[2024-01-24 13:18:41,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg5cc62e9f-961d-4770-b16d-3ffa09812a00/dqc_reference
[2024-01-24 13:18:42,291] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,292] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,292] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d8f2d5f-2038-45a5-a333-2c41279b5858/GCF_014653855.1_ASM1465385v1_genomic.fna.gz | prodigal -d GCF_014653855.1_ASM1465385v1_genomic.fna/cds.fna -a GCF_014653855.1_ASM1465385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:14,351] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:14,351] [INFO] Task started: HMMsearch
[2024-01-24 13:19:14,352] [INFO] Running command: hmmsearch --tblout GCF_014653855.1_ASM1465385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5cc62e9f-961d-4770-b16d-3ffa09812a00/dqc_reference/reference_markers.hmm GCF_014653855.1_ASM1465385v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:14,746] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:14,748] [INFO] Found 6/6 markers.
[2024-01-24 13:19:14,833] [INFO] Query marker FASTA was written to GCF_014653855.1_ASM1465385v1_genomic.fna/markers.fasta
[2024-01-24 13:19:14,833] [INFO] Task started: Blastn
[2024-01-24 13:19:14,833] [INFO] Running command: blastn -query GCF_014653855.1_ASM1465385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc62e9f-961d-4770-b16d-3ffa09812a00/dqc_reference/reference_markers.fasta -out GCF_014653855.1_ASM1465385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:16,108] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:16,113] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:16,114] [INFO] Target genome list was writen to GCF_014653855.1_ASM1465385v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:16,199] [INFO] Task started: fastANI
[2024-01-24 13:19:16,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d8f2d5f-2038-45a5-a333-2c41279b5858/GCF_014653855.1_ASM1465385v1_genomic.fna.gz --refList GCF_014653855.1_ASM1465385v1_genomic.fna/target_genomes.txt --output GCF_014653855.1_ASM1465385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:56,726] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:56,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5cc62e9f-961d-4770-b16d-3ffa09812a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:56,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5cc62e9f-961d-4770-b16d-3ffa09812a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:56,748] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:56,748] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:56,748] [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 capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	100.0	3502	3511	95	conclusive
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	99.9528	3496	3511	95	conclusive
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	93.2954	2347	3511	95	below_threshold
Streptomyces adelaidensis	strain=CAP261	GCA_016598475.1	2796465	2796465	type	True	88.5617	2102	3511	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	87.9576	2236	3511	95	below_threshold
Streptomyces neyagawaensis	strain=NRRL B-3092	GCA_001418645.1	42238	42238	type	True	87.8556	1659	3511	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	87.818	2205	3511	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	87.7191	1861	3511	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	87.7166	2256	3511	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	87.5472	2251	3511	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	87.5452	2101	3511	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	87.5395	2104	3511	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	84.1746	1924	3511	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	83.8985	1541	3511	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	83.0323	1637	3511	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	76.1477	294	3511	95	below_threshold
Demequina salsinemoris	strain=NBRC 105323	GCA_000974805.1	577470	577470	type	True	76.0981	241	3511	95	below_threshold
Glycomyces paridis	strain=CPCC 204357	GCA_004912155.1	2126555	2126555	type	True	75.8769	473	3511	95	below_threshold
Parenemella sanctibonifatiensis	strain=NML 150081	GCA_002250565.1	2016505	2016505	type	True	75.8252	187	3511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:56,750] [INFO] DFAST Taxonomy check result was written to GCF_014653855.1_ASM1465385v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:56,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:56,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:56,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5cc62e9f-961d-4770-b16d-3ffa09812a00/dqc_reference/checkm_data
[2024-01-24 13:19:56,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:56,855] [INFO] Task started: CheckM
[2024-01-24 13:19:56,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653855.1_ASM1465385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653855.1_ASM1465385v1_genomic.fna/checkm_input GCF_014653855.1_ASM1465385v1_genomic.fna/checkm_result
[2024-01-24 13:21:45,541] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:45,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:21:45,571] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:45,572] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:45,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653855.1_ASM1465385v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:45,573] [INFO] Task started: Blastn
[2024-01-24 13:21:45,573] [INFO] Running command: blastn -query GCF_014653855.1_ASM1465385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5cc62e9f-961d-4770-b16d-3ffa09812a00/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653855.1_ASM1465385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:47,638] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:47,641] [INFO] Selected 21 target genomes.
[2024-01-24 13:21:47,641] [INFO] Target genome list was writen to GCF_014653855.1_ASM1465385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:47,735] [INFO] Task started: fastANI
[2024-01-24 13:21:47,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d8f2d5f-2038-45a5-a333-2c41279b5858/GCF_014653855.1_ASM1465385v1_genomic.fna.gz --refList GCF_014653855.1_ASM1465385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653855.1_ASM1465385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:34,998] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:35,020] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:35,021] [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_002214185.1	s__Streptomyces capitiformicae	99.9528	3496	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.95	1.00	1.00	2	conclusive
GCF_008386495.1	s__Streptomyces tailanensis	93.2954	2347	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317595.1	s__Streptomyces ipomoeae	88.8488	2066	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_016598475.1	s__Streptomyces adelaidensis	88.5295	2108	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550375.1	s__Streptomyces europaeiscabiei	88.0934	1996	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.72	96.30	0.83	0.82	3	-
GCF_001418645.1	s__Streptomyces neyagawaensis	87.8643	1657	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCF_014203845.1	s__Streptomyces scabiei_E	87.8443	2275	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_014873495.1	s__Streptomyces stelliscabiei	87.8114	2206	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.87	99.68	0.98	0.96	4	-
GCF_001419765.1	s__Streptomyces torulosus	87.7779	1851	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
GCF_900290235.1	s__Streptomyces sp900290235	87.7244	2225	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	96.28	96.28	0.86	0.86	2	-
GCF_000383595.1	s__Streptomyces bottropensis	87.525	2105	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_009857135.1	s__Streptomyces sp009857135	87.4098	1905	3511	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	84.3353	1953	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	84.1304	1884	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746365.1	s__Streptomyces sp001746365	83.3385	1711	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920535.1	s__Streptomyces sp002920535	83.2647	1609	3511	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	83.2011	1669	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514035.1	s__Streptomyces yokosukanensis	82.9498	1671	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832925.1	s__Streptomyces sp009832925	80.9123	1321	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	76.5024	479	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912155.1	s__Glycomyces paridis	75.8928	467	3511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:35,022] [INFO] GTDB search result was written to GCF_014653855.1_ASM1465385v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:35,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:35,027] [INFO] DFAST_QC result json was written to GCF_014653855.1_ASM1465385v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:35,027] [INFO] DFAST_QC completed!
[2024-01-24 13:22:35,027] [INFO] Total running time: 0h3m54s