[2024-01-25 20:00:20,759] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:20,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:20,761] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdb68828-4c4c-4d72-b4dd-9c9d5191e968/dqc_reference
[2024-01-25 20:00:21,959] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:21,960] [INFO] Task started: Prodigal
[2024-01-25 20:00:21,960] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d1baba3-72ad-4154-b27c-74ceceb772e0/GCF_003112555.1_ASM311255v1_genomic.fna.gz | prodigal -d GCF_003112555.1_ASM311255v1_genomic.fna/cds.fna -a GCF_003112555.1_ASM311255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:44,363] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:44,363] [INFO] Task started: HMMsearch
[2024-01-25 20:00:44,363] [INFO] Running command: hmmsearch --tblout GCF_003112555.1_ASM311255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdb68828-4c4c-4d72-b4dd-9c9d5191e968/dqc_reference/reference_markers.hmm GCF_003112555.1_ASM311255v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:44,696] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:44,697] [INFO] Found 6/6 markers.
[2024-01-25 20:00:44,762] [INFO] Query marker FASTA was written to GCF_003112555.1_ASM311255v1_genomic.fna/markers.fasta
[2024-01-25 20:00:44,762] [INFO] Task started: Blastn
[2024-01-25 20:00:44,762] [INFO] Running command: blastn -query GCF_003112555.1_ASM311255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdb68828-4c4c-4d72-b4dd-9c9d5191e968/dqc_reference/reference_markers.fasta -out GCF_003112555.1_ASM311255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:46,018] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:46,021] [INFO] Selected 14 target genomes.
[2024-01-25 20:00:46,021] [INFO] Target genome list was writen to GCF_003112555.1_ASM311255v1_genomic.fna/target_genomes.txt
[2024-01-25 20:00:46,030] [INFO] Task started: fastANI
[2024-01-25 20:00:46,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d1baba3-72ad-4154-b27c-74ceceb772e0/GCF_003112555.1_ASM311255v1_genomic.fna.gz --refList GCF_003112555.1_ASM311255v1_genomic.fna/target_genomes.txt --output GCF_003112555.1_ASM311255v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:17,705] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:17,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdb68828-4c4c-4d72-b4dd-9c9d5191e968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:17,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdb68828-4c4c-4d72-b4dd-9c9d5191e968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:17,715] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:01:17,715] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:01:17,715] [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 anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	92.7573	2194	2890	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	92.7506	2213	2890	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	92.6988	2195	2890	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	92.6229	2105	2890	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	92.5859	2061	2890	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	92.2957	1986	2890	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_015645455.1	47716	47716	type	True	89.8721	1989	2890	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	89.7778	2033	2890	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	89.4771	1977	2890	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	87.8478	1905	2890	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.114	1533	2890	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.3137	1784	2890	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.8703	1564	2890	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.4589	1597	2890	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:17,717] [INFO] DFAST Taxonomy check result was written to GCF_003112555.1_ASM311255v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:17,717] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:17,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:17,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdb68828-4c4c-4d72-b4dd-9c9d5191e968/dqc_reference/checkm_data
[2024-01-25 20:01:17,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:17,795] [INFO] Task started: CheckM
[2024-01-25 20:01:17,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003112555.1_ASM311255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003112555.1_ASM311255v1_genomic.fna/checkm_input GCF_003112555.1_ASM311255v1_genomic.fna/checkm_result
[2024-01-25 20:03:31,401] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:31,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:31,423] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:31,423] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:31,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003112555.1_ASM311255v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:31,424] [INFO] Task started: Blastn
[2024-01-25 20:03:31,424] [INFO] Running command: blastn -query GCF_003112555.1_ASM311255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdb68828-4c4c-4d72-b4dd-9c9d5191e968/dqc_reference/reference_markers_gtdb.fasta -out GCF_003112555.1_ASM311255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:33,544] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:33,550] [INFO] Selected 12 target genomes.
[2024-01-25 20:03:33,551] [INFO] Target genome list was writen to GCF_003112555.1_ASM311255v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:33,569] [INFO] Task started: fastANI
[2024-01-25 20:03:33,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d1baba3-72ad-4154-b27c-74ceceb772e0/GCF_003112555.1_ASM311255v1_genomic.fna.gz --refList GCF_003112555.1_ASM311255v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003112555.1_ASM311255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:00,776] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:00,784] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:00,784] [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_003112555.1	s__Streptomyces coelicoflavus	100.0	2887	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	conclusive
GCF_000772045.1	s__Streptomyces sp000772045	93.3008	2274	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_003369795.1	s__Streptomyces sp003369795	92.811	2065	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3499	N/A	N/A	N/A	N/A	1	-
GCF_002939385.1	s__Streptomyces sp002939385	92.7945	2035	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_014651155.1	s__Streptomyces anthocyanicus	92.7823	2191	2890	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	92.7734	2210	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_014650435.1	s__Streptomyces tendae	92.7131	2193	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.72	95.62	0.85	0.82	7	-
GCF_003112575.1	s__Streptomyces ardesiacus	92.6478	2102	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCA_000720845.1	s__Streptomyces sp000720845	92.5473	2132	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717995.1	s__Streptomyces violaceorubidus	92.3136	1984	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364245.1	s__Streptomyces sp004364245	92.0492	2071	2890	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	89.8134	2027	2890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.53	98.10	0.91	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:00,785] [INFO] GTDB search result was written to GCF_003112555.1_ASM311255v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:00,786] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:00,789] [INFO] DFAST_QC result json was written to GCF_003112555.1_ASM311255v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:00,789] [INFO] DFAST_QC completed!
[2024-01-25 20:04:00,789] [INFO] Total running time: 0h3m40s