[2024-01-24 14:02:50,318] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:50,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:50,321] [INFO] DQC Reference Directory: /var/lib/cwl/stge35ddfef-9b1d-4fa1-b732-8a5b1f64b301/dqc_reference
[2024-01-24 14:02:51,570] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:51,572] [INFO] Task started: Prodigal
[2024-01-24 14:02:51,572] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c971a44-dd69-44e2-ba99-9a70a68f15eb/GCF_014534645.1_ASM1453464v1_genomic.fna.gz | prodigal -d GCF_014534645.1_ASM1453464v1_genomic.fna/cds.fna -a GCF_014534645.1_ASM1453464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:18,802] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:18,802] [INFO] Task started: HMMsearch
[2024-01-24 14:03:18,803] [INFO] Running command: hmmsearch --tblout GCF_014534645.1_ASM1453464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge35ddfef-9b1d-4fa1-b732-8a5b1f64b301/dqc_reference/reference_markers.hmm GCF_014534645.1_ASM1453464v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:19,154] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:19,156] [INFO] Found 6/6 markers.
[2024-01-24 14:03:19,232] [INFO] Query marker FASTA was written to GCF_014534645.1_ASM1453464v1_genomic.fna/markers.fasta
[2024-01-24 14:03:19,232] [INFO] Task started: Blastn
[2024-01-24 14:03:19,233] [INFO] Running command: blastn -query GCF_014534645.1_ASM1453464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge35ddfef-9b1d-4fa1-b732-8a5b1f64b301/dqc_reference/reference_markers.fasta -out GCF_014534645.1_ASM1453464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:20,669] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:20,673] [INFO] Selected 17 target genomes.
[2024-01-24 14:03:20,674] [INFO] Target genome list was writen to GCF_014534645.1_ASM1453464v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:20,696] [INFO] Task started: fastANI
[2024-01-24 14:03:20,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c971a44-dd69-44e2-ba99-9a70a68f15eb/GCF_014534645.1_ASM1453464v1_genomic.fna.gz --refList GCF_014534645.1_ASM1453464v1_genomic.fna/target_genomes.txt --output GCF_014534645.1_ASM1453464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:58,004] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:58,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge35ddfef-9b1d-4fa1-b732-8a5b1f64b301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:58,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge35ddfef-9b1d-4fa1-b732-8a5b1f64b301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:58,018] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:58,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:58,018] [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 griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	100.0	2853	2866	95	conclusive
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	92.1058	2187	2866	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	88.9183	1929	2866	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	88.9068	1963	2866	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	88.3252	1895	2866	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	88.0423	1885	2866	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	87.1598	1786	2866	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	87.1091	1598	2866	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	86.8423	1859	2866	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	86.6883	1860	2866	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	86.5818	1886	2866	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	86.5119	1818	2866	95	below_threshold
Streptomyces purpurascens	strain=JCM 4509	GCA_014650155.1	1924	1924	type	True	86.1666	1786	2866	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	86.1096	1800	2866	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.8446	1476	2866	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	85.5818	1593	2866	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.2257	1617	2866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:58,020] [INFO] DFAST Taxonomy check result was written to GCF_014534645.1_ASM1453464v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:58,021] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:58,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:58,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge35ddfef-9b1d-4fa1-b732-8a5b1f64b301/dqc_reference/checkm_data
[2024-01-24 14:03:58,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:58,105] [INFO] Task started: CheckM
[2024-01-24 14:03:58,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014534645.1_ASM1453464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014534645.1_ASM1453464v1_genomic.fna/checkm_input GCF_014534645.1_ASM1453464v1_genomic.fna/checkm_result
[2024-01-24 14:06:09,050] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:09,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:09,074] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:09,075] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:09,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014534645.1_ASM1453464v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:09,075] [INFO] Task started: Blastn
[2024-01-24 14:06:09,075] [INFO] Running command: blastn -query GCF_014534645.1_ASM1453464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge35ddfef-9b1d-4fa1-b732-8a5b1f64b301/dqc_reference/reference_markers_gtdb.fasta -out GCF_014534645.1_ASM1453464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:11,395] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:11,398] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:11,398] [INFO] Target genome list was writen to GCF_014534645.1_ASM1453464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:11,440] [INFO] Task started: fastANI
[2024-01-24 14:06:11,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c971a44-dd69-44e2-ba99-9a70a68f15eb/GCF_014534645.1_ASM1453464v1_genomic.fna.gz --refList GCF_014534645.1_ASM1453464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014534645.1_ASM1453464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:49,138] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:49,158] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:49,158] [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_014534645.1	s__Streptomyces sp014534645	100.0	2853	2866	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_014650995.1	s__Streptomyces viridiviolaceus	92.0824	2190	2866	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	88.9242	1961	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	88.7803	1765	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005225.1	s__Streptomyces pactum_A	88.5854	1908	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_002939385.1	s__Streptomyces sp002939385	88.1634	1836	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_000772045.1	s__Streptomyces sp000772045	87.94	1900	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_003112555.1	s__Streptomyces coelicoflavus	87.8004	1906	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCA_003248315.1	s__Streptomyces sp003248315	87.5985	1855	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	87.2306	1814	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCF_000721235.1	s__Streptomyces olivaceus	87.198	1781	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.53	98.10	0.91	0.89	6	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	86.8304	1861	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	86.7612	1885	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	86.6001	1883	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	85.5774	1593	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014655195.1	s__Streptomyces cellulosae	85.5406	1682	2866	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.87	0.87	0.85	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:49,160] [INFO] GTDB search result was written to GCF_014534645.1_ASM1453464v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:49,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:49,165] [INFO] DFAST_QC result json was written to GCF_014534645.1_ASM1453464v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:49,166] [INFO] DFAST_QC completed!
[2024-01-24 14:06:49,166] [INFO] Total running time: 0h3m59s