[2024-01-24 15:10:22,879] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd8f99b7-8e78-4798-9f7c-64094c9631da/dqc_reference
[2024-01-24 15:10:24,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,486] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a02977e-7e8d-4f45-807b-26566a88c1b8/GCF_014203475.1_ASM1420347v1_genomic.fna.gz | prodigal -d GCF_014203475.1_ASM1420347v1_genomic.fna/cds.fna -a GCF_014203475.1_ASM1420347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:03,650] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:03,650] [INFO] Task started: HMMsearch
[2024-01-24 15:11:03,650] [INFO] Running command: hmmsearch --tblout GCF_014203475.1_ASM1420347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd8f99b7-8e78-4798-9f7c-64094c9631da/dqc_reference/reference_markers.hmm GCF_014203475.1_ASM1420347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:04,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:04,049] [INFO] Found 6/6 markers.
[2024-01-24 15:11:04,135] [INFO] Query marker FASTA was written to GCF_014203475.1_ASM1420347v1_genomic.fna/markers.fasta
[2024-01-24 15:11:04,136] [INFO] Task started: Blastn
[2024-01-24 15:11:04,136] [INFO] Running command: blastn -query GCF_014203475.1_ASM1420347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd8f99b7-8e78-4798-9f7c-64094c9631da/dqc_reference/reference_markers.fasta -out GCF_014203475.1_ASM1420347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:05,480] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:05,493] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:05,494] [INFO] Target genome list was writen to GCF_014203475.1_ASM1420347v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:05,501] [INFO] Task started: fastANI
[2024-01-24 15:11:05,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a02977e-7e8d-4f45-807b-26566a88c1b8/GCF_014203475.1_ASM1420347v1_genomic.fna.gz --refList GCF_014203475.1_ASM1420347v1_genomic.fna/target_genomes.txt --output GCF_014203475.1_ASM1420347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:49,011] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:49,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd8f99b7-8e78-4798-9f7c-64094c9631da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:49,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd8f99b7-8e78-4798-9f7c-64094c9631da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:49,028] [INFO] Found 17 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 15:11:49,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:49,028] [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 spectabilis	strain=CECT 3146	GCA_014203475.1	68270	68270	type	True	100.0	3518	3523	95	conclusive
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	99.9895	3451	3523	95	conclusive
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	99.9836	3280	3523	95	conclusive
Streptomyces spectabilis	strain=ATCC 27465	GCA_008704795.1	68270	68270	type	True	99.9831	3237	3523	95	conclusive
Streptomyces longispororuber	strain=JCM 4784	GCA_014656095.1	68230	68230	type	True	88.4902	2138	3523	95	below_threshold
Streptomyces aureoverticillatus	strain=JCM 4347	GCA_014649395.1	66871	66871	type	True	86.7565	2241	3523	95	below_threshold
Streptomyces atriruber	strain=NRRL B-24165	GCA_001418325.1	545121	545121	type	True	84.3553	1773	3523	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	83.861	1997	3523	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	82.2843	1523	3523	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	82.2208	1373	3523	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	82.1027	1561	3523	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	82.0976	1596	3523	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.9999	1451	3523	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	81.9581	1408	3523	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.9165	1701	3523	95	below_threshold
Streptomyces thermovulgaris	strain=NRRL B-12375	GCA_002155915.1	1934	1934	type	True	81.8763	1096	3523	95	below_threshold
Streptomyces calidiresistens	strain=DSM 42108	GCA_014141525.1	1485586	1485586	type	True	78.7119	609	3523	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:49,030] [INFO] DFAST Taxonomy check result was written to GCF_014203475.1_ASM1420347v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:49,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:49,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:49,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd8f99b7-8e78-4798-9f7c-64094c9631da/dqc_reference/checkm_data
[2024-01-24 15:11:49,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:49,134] [INFO] Task started: CheckM
[2024-01-24 15:11:49,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203475.1_ASM1420347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203475.1_ASM1420347v1_genomic.fna/checkm_input GCF_014203475.1_ASM1420347v1_genomic.fna/checkm_result
[2024-01-24 15:13:54,014] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:54,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:13:54,044] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:54,044] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:54,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203475.1_ASM1420347v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:54,045] [INFO] Task started: Blastn
[2024-01-24 15:13:54,045] [INFO] Running command: blastn -query GCF_014203475.1_ASM1420347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd8f99b7-8e78-4798-9f7c-64094c9631da/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203475.1_ASM1420347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:56,088] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:56,094] [INFO] Selected 18 target genomes.
[2024-01-24 15:13:56,094] [INFO] Target genome list was writen to GCF_014203475.1_ASM1420347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:56,106] [INFO] Task started: fastANI
[2024-01-24 15:13:56,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a02977e-7e8d-4f45-807b-26566a88c1b8/GCF_014203475.1_ASM1420347v1_genomic.fna.gz --refList GCF_014203475.1_ASM1420347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203475.1_ASM1420347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:14:40,921] [INFO] Task succeeded: fastANI
[2024-01-24 15:14:40,935] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:14:40,935] [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_008704795.1	s__Streptomyces spectabilis	99.9831	3237	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	96.21	0.96	0.90	4	conclusive
GCF_000720325.1	s__Streptomyces sp000720325	94.209	2763	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006088715.1	s__Streptomyces sp006088715	92.8313	2832	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	98.04	0.88	0.88	2	-
GCF_014656095.1	s__Streptomyces longispororuber	88.494	2136	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649395.1	s__Streptomyces aureoverticillatus	86.7772	2238	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414115.1	s__Streptomyces aurantiacus_A	86.7458	2002	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418325.1	s__Streptomyces atriruber	84.3768	1768	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008642355.1	s__Streptomyces venezuelae_B	84.2564	1859	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.58	99.56	0.88	0.87	4	-
GCA_000720845.1	s__Streptomyces sp000720845	82.2119	1548	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513975.1	s__Streptomyces curacoi	82.1713	1562	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	82.1348	1588	3523	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	82.1326	1558	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_007176755.1	s__Streptomyces sp007176755	82.0428	1508	3523	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	81.8974	1635	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612545.1	s__Streptomyces sp016612545	81.6207	1502	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001278075.1	s__Streptomyces pristinaespiralis	81.2368	1490	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.86	99.72	0.99	0.98	3	-
GCF_016919245.1	s__Streptomyces zhihengii	81.1755	1594	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	80.6895	1450	3523	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:14:40,938] [INFO] GTDB search result was written to GCF_014203475.1_ASM1420347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:14:40,938] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:14:40,942] [INFO] DFAST_QC result json was written to GCF_014203475.1_ASM1420347v1_genomic.fna/dqc_result.json
[2024-01-24 15:14:40,942] [INFO] DFAST_QC completed!
[2024-01-24 15:14:40,942] [INFO] Total running time: 0h4m18s