[2024-01-24 12:37:37,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg22b2c040-f417-4408-8885-742607d80b05/dqc_reference
[2024-01-24 12:37:41,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,015] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgbca00552-3580-40ee-9d2f-08ee36e950ad/GCF_014656235.1_ASM1465623v1_genomic.fna.gz | prodigal -d GCF_014656235.1_ASM1465623v1_genomic.fna/cds.fna -a GCF_014656235.1_ASM1465623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:38:04,647] [INFO] Task succeeded: Prodigal
[2024-01-24 12:38:04,648] [INFO] Task started: HMMsearch
[2024-01-24 12:38:04,648] [INFO] Running command: hmmsearch --tblout GCF_014656235.1_ASM1465623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22b2c040-f417-4408-8885-742607d80b05/dqc_reference/reference_markers.hmm GCF_014656235.1_ASM1465623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:38:05,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:38:05,037] [INFO] Found 6/6 markers.
[2024-01-24 12:38:05,113] [INFO] Query marker FASTA was written to GCF_014656235.1_ASM1465623v1_genomic.fna/markers.fasta
[2024-01-24 12:38:05,113] [INFO] Task started: Blastn
[2024-01-24 12:38:05,113] [INFO] Running command: blastn -query GCF_014656235.1_ASM1465623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22b2c040-f417-4408-8885-742607d80b05/dqc_reference/reference_markers.fasta -out GCF_014656235.1_ASM1465623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:06,476] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:06,480] [INFO] Selected 12 target genomes.
[2024-01-24 12:38:06,480] [INFO] Target genome list was writen to GCF_014656235.1_ASM1465623v1_genomic.fna/target_genomes.txt
[2024-01-24 12:38:06,489] [INFO] Task started: fastANI
[2024-01-24 12:38:06,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca00552-3580-40ee-9d2f-08ee36e950ad/GCF_014656235.1_ASM1465623v1_genomic.fna.gz --refList GCF_014656235.1_ASM1465623v1_genomic.fna/target_genomes.txt --output GCF_014656235.1_ASM1465623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:32,382] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:32,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22b2c040-f417-4408-8885-742607d80b05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:32,383] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22b2c040-f417-4408-8885-742607d80b05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:32,394] [INFO] Found 12 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:38:32,394] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:38:32,394] [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 glebosus	strain=JCM 4954	GCA_014656235.1	249580	249580	type	True	100.0	2753	2757	95	inconclusive
Streptomyces glebosus	strain=NBRC 13786	GCA_009811575.1	249580	249580	type	True	99.9991	2756	2757	95	inconclusive
Streptomyces platensis	strain=DSM 40041	GCA_002119195.1	58346	58346	type	True	97.6576	2397	2757	95	inconclusive
Streptomyces platensis	strain=ATCC 23948	GCA_008704855.1	58346	58346	type	True	97.6338	2451	2757	95	inconclusive
Streptomyces lydicamycinicus	strain=NBRC 110027	GCA_000829715.2	1546107	1546107	type	True	95.2646	2340	2757	95	inconclusive
Streptomyces caniferus	strain=NBRC 15389	GCA_009811555.1	285557	285557	type	True	89.7562	2153	2757	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	88.9581	1894	2757	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	85.5249	1567	2757	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	84.4401	1272	2757	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_022271435.1	371720	371720	type	True	83.6973	1569	2757	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	83.6411	1637	2757	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	83.5974	1620	2757	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:32,396] [INFO] DFAST Taxonomy check result was written to GCF_014656235.1_ASM1465623v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:32,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:32,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:32,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22b2c040-f417-4408-8885-742607d80b05/dqc_reference/checkm_data
[2024-01-24 12:38:32,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:32,478] [INFO] Task started: CheckM
[2024-01-24 12:38:32,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656235.1_ASM1465623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656235.1_ASM1465623v1_genomic.fna/checkm_input GCF_014656235.1_ASM1465623v1_genomic.fna/checkm_result
[2024-01-24 12:39:51,386] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:51,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.29%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:51,418] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:51,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:51,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656235.1_ASM1465623v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:51,422] [INFO] Task started: Blastn
[2024-01-24 12:39:51,422] [INFO] Running command: blastn -query GCF_014656235.1_ASM1465623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22b2c040-f417-4408-8885-742607d80b05/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656235.1_ASM1465623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:53,557] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:53,561] [INFO] Selected 9 target genomes.
[2024-01-24 12:39:53,561] [INFO] Target genome list was writen to GCF_014656235.1_ASM1465623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:53,569] [INFO] Task started: fastANI
[2024-01-24 12:39:53,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca00552-3580-40ee-9d2f-08ee36e950ad/GCF_014656235.1_ASM1465623v1_genomic.fna.gz --refList GCF_014656235.1_ASM1465623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656235.1_ASM1465623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:14,946] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:14,957] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:14,957] [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_008704855.1	s__Streptomyces platensis	97.6338	2451	2757	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.55	95.21	0.91	0.87	7	conclusive
GCF_009811595.1	s__Streptomyces libani	92.6095	2343	2757	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.04	96.45	0.91	0.86	12	-
GCF_009811635.1	s__Streptomyces tubercidicus	92.4054	2081	2757	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270575.1	s__Streptomyces decoyicus	90.1155	2114	2757	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.25	96.25	0.87	0.87	2	-
GCF_009811555.1	s__Streptomyces caniferus	89.774	2150	2757	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187385.1	s__Streptomyces sp900187385	89.4957	2050	2757	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.51	0.98	0.96	9	-
GCF_004122735.1	s__Streptomyces sioyaensis	89.4181	1858	2757	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.26	95.36	0.89	0.84	9	-
GCF_004125265.1	s__Streptomyces lydicus_C	89.3732	2000	2757	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646275.1	s__Streptomyces kronopolitis	88.9282	1899	2757	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 12:40:14,959] [INFO] GTDB search result was written to GCF_014656235.1_ASM1465623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:14,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:14,964] [INFO] DFAST_QC result json was written to GCF_014656235.1_ASM1465623v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:14,965] [INFO] DFAST_QC completed!
[2024-01-24 12:40:14,965] [INFO] Total running time: 0h2m37s