[2024-01-25 20:11:50,775] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:11:50,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:11:50,777] [INFO] DQC Reference Directory: /var/lib/cwl/stgf26c3bbe-94e6-45c6-adcd-3ff34fd44310/dqc_reference
[2024-01-25 20:11:51,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:11:51,904] [INFO] Task started: Prodigal
[2024-01-25 20:11:51,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg58a82e8f-6eb5-43f6-b081-591996e1da93/GCF_014649815.1_ASM1464981v1_genomic.fna.gz | prodigal -d GCF_014649815.1_ASM1464981v1_genomic.fna/cds.fna -a GCF_014649815.1_ASM1464981v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:11,315] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:11,315] [INFO] Task started: HMMsearch
[2024-01-25 20:12:11,316] [INFO] Running command: hmmsearch --tblout GCF_014649815.1_ASM1464981v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf26c3bbe-94e6-45c6-adcd-3ff34fd44310/dqc_reference/reference_markers.hmm GCF_014649815.1_ASM1464981v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:11,621] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:11,623] [INFO] Found 6/6 markers.
[2024-01-25 20:12:11,679] [INFO] Query marker FASTA was written to GCF_014649815.1_ASM1464981v1_genomic.fna/markers.fasta
[2024-01-25 20:12:11,679] [INFO] Task started: Blastn
[2024-01-25 20:12:11,679] [INFO] Running command: blastn -query GCF_014649815.1_ASM1464981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf26c3bbe-94e6-45c6-adcd-3ff34fd44310/dqc_reference/reference_markers.fasta -out GCF_014649815.1_ASM1464981v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:12,915] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:12,918] [INFO] Selected 16 target genomes.
[2024-01-25 20:12:12,918] [INFO] Target genome list was writen to GCF_014649815.1_ASM1464981v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:12,927] [INFO] Task started: fastANI
[2024-01-25 20:12:12,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg58a82e8f-6eb5-43f6-b081-591996e1da93/GCF_014649815.1_ASM1464981v1_genomic.fna.gz --refList GCF_014649815.1_ASM1464981v1_genomic.fna/target_genomes.txt --output GCF_014649815.1_ASM1464981v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:45,246] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:45,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf26c3bbe-94e6-45c6-adcd-3ff34fd44310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:45,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf26c3bbe-94e6-45c6-adcd-3ff34fd44310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:45,257] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:45,257] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:45,257] [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 mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	100.0	2481	2482	95	conclusive
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	90.0331	1929	2482	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	89.6855	1831	2482	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	89.4892	1881	2482	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	89.4234	1879	2482	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	89.2805	1786	2482	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	89.1798	1822	2482	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	89.1609	1822	2482	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	89.0188	1822	2482	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	88.7032	1801	2482	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	88.3573	1794	2482	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.3339	1491	2482	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	85.8562	1749	2482	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	85.2877	1454	2482	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.867	1470	2482	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.6573	1513	2482	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:45,259] [INFO] DFAST Taxonomy check result was written to GCF_014649815.1_ASM1464981v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:45,259] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:45,259] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:45,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf26c3bbe-94e6-45c6-adcd-3ff34fd44310/dqc_reference/checkm_data
[2024-01-25 20:12:45,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:45,336] [INFO] Task started: CheckM
[2024-01-25 20:12:45,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649815.1_ASM1464981v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649815.1_ASM1464981v1_genomic.fna/checkm_input GCF_014649815.1_ASM1464981v1_genomic.fna/checkm_result
[2024-01-25 20:14:10,437] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:10,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:10,470] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:10,470] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:10,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649815.1_ASM1464981v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:10,472] [INFO] Task started: Blastn
[2024-01-25 20:14:10,472] [INFO] Running command: blastn -query GCF_014649815.1_ASM1464981v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf26c3bbe-94e6-45c6-adcd-3ff34fd44310/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649815.1_ASM1464981v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:12,587] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:12,590] [INFO] Selected 13 target genomes.
[2024-01-25 20:14:12,590] [INFO] Target genome list was writen to GCF_014649815.1_ASM1464981v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:12,598] [INFO] Task started: fastANI
[2024-01-25 20:14:12,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg58a82e8f-6eb5-43f6-b081-591996e1da93/GCF_014649815.1_ASM1464981v1_genomic.fna.gz --refList GCF_014649815.1_ASM1464981v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649815.1_ASM1464981v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:39,158] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:39,167] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:39,167] [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_014649815.1	s__Streptomyces mutabilis	100.0	2481	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.69	95.91	0.82	0.76	4	conclusive
GCF_001905385.1	s__Streptomyces sp001905385	92.7659	1968	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCA_002155895.1	s__Streptomyces rochei	91.9981	1678	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.25	0.91	0.79	28	-
GCF_002005225.1	s__Streptomyces pactum_A	90.5015	1961	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001267885.1	s__Streptomyces ambofaciens	89.9982	1935	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.23	99.23	0.92	0.92	2	-
GCF_000772045.1	s__Streptomyces sp000772045	89.654	1861	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_003112595.1	s__Streptomyces rubrogriseus	89.5051	1879	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_000717995.1	s__Streptomyces violaceorubidus	89.5039	1816	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	89.4043	1876	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_014648815.1	s__Streptomyces flaveolus	89.2261	1816	2482	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	89.1462	1823	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_002005565.1	s__Streptomyces sp002005565	89.0847	1698	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614415.1	s__Streptomyces sp018614415	86.758	1657	2482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:39,168] [INFO] GTDB search result was written to GCF_014649815.1_ASM1464981v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:39,169] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:39,172] [INFO] DFAST_QC result json was written to GCF_014649815.1_ASM1464981v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:39,173] [INFO] DFAST_QC completed!
[2024-01-25 20:14:39,173] [INFO] Total running time: 0h2m48s