[2024-01-25 18:15:35,548] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,550] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,550] [INFO] DQC Reference Directory: /var/lib/cwl/stge3b4c5a6-efd7-4470-b97d-abc98e0f449b/dqc_reference
[2024-01-25 18:15:36,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,704] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,705] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d638df0-6930-4e17-8ff6-741afed659d8/GCF_009299385.1_ASM929938v1_genomic.fna.gz | prodigal -d GCF_009299385.1_ASM929938v1_genomic.fna/cds.fna -a GCF_009299385.1_ASM929938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:54,044] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:54,044] [INFO] Task started: HMMsearch
[2024-01-25 18:15:54,044] [INFO] Running command: hmmsearch --tblout GCF_009299385.1_ASM929938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3b4c5a6-efd7-4470-b97d-abc98e0f449b/dqc_reference/reference_markers.hmm GCF_009299385.1_ASM929938v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:54,520] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:54,522] [INFO] Found 6/6 markers.
[2024-01-25 18:15:54,579] [INFO] Query marker FASTA was written to GCF_009299385.1_ASM929938v1_genomic.fna/markers.fasta
[2024-01-25 18:15:54,579] [INFO] Task started: Blastn
[2024-01-25 18:15:54,579] [INFO] Running command: blastn -query GCF_009299385.1_ASM929938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3b4c5a6-efd7-4470-b97d-abc98e0f449b/dqc_reference/reference_markers.fasta -out GCF_009299385.1_ASM929938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:55,968] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:55,972] [INFO] Selected 15 target genomes.
[2024-01-25 18:15:55,972] [INFO] Target genome list was writen to GCF_009299385.1_ASM929938v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:55,994] [INFO] Task started: fastANI
[2024-01-25 18:15:55,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d638df0-6930-4e17-8ff6-741afed659d8/GCF_009299385.1_ASM929938v1_genomic.fna.gz --refList GCF_009299385.1_ASM929938v1_genomic.fna/target_genomes.txt --output GCF_009299385.1_ASM929938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:28,890] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:28,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3b4c5a6-efd7-4470-b97d-abc98e0f449b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:28,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3b4c5a6-efd7-4470-b97d-abc98e0f449b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:28,901] [INFO] Found 15 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 18:16:28,901] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:28,902] [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 cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	100.0	2503	2505	95	conclusive
Streptomyces cinereoruber	strain=DSM 41512	GCA_011758705.1	67260	67260	type	True	99.9931	2479	2505	95	conclusive
Streptomyces cinereoruber	strain=NRRL ISP-5012	GCA_014197485.1	67260	67260	type	True	99.9931	2475	2505	95	conclusive
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	99.9882	2446	2505	95	conclusive
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	99.9797	2330	2505	95	conclusive
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.3199	1777	2505	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.2583	1797	2505	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	89.2575	1801	2505	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	89.077	1762	2505	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.0223	1771	2505	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	88.5326	1405	2505	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	88.4667	1760	2505	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.3535	1405	2505	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	83.1957	1171	2505	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.7674	1402	2505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:28,903] [INFO] DFAST Taxonomy check result was written to GCF_009299385.1_ASM929938v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:28,903] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:28,903] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:28,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3b4c5a6-efd7-4470-b97d-abc98e0f449b/dqc_reference/checkm_data
[2024-01-25 18:16:28,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:28,976] [INFO] Task started: CheckM
[2024-01-25 18:16:28,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009299385.1_ASM929938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009299385.1_ASM929938v1_genomic.fna/checkm_input GCF_009299385.1_ASM929938v1_genomic.fna/checkm_result
[2024-01-25 18:18:13,614] [INFO] Task succeeded: CheckM
[2024-01-25 18:18:13,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:18:13,641] [INFO] ===== Completeness check finished =====
[2024-01-25 18:18:13,641] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:18:13,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009299385.1_ASM929938v1_genomic.fna/markers.fasta)
[2024-01-25 18:18:13,643] [INFO] Task started: Blastn
[2024-01-25 18:18:13,643] [INFO] Running command: blastn -query GCF_009299385.1_ASM929938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3b4c5a6-efd7-4470-b97d-abc98e0f449b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009299385.1_ASM929938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:18:15,838] [INFO] Task succeeded: Blastn
[2024-01-25 18:18:15,841] [INFO] Selected 16 target genomes.
[2024-01-25 18:18:15,841] [INFO] Target genome list was writen to GCF_009299385.1_ASM929938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:18:15,861] [INFO] Task started: fastANI
[2024-01-25 18:18:15,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d638df0-6930-4e17-8ff6-741afed659d8/GCF_009299385.1_ASM929938v1_genomic.fna.gz --refList GCF_009299385.1_ASM929938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009299385.1_ASM929938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:52,394] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:52,405] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:18:52,405] [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
GCA_000716465.1	s__Streptomyces bikiniensis	95.7691	1974	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.67	95.67	0.86	0.82	10	conclusive
GCF_001280125.1	s__Streptomyces sp001280125	93.8817	1901	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.57	95.16	0.89	0.81	3	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.297	1780	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_000830005.1	s__Streptomyces vietnamensis	89.2663	1800	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105415.1	s__Streptomyces sp900105415	89.197	1824	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_014649755.1	s__Streptomyces litmocidini	89.1273	1756	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_003386135.1	s__Streptomyces sp003386135	88.9997	1803	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_008639165.1	s__Streptomyces venezuelae	88.8144	1790	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	-
GCF_000725545.1	s__Streptomyces exfoliatus	88.7442	1774	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	88.7087	1727	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_014656215.1	s__Streptomyces zaomyceticus	88.6112	1789	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539185.1	s__Streptomyces gardneri	88.5115	1734	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCF_014451325.1	s__Streptomyces sp014451325	88.1974	1245	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008345.1	s__Streptomyces showdoensis	86.3623	1627	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002355495.1	s__Streptomyces laurentii	85.1853	1566	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008973465.1	s__Streptomyces sp008973465	82.1903	1377	2505	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 18:18:52,406] [INFO] GTDB search result was written to GCF_009299385.1_ASM929938v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:52,408] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:52,411] [INFO] DFAST_QC result json was written to GCF_009299385.1_ASM929938v1_genomic.fna/dqc_result.json
[2024-01-25 18:18:52,411] [INFO] DFAST_QC completed!
[2024-01-25 18:18:52,411] [INFO] Total running time: 0h3m17s