[2024-01-24 12:22:28,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:28,093] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:28,093] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6c9317b-ac80-40fd-92ba-bc5c9830e594/dqc_reference
[2024-01-24 12:22:29,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:29,532] [INFO] Task started: Prodigal
[2024-01-24 12:22:29,533] [INFO] Running command: gunzip -c /var/lib/cwl/stge402b110-26a3-4b72-a33e-885852315499/GCF_011045015.1_ASM1104501v1_genomic.fna.gz | prodigal -d GCF_011045015.1_ASM1104501v1_genomic.fna/cds.fna -a GCF_011045015.1_ASM1104501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:04,770] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:04,771] [INFO] Task started: HMMsearch
[2024-01-24 12:23:04,771] [INFO] Running command: hmmsearch --tblout GCF_011045015.1_ASM1104501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6c9317b-ac80-40fd-92ba-bc5c9830e594/dqc_reference/reference_markers.hmm GCF_011045015.1_ASM1104501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:05,223] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:05,224] [INFO] Found 6/6 markers.
[2024-01-24 12:23:05,330] [INFO] Query marker FASTA was written to GCF_011045015.1_ASM1104501v1_genomic.fna/markers.fasta
[2024-01-24 12:23:05,330] [INFO] Task started: Blastn
[2024-01-24 12:23:05,330] [INFO] Running command: blastn -query GCF_011045015.1_ASM1104501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6c9317b-ac80-40fd-92ba-bc5c9830e594/dqc_reference/reference_markers.fasta -out GCF_011045015.1_ASM1104501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:06,848] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:06,853] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:06,853] [INFO] Target genome list was writen to GCF_011045015.1_ASM1104501v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:06,861] [INFO] Task started: fastANI
[2024-01-24 12:23:06,861] [INFO] Running command: fastANI --query /var/lib/cwl/stge402b110-26a3-4b72-a33e-885852315499/GCF_011045015.1_ASM1104501v1_genomic.fna.gz --refList GCF_011045015.1_ASM1104501v1_genomic.fna/target_genomes.txt --output GCF_011045015.1_ASM1104501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:55,357] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:55,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6c9317b-ac80-40fd-92ba-bc5c9830e594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:55,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6c9317b-ac80-40fd-92ba-bc5c9830e594/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:55,387] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:55,387] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:55,387] [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 scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	100.0	3441	3472	95	conclusive
Streptomyces montanus	strain=NEAU-C151	GCA_005786655.1	2580423	2580423	type	True	88.2203	2133	3472	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	88.1964	2149	3472	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	88.1881	2149	3472	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	86.1818	2222	3472	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	86.1712	2037	3472	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	85.3374	1655	3472	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.9329	1625	3472	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	84.7451	1922	3472	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	84.1215	1884	3472	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.9992	1653	3472	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	83.9622	1764	3472	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.64	1851	3472	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.3673	1881	3472	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.0488	1690	3472	95	below_threshold
Streptomyces bungoensis	strain=DSM 41781	GCA_001514215.1	285568	285568	type	True	82.7213	1495	3472	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.5245	1663	3472	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	82.2258	1430	3472	95	below_threshold
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	82.0319	1277	3472	95	below_threshold
Streptomyces clavifer	strain=DSM 40843	GCA_017876255.1	68188	68188	type	True	80.7635	1244	3472	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	80.7164	1255	3472	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.1929	995	3472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:55,389] [INFO] DFAST Taxonomy check result was written to GCF_011045015.1_ASM1104501v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:55,389] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:55,389] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:55,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6c9317b-ac80-40fd-92ba-bc5c9830e594/dqc_reference/checkm_data
[2024-01-24 12:23:55,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:55,492] [INFO] Task started: CheckM
[2024-01-24 12:23:55,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011045015.1_ASM1104501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011045015.1_ASM1104501v1_genomic.fna/checkm_input GCF_011045015.1_ASM1104501v1_genomic.fna/checkm_result
[2024-01-24 12:25:48,530] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:48,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 12:25:48,563] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:48,564] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:48,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011045015.1_ASM1104501v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:48,564] [INFO] Task started: Blastn
[2024-01-24 12:25:48,565] [INFO] Running command: blastn -query GCF_011045015.1_ASM1104501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6c9317b-ac80-40fd-92ba-bc5c9830e594/dqc_reference/reference_markers_gtdb.fasta -out GCF_011045015.1_ASM1104501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:50,870] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:50,875] [INFO] Selected 13 target genomes.
[2024-01-24 12:25:50,876] [INFO] Target genome list was writen to GCF_011045015.1_ASM1104501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:50,896] [INFO] Task started: fastANI
[2024-01-24 12:25:50,897] [INFO] Running command: fastANI --query /var/lib/cwl/stge402b110-26a3-4b72-a33e-885852315499/GCF_011045015.1_ASM1104501v1_genomic.fna.gz --refList GCF_011045015.1_ASM1104501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011045015.1_ASM1104501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:22,621] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:22,637] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:22,637] [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_011045015.1	s__Streptomyces scabichelini	100.0	3441	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014647675.1	s__Streptomyces flaveus	90.3104	2310	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.63	96.63	0.83	0.83	2	-
GCF_011045025.1	s__Streptomyces ureilyticus	89.6917	2127	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005768555.2	s__Streptomyces sporangiiformans	88.1721	2153	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.93	95.85	0.91	0.82	3	-
GCF_008905045.1	s__Streptomyces albicerus	87.3444	2320	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	86.259	2214	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418655.1	s__Streptomyces phaeochromogenes	86.1775	2035	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	-
GCF_019090165.1	s__Streptomyces sp019090165	85.8785	1956	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418335.1	s__Streptomyces aurantiacus	85.3296	1656	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_017948455.1	s__Streptomyces sp017948455	84.9381	2001	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002946835.1	s__Streptomyces dengpaensis	84.9036	1630	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009769735.1	s__Streptomyces sp009769735	82.5274	1665	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004127445.1	s__Streptomyces alfalfae	82.2097	1476	3472	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.46	98.55	0.94	0.88	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:22,640] [INFO] GTDB search result was written to GCF_011045015.1_ASM1104501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:22,640] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:22,644] [INFO] DFAST_QC result json was written to GCF_011045015.1_ASM1104501v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:22,645] [INFO] DFAST_QC completed!
[2024-01-24 12:26:22,645] [INFO] Total running time: 0h3m55s