[2024-01-24 12:44:18,438] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:18,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:18,440] [INFO] DQC Reference Directory: /var/lib/cwl/stgd707bbce-0d7e-4a80-a0e7-a22b3e506be7/dqc_reference
[2024-01-24 12:44:19,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:19,613] [INFO] Task started: Prodigal
[2024-01-24 12:44:19,614] [INFO] Running command: gunzip -c /var/lib/cwl/stgf183d29d-a387-49bf-90cb-ce7115258e7a/GCF_027947595.1_ASM2794759v1_genomic.fna.gz | prodigal -d GCF_027947595.1_ASM2794759v1_genomic.fna/cds.fna -a GCF_027947595.1_ASM2794759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:41,278] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:41,279] [INFO] Task started: HMMsearch
[2024-01-24 12:44:41,279] [INFO] Running command: hmmsearch --tblout GCF_027947595.1_ASM2794759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd707bbce-0d7e-4a80-a0e7-a22b3e506be7/dqc_reference/reference_markers.hmm GCF_027947595.1_ASM2794759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:41,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:41,636] [INFO] Found 6/6 markers.
[2024-01-24 12:44:41,697] [INFO] Query marker FASTA was written to GCF_027947595.1_ASM2794759v1_genomic.fna/markers.fasta
[2024-01-24 12:44:41,698] [INFO] Task started: Blastn
[2024-01-24 12:44:41,698] [INFO] Running command: blastn -query GCF_027947595.1_ASM2794759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd707bbce-0d7e-4a80-a0e7-a22b3e506be7/dqc_reference/reference_markers.fasta -out GCF_027947595.1_ASM2794759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:42,992] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:42,996] [INFO] Selected 13 target genomes.
[2024-01-24 12:44:42,996] [INFO] Target genome list was writen to GCF_027947595.1_ASM2794759v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:43,053] [INFO] Task started: fastANI
[2024-01-24 12:44:43,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgf183d29d-a387-49bf-90cb-ce7115258e7a/GCF_027947595.1_ASM2794759v1_genomic.fna.gz --refList GCF_027947595.1_ASM2794759v1_genomic.fna/target_genomes.txt --output GCF_027947595.1_ASM2794759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:10,939] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:10,940] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd707bbce-0d7e-4a80-a0e7-a22b3e506be7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:10,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd707bbce-0d7e-4a80-a0e7-a22b3e506be7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:10,962] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:10,962] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:10,963] [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 rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	92.0641	2142	2621	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	92.0383	2132	2621	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	91.9197	2134	2621	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	91.7941	2040	2621	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	91.6849	1952	2621	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	91.5416	2035	2621	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_015645455.1	47716	47716	type	True	90.1985	1952	2621	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	90.1741	1962	2621	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.7707	1867	2621	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.1852	1479	2621	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.3242	1434	2621	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	85.2589	1724	2621	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.4804	1566	2621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:10,964] [INFO] DFAST Taxonomy check result was written to GCF_027947595.1_ASM2794759v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:10,965] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:10,965] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:10,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd707bbce-0d7e-4a80-a0e7-a22b3e506be7/dqc_reference/checkm_data
[2024-01-24 12:45:10,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:11,041] [INFO] Task started: CheckM
[2024-01-24 12:45:11,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027947595.1_ASM2794759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027947595.1_ASM2794759v1_genomic.fna/checkm_input GCF_027947595.1_ASM2794759v1_genomic.fna/checkm_result
[2024-01-24 12:47:19,896] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:19,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:19,929] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:19,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:19,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027947595.1_ASM2794759v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:19,930] [INFO] Task started: Blastn
[2024-01-24 12:47:19,930] [INFO] Running command: blastn -query GCF_027947595.1_ASM2794759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd707bbce-0d7e-4a80-a0e7-a22b3e506be7/dqc_reference/reference_markers_gtdb.fasta -out GCF_027947595.1_ASM2794759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:22,204] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:22,208] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:22,208] [INFO] Target genome list was writen to GCF_027947595.1_ASM2794759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:22,219] [INFO] Task started: fastANI
[2024-01-24 12:47:22,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgf183d29d-a387-49bf-90cb-ce7115258e7a/GCF_027947595.1_ASM2794759v1_genomic.fna.gz --refList GCF_027947595.1_ASM2794759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027947595.1_ASM2794759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:53,455] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:53,468] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:47:53,469] [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_002939385.1	s__Streptomyces sp002939385	92.1774	1978	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_003112555.1	s__Streptomyces coelicoflavus	92.1539	2140	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_003369795.1	s__Streptomyces sp003369795	92.0919	2010	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3499	N/A	N/A	N/A	N/A	1	-
GCF_014651155.1	s__Streptomyces anthocyanicus	92.0427	2131	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	99.40	98.26	0.96	0.83	31	-
GCF_003112595.1	s__Streptomyces rubrogriseus	92.0395	2145	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCA_000720845.1	s__Streptomyces sp000720845	91.9332	2083	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	91.9034	2136	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_000772045.1	s__Streptomyces sp000772045	91.8785	2092	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_000717995.1	s__Streptomyces violaceorubidus	91.7025	1950	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049325.1	s__Streptomyces sp019049325	91.5908	2090	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112575.1	s__Streptomyces ardesiacus	91.5387	2036	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_004364245.1	s__Streptomyces sp004364245	91.4009	1982	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721235.1	s__Streptomyces olivaceus	90.1764	1962	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.53	98.10	0.91	0.89	6	-
GCF_002005225.1	s__Streptomyces pactum_A	89.9349	1959	2621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:53,477] [INFO] GTDB search result was written to GCF_027947595.1_ASM2794759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:53,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:53,482] [INFO] DFAST_QC result json was written to GCF_027947595.1_ASM2794759v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:53,483] [INFO] DFAST_QC completed!
[2024-01-24 12:47:53,483] [INFO] Total running time: 0h3m35s