[2024-01-25 19:06:05,584] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:05,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:05,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg80b992fb-5ada-45ae-a73f-850417454a00/dqc_reference
[2024-01-25 19:06:06,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:06,771] [INFO] Task started: Prodigal
[2024-01-25 19:06:06,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a40a65f-9a74-4cb8-869a-e5da54c5662e/GCF_008905045.1_ASM890504v1_genomic.fna.gz | prodigal -d GCF_008905045.1_ASM890504v1_genomic.fna/cds.fna -a GCF_008905045.1_ASM890504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:39,860] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:39,860] [INFO] Task started: HMMsearch
[2024-01-25 19:06:39,860] [INFO] Running command: hmmsearch --tblout GCF_008905045.1_ASM890504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80b992fb-5ada-45ae-a73f-850417454a00/dqc_reference/reference_markers.hmm GCF_008905045.1_ASM890504v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:40,313] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:40,314] [INFO] Found 6/6 markers.
[2024-01-25 19:06:40,399] [INFO] Query marker FASTA was written to GCF_008905045.1_ASM890504v1_genomic.fna/markers.fasta
[2024-01-25 19:06:40,400] [INFO] Task started: Blastn
[2024-01-25 19:06:40,400] [INFO] Running command: blastn -query GCF_008905045.1_ASM890504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80b992fb-5ada-45ae-a73f-850417454a00/dqc_reference/reference_markers.fasta -out GCF_008905045.1_ASM890504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:41,803] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:41,806] [INFO] Selected 25 target genomes.
[2024-01-25 19:06:41,806] [INFO] Target genome list was writen to GCF_008905045.1_ASM890504v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:41,825] [INFO] Task started: fastANI
[2024-01-25 19:06:41,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a40a65f-9a74-4cb8-869a-e5da54c5662e/GCF_008905045.1_ASM890504v1_genomic.fna.gz --refList GCF_008905045.1_ASM890504v1_genomic.fna/target_genomes.txt --output GCF_008905045.1_ASM890504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:41,107] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:41,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80b992fb-5ada-45ae-a73f-850417454a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:41,109] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80b992fb-5ada-45ae-a73f-850417454a00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:41,123] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:07:41,123] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:07:41,123] [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 umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	89.4156	2599	3892	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	89.2922	2330	3892	95	below_threshold
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	87.8111	1816	3892	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	87.3729	2285	3892	95	below_threshold
Streptomyces montanus	strain=NEAU-C151	GCA_005786655.1	2580423	2580423	type	True	86.8242	2227	3892	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	86.814	2246	3892	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	86.7986	2249	3892	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.6426	2033	3892	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	85.4082	2209	3892	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	85.1504	1964	3892	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	85.12	1959	3892	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	85.0441	2064	3892	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.1542	1828	3892	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.7485	2121	3892	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.4778	1882	3892	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.4375	1635	3892	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	83.0975	1678	3892	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	83.0339	1703	3892	95	below_threshold
Streptomyces olivaceoviridis	strain=JCM 4499	GCA_014650115.1	1921	1921	type	True	83.0014	1787	3892	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	82.9557	1382	3892	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.7693	1876	3892	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	82.7691	1623	3892	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	81.6988	1569	3892	95	below_threshold
Streptomyces clavifer	strain=JCM 5059	GCA_014651175.1	68188	68188	type	True	80.7762	1397	3892	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.169	1133	3892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:41,125] [INFO] DFAST Taxonomy check result was written to GCF_008905045.1_ASM890504v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:41,126] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:41,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:41,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80b992fb-5ada-45ae-a73f-850417454a00/dqc_reference/checkm_data
[2024-01-25 19:07:41,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:41,236] [INFO] Task started: CheckM
[2024-01-25 19:07:41,236] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008905045.1_ASM890504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008905045.1_ASM890504v1_genomic.fna/checkm_input GCF_008905045.1_ASM890504v1_genomic.fna/checkm_result
[2024-01-25 19:09:46,616] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:46,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:46,642] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:46,642] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:46,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008905045.1_ASM890504v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:46,643] [INFO] Task started: Blastn
[2024-01-25 19:09:46,643] [INFO] Running command: blastn -query GCF_008905045.1_ASM890504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80b992fb-5ada-45ae-a73f-850417454a00/dqc_reference/reference_markers_gtdb.fasta -out GCF_008905045.1_ASM890504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:49,059] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:49,062] [INFO] Selected 18 target genomes.
[2024-01-25 19:09:49,062] [INFO] Target genome list was writen to GCF_008905045.1_ASM890504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:49,091] [INFO] Task started: fastANI
[2024-01-25 19:09:49,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a40a65f-9a74-4cb8-869a-e5da54c5662e/GCF_008905045.1_ASM890504v1_genomic.fna.gz --refList GCF_008905045.1_ASM890504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008905045.1_ASM890504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:35,207] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:35,218] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:35,219] [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_008905045.1	s__Streptomyces albicerus	100.0	3879	3892	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_007050945.1	s__Streptomyces sp007050945	89.7516	2638	3892	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	89.6072	2573	3892	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	89.2913	2331	3892	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	88.6357	2292	3892	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	87.7714	1822	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	-
GCF_014650955.1	s__Streptomyces tauricus	87.7523	2228	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070025.1	s__Streptomyces sp018070025	87.4413	2309	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	87.3343	2294	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369065.1	s__Streptomyces sp008369065	87.1271	1969	3892	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	86.7969	2251	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.93	95.85	0.91	0.82	3	-
GCF_014651055.1	s__Streptomyces fructofermentans	86.6439	2033	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645835.1	s__Streptomyces albiflavescens	85.4209	2205	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948455.1	s__Streptomyces sp017948455	84.6785	2123	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664315.1	s__Streptomyces sp003664315	84.6206	1881	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648855.1	s__Streptomyces parvulus	83.0014	1710	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_009769735.1	s__Streptomyces sp009769735	82.632	1854	3892	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203645.1	s__Streptomyces zagrosensis	79.138	1140	3892	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 19:10:35,221] [INFO] GTDB search result was written to GCF_008905045.1_ASM890504v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:35,222] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:35,225] [INFO] DFAST_QC result json was written to GCF_008905045.1_ASM890504v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:35,225] [INFO] DFAST_QC completed!
[2024-01-25 19:10:35,226] [INFO] Total running time: 0h4m30s