[2024-01-24 13:55:18,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:18,948] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:18,948] [INFO] DQC Reference Directory: /var/lib/cwl/stgd84d3ccd-5234-4549-9542-59f05f2d7979/dqc_reference
[2024-01-24 13:55:20,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:20,339] [INFO] Task started: Prodigal
[2024-01-24 13:55:20,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg61b5ddb8-e346-4f49-85e8-bafe6f333b1f/GCF_000225525.1_ASM22552v1_genomic.fna.gz | prodigal -d GCF_000225525.1_ASM22552v1_genomic.fna/cds.fna -a GCF_000225525.1_ASM22552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:41,802] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:41,803] [INFO] Task started: HMMsearch
[2024-01-24 13:55:41,803] [INFO] Running command: hmmsearch --tblout GCF_000225525.1_ASM22552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd84d3ccd-5234-4549-9542-59f05f2d7979/dqc_reference/reference_markers.hmm GCF_000225525.1_ASM22552v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:42,283] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:42,285] [INFO] Found 6/6 markers.
[2024-01-24 13:55:42,348] [INFO] Query marker FASTA was written to GCF_000225525.1_ASM22552v1_genomic.fna/markers.fasta
[2024-01-24 13:55:42,349] [INFO] Task started: Blastn
[2024-01-24 13:55:42,349] [INFO] Running command: blastn -query GCF_000225525.1_ASM22552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd84d3ccd-5234-4549-9542-59f05f2d7979/dqc_reference/reference_markers.fasta -out GCF_000225525.1_ASM22552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:43,707] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:43,719] [INFO] Selected 20 target genomes.
[2024-01-24 13:55:43,720] [INFO] Target genome list was writen to GCF_000225525.1_ASM22552v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:43,737] [INFO] Task started: fastANI
[2024-01-24 13:55:43,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg61b5ddb8-e346-4f49-85e8-bafe6f333b1f/GCF_000225525.1_ASM22552v1_genomic.fna.gz --refList GCF_000225525.1_ASM22552v1_genomic.fna/target_genomes.txt --output GCF_000225525.1_ASM22552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:26,460] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:26,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd84d3ccd-5234-4549-9542-59f05f2d7979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:26,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd84d3ccd-5234-4549-9542-59f05f2d7979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:26,481] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:26,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:26,481] [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 zinciresistens	strain=K42	GCA_000225525.2	1073330	1073330	type	True	100.0	2468	2493	95	conclusive
Streptomyces chartreusis	strain=ATCC 14922	GCA_008704715.1	1969	1969	suspected-type	True	87.476	1756	2493	95	below_threshold
Streptomyces chartreusis	strain=JCM 4570	GCA_014650315.1	1969	1969	suspected-type	True	87.4478	1759	2493	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	87.3099	1661	2493	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	87.2349	1591	2493	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	87.1866	1677	2493	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	87.0434	1686	2493	95	below_threshold
Streptomyces cyaneus	strain=CGMCC 4.1671	GCA_004028635.1	1904	1904	type	True	86.9969	1638	2493	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	86.9387	1703	2493	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	86.8511	1702	2493	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	85.2277	1533	2493	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	85.1783	1571	2493	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.1477	1505	2493	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.0542	1588	2493	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.0007	1510	2493	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.9341	1483	2493	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	84.7454	1492	2493	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	84.2863	1504	2493	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.2821	1502	2493	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	83.4809	1303	2493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:26,483] [INFO] DFAST Taxonomy check result was written to GCF_000225525.1_ASM22552v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:26,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:26,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:26,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd84d3ccd-5234-4549-9542-59f05f2d7979/dqc_reference/checkm_data
[2024-01-24 13:56:26,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:26,561] [INFO] Task started: CheckM
[2024-01-24 13:56:26,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000225525.1_ASM22552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000225525.1_ASM22552v1_genomic.fna/checkm_input GCF_000225525.1_ASM22552v1_genomic.fna/checkm_result
[2024-01-24 13:57:43,986] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:43,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.51%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:44,007] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:44,008] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:44,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000225525.1_ASM22552v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:44,008] [INFO] Task started: Blastn
[2024-01-24 13:57:44,008] [INFO] Running command: blastn -query GCF_000225525.1_ASM22552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd84d3ccd-5234-4549-9542-59f05f2d7979/dqc_reference/reference_markers_gtdb.fasta -out GCF_000225525.1_ASM22552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:46,194] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:46,197] [INFO] Selected 20 target genomes.
[2024-01-24 13:57:46,198] [INFO] Target genome list was writen to GCF_000225525.1_ASM22552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:46,214] [INFO] Task started: fastANI
[2024-01-24 13:57:46,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg61b5ddb8-e346-4f49-85e8-bafe6f333b1f/GCF_000225525.1_ASM22552v1_genomic.fna.gz --refList GCF_000225525.1_ASM22552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000225525.1_ASM22552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:29,231] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:29,247] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:29,247] [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_000225525.1	s__Streptomyces zinciresistens	100.0	2468	2493	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_008704715.1	s__Streptomyces chartreusis	87.4628	1756	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.83	96.55	0.93	0.86	10	-
GCF_001509795.1	s__Streptomyces sp001509795	87.461	1621	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_003074055.1	s__Streptomyces nigra	87.3275	1658	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.21	97.15	0.92	0.91	4	-
GCF_001513975.1	s__Streptomyces curacoi	87.2114	1596	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_015160855.1	s__Streptomyces ferrugineus	87.204	1676	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042075.1	s__Streptomyces sp008042075	87.2031	1697	2493	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	87.1513	1661	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	87.0372	1687	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514235.1	s__Streptomyces caeruleatus	86.957	1700	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049285.1	s__Streptomyces sp019049285	86.8931	1611	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655715.1	s__Streptomyces lanatus	86.879	1698	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	86.8398	1693	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509475.1	s__Streptomyces regalis	86.7498	1651	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014257025.1	s__Streptomyces sp014257025	85.2652	1531	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349325.1	s__Streptomyces davaonensis	85.1738	1572	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411315.1	s__Streptomyces sp000411315	85.1011	1553	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	84.8753	1503	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342105.1	s__Streptomyces sp004342105	84.0978	1504	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418475.1	s__Streptomyces ossamyceticus	83.4555	1306	2493	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6547	98.97	98.97	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:29,249] [INFO] GTDB search result was written to GCF_000225525.1_ASM22552v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:29,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:29,253] [INFO] DFAST_QC result json was written to GCF_000225525.1_ASM22552v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:29,254] [INFO] DFAST_QC completed!
[2024-01-24 13:58:29,254] [INFO] Total running time: 0h3m10s