM2269814v1_genomic.fna/markers.fasta
[2024-01-24 12:54:36,379] [INFO] Task started: Blastn
[2024-01-24 12:54:36,379] [INFO] Running command: blastn -query GCF_022698145.1_ASM2269814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68824b2e-1631-4216-8f51-120fc52bfa0b/dqc_reference/reference_markers.fasta -out GCF_022698145.1_ASM2269814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:37,702] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:37,706] [INFO] Selected 27 target genomes.
[2024-01-24 12:54:37,707] [INFO] Target genome list was writen to GCF_022698145.1_ASM2269814v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:37,731] [INFO] Task started: fastANI
[2024-01-24 12:54:37,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ed84a7f-3e4f-4071-b51f-de3711eab365/GCF_022698145.1_ASM2269814v1_genomic.fna.gz --refList GCF_022698145.1_ASM2269814v1_genomic.fna/target_genomes.txt --output GCF_022698145.1_ASM2269814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:36,648] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:36,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68824b2e-1631-4216-8f51-120fc52bfa0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:36,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68824b2e-1631-4216-8f51-120fc52bfa0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:36,675] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:55:36,675] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:55:36,675] [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 plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	94.0536	2465	3102	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	87.2017	1990	3102	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.9622	2079	3102	95	below_threshold
Streptomyces antibioticus	strain=DSM 40234	GCA_001514065.1	1890	1890	suspected-type	True	85.8962	2019	3102	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	85.7946	1999	3102	95	below_threshold
Streptomyces griseorubiginosus	strain=DSM 40469	GCA_001514195.1	67304	67304	type	True	85.5087	1964	3102	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.3689	1726	3102	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	85.2202	1833	3102	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.1384	1849	3102	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.1137	1783	3102	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.0808	1739	3102	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	85.0686	1843	3102	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	85.0574	1707	3102	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	85.0137	1953	3102	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	84.98	1425	3102	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	84.9232	1359	3102	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	84.9119	1735	3102	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	84.8949	1870	3102	95	below_threshold
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	84.8798	2012	3102	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	84.8656	1733	3102	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	84.8594	1539	3102	95	below_threshold
Streptomyces humi	strain=MUSC 119	GCA_001005085.2	1428620	1428620	type	True	84.7937	1977	3102	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.7104	1860	3102	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	84.6244	1675	3102	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	84.5806	1850	3102	95	below_threshold
Streptomyces hirsutus	strain=NRRL B-2713	GCA_001418415.1	35620	35620	type	True	84.015	1395	3102	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	83.8169	1449	3102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:36,677] [INFO] DFAST Taxonomy check result was written to GCF_022698145.1_ASM2269814v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:36,678] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:36,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:36,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68824b2e-1631-4216-8f51-120fc52bfa0b/dqc_reference/checkm_data
[2024-01-24 12:55:36,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:36,761] [INFO] Task started: CheckM
[2024-01-24 12:55:36,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022698145.1_ASM2269814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022698145.1_ASM2269814v1_genomic.fna/checkm_input GCF_022698145.1_ASM2269814v1_genomic.fna/checkm_result
[2024-01-24 12:57:52,569] [INFO] Task succeeded: CheckM
[2024-01-24 12:57:52,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 12:57:52,600] [INFO] ===== Completeness check finished =====
[2024-01-24 12:57:52,601] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:57:52,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022698145.1_ASM2269814v1_genomic.fna/markers.fasta)
[2024-01-24 12:57:52,601] [INFO] Task started: Blastn
[2024-01-24 12:57:52,602] [INFO] Running command: blastn -query GCF_022698145.1_ASM2269814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68824b2e-1631-4216-8f51-120fc52bfa0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_022698145.1_ASM2269814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:57:54,678] [INFO] Task succeeded: Blastn
[2024-01-24 12:57:54,683] [INFO] Selected 16 target genomes.
[2024-01-24 12:57:54,683] [INFO] Target genome list was writen to GCF_022698145.1_ASM2269814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:57:54,709] [INFO] Task started: fastANI
[2024-01-24 12:57:54,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ed84a7f-3e4f-4071-b51f-de3711eab365/GCF_022698145.1_ASM2269814v1_genomic.fna.gz --refList GCF_022698145.1_ASM2269814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022698145.1_ASM2269814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:58:31,578] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:31,603] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:58:31,604] [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_000411315.1	s__Streptomyces sp000411315	98.6949	2865	3102	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_004104505.1	s__Streptomyces sp003046555	94.0802	2558	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.74	99.48	0.99	0.97	3	-
GCF_000720765.1	s__Streptomyces sp000720765	88.1491	2188	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.07	96.07	0.83	0.83	2	-
GCF_002754715.1	s__Streptomyces sp002754715	88.0001	2136	3102	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	87.9851	2065	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343515.1	s__Streptomyces sp004343515	87.1423	2126	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.56	96.56	0.86	0.86	2	-
GCF_001484565.1	s__Streptomyces sp001484565	87.0431	2121	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282115.1	s__Streptomyces sp001282115	85.815	1778	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	0.95	0.95	2	-
GCF_018128905.1	s__Streptomyces sp003814525	85.7945	2045	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	99.42	0.94	0.94	2	-
GCF_001514195.1	s__Streptomyces griseorubiginosus	85.5278	1960	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.34	95.64	0.90	0.86	7	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	85.3641	1888	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014534645.1	s__Streptomyces sp014534645	85.1506	1777	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	85.0338	1747	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217755.1	s__Streptomyces hyaluromycini	84.8842	2011	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.22	96.22	0.84	0.84	2	-
GCF_004342105.1	s__Streptomyces sp004342105	84.8046	1861	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418415.1	s__Streptomyces hirsutus	83.9937	1399	3102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.60	97.60	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:58:31,606] [INFO] GTDB search result was written to GCF_022698145.1_ASM2269814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:58:31,607] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:58:31,614] [INFO] DFAST_QC result json was written to GCF_022698145.1_ASM2269814v1_genomic.fna/dqc_result.json
[2024-01-24 12:58:31,614] [INFO] DFAST_QC completed!
[2024-01-24 12:58:31,614] [INFO] Total running time: 0h4m26s