[2024-01-24 13:18:27,598] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:27,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:27,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg44725188-d426-4720-b01a-bef02d765b06/dqc_reference
[2024-01-24 13:18:28,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:28,862] [INFO] Task started: Prodigal
[2024-01-24 13:18:28,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bfa7dc1-c346-4c52-85ae-537450ac748e/GCF_014650195.1_ASM1465019v1_genomic.fna.gz | prodigal -d GCF_014650195.1_ASM1465019v1_genomic.fna/cds.fna -a GCF_014650195.1_ASM1465019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:07,885] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:07,885] [INFO] Task started: HMMsearch
[2024-01-24 13:19:07,886] [INFO] Running command: hmmsearch --tblout GCF_014650195.1_ASM1465019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44725188-d426-4720-b01a-bef02d765b06/dqc_reference/reference_markers.hmm GCF_014650195.1_ASM1465019v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:08,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:08,334] [INFO] Found 6/6 markers.
[2024-01-24 13:19:08,425] [INFO] Query marker FASTA was written to GCF_014650195.1_ASM1465019v1_genomic.fna/markers.fasta
[2024-01-24 13:19:08,425] [INFO] Task started: Blastn
[2024-01-24 13:19:08,425] [INFO] Running command: blastn -query GCF_014650195.1_ASM1465019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44725188-d426-4720-b01a-bef02d765b06/dqc_reference/reference_markers.fasta -out GCF_014650195.1_ASM1465019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:09,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:09,677] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:09,677] [INFO] Target genome list was writen to GCF_014650195.1_ASM1465019v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:09,683] [INFO] Task started: fastANI
[2024-01-24 13:19:09,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bfa7dc1-c346-4c52-85ae-537450ac748e/GCF_014650195.1_ASM1465019v1_genomic.fna.gz --refList GCF_014650195.1_ASM1465019v1_genomic.fna/target_genomes.txt --output GCF_014650195.1_ASM1465019v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:55,733] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:55,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44725188-d426-4720-b01a-bef02d765b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:55,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44725188-d426-4720-b01a-bef02d765b06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:55,748] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:55,748] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:19:55,748] [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	100.0	3914	3918	95	inconclusive
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	95.8173	2885	3918	95	inconclusive
Streptomyces aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	87.8381	1942	3918	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.4899	2135	3918	95	below_threshold
Streptomyces scabichelini	strain=HC44	GCA_011045015.1	2711217	2711217	type	True	86.109	2200	3918	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_003568675.1	2315329	2315329	type	True	85.7531	2192	3918	95	below_threshold
Streptomyces sporangiiformans	strain=NEAU-SSA 1	GCA_005768555.2	2315329	2315329	type	True	85.7336	2197	3918	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	84.9908	2274	3918	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	84.8519	2224	3918	95	below_threshold
Streptomyces lacrimifluminis	strain=CGMCC 4.7272	GCA_014646095.1	1500077	1500077	type	True	84.0558	1981	3918	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.8587	2222	3918	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.8579	1811	3918	95	below_threshold
Streptomyces geranii	strain=A301	GCA_002954775.1	2058923	2058923	type	True	83.8529	1990	3918	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.8431	2073	3918	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.3906	1920	3918	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	83.229	1702	3918	95	below_threshold
Streptomyces silaceus	strain=NRRL B-24166	GCA_001419745.1	545123	545123	type	True	82.9597	1552	3918	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	82.8643	1778	3918	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,750] [INFO] DFAST Taxonomy check result was written to GCF_014650195.1_ASM1465019v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:55,751] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:55,751] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:55,751] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44725188-d426-4720-b01a-bef02d765b06/dqc_reference/checkm_data
[2024-01-24 13:19:55,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:55,860] [INFO] Task started: CheckM
[2024-01-24 13:19:55,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014650195.1_ASM1465019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014650195.1_ASM1465019v1_genomic.fna/checkm_input GCF_014650195.1_ASM1465019v1_genomic.fna/checkm_result
[2024-01-24 13:22:16,372] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:16,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:16,401] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:16,402] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:16,402] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014650195.1_ASM1465019v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:16,402] [INFO] Task started: Blastn
[2024-01-24 13:22:16,402] [INFO] Running command: blastn -query GCF_014650195.1_ASM1465019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44725188-d426-4720-b01a-bef02d765b06/dqc_reference/reference_markers_gtdb.fasta -out GCF_014650195.1_ASM1465019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:18,495] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:18,499] [INFO] Selected 9 target genomes.
[2024-01-24 13:22:18,500] [INFO] Target genome list was writen to GCF_014650195.1_ASM1465019v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:18,524] [INFO] Task started: fastANI
[2024-01-24 13:22:18,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bfa7dc1-c346-4c52-85ae-537450ac748e/GCF_014650195.1_ASM1465019v1_genomic.fna.gz --refList GCF_014650195.1_ASM1465019v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014650195.1_ASM1465019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:44,638] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:44,651] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:44,651] [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_001418655.1	s__Streptomyces phaeochromogenes	95.806	2886	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.97	95.89	0.88	0.87	3	conclusive
GCF_016598615.1	s__Streptomyces sp016598615	94.4589	3132	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050945.1	s__Streptomyces sp007050945	94.3306	3019	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	89.2661	2612	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090165.1	s__Streptomyces sp019090165	88.893	2382	3918	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	87.9215	2455	3918	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	87.2976	2088	3918	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	84.5759	1925	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418565.1	s__Streptomyces graminilatus	83.8017	1573	3918	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:44,653] [INFO] GTDB search result was written to GCF_014650195.1_ASM1465019v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:44,654] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:44,659] [INFO] DFAST_QC result json was written to GCF_014650195.1_ASM1465019v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:44,660] [INFO] DFAST_QC completed!
[2024-01-24 13:22:44,660] [INFO] Total running time: 0h4m17s