[2024-01-25 19:34:21,019] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c159f59-e580-4828-830c-02044908fab7/dqc_reference
[2024-01-25 19:34:22,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,160] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg57881641-be83-457d-ba2a-66696a740418/GCF_014651115.1_ASM1465111v1_genomic.fna.gz | prodigal -d GCF_014651115.1_ASM1465111v1_genomic.fna/cds.fna -a GCF_014651115.1_ASM1465111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:42,300] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:42,301] [INFO] Task started: HMMsearch
[2024-01-25 19:34:42,301] [INFO] Running command: hmmsearch --tblout GCF_014651115.1_ASM1465111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c159f59-e580-4828-830c-02044908fab7/dqc_reference/reference_markers.hmm GCF_014651115.1_ASM1465111v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:42,598] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:42,599] [INFO] Found 6/6 markers.
[2024-01-25 19:34:42,656] [INFO] Query marker FASTA was written to GCF_014651115.1_ASM1465111v1_genomic.fna/markers.fasta
[2024-01-25 19:34:42,656] [INFO] Task started: Blastn
[2024-01-25 19:34:42,657] [INFO] Running command: blastn -query GCF_014651115.1_ASM1465111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c159f59-e580-4828-830c-02044908fab7/dqc_reference/reference_markers.fasta -out GCF_014651115.1_ASM1465111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:43,848] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:43,852] [INFO] Selected 20 target genomes.
[2024-01-25 19:34:43,853] [INFO] Target genome list was writen to GCF_014651115.1_ASM1465111v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:43,869] [INFO] Task started: fastANI
[2024-01-25 19:34:43,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg57881641-be83-457d-ba2a-66696a740418/GCF_014651115.1_ASM1465111v1_genomic.fna.gz --refList GCF_014651115.1_ASM1465111v1_genomic.fna/target_genomes.txt --output GCF_014651115.1_ASM1465111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:20,601] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:20,602] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c159f59-e580-4828-830c-02044908fab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:20,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c159f59-e580-4828-830c-02044908fab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:20,615] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:20,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:20,615] [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 inusitatus	strain=JCM 4988	GCA_014651115.1	68221	68221	type	True	100.0	2572	2576	95	conclusive
Streptomyces clavuligerus	strain=ATCC 27064	GCA_015912925.1	1901	1901	type	True	84.4567	1197	2576	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000148465.1	1901	1901	type	True	84.3141	1580	2576	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000163875.1	1901	1901	suspected-type	True	84.2752	1569	2576	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_000154925.1	1901	1901	suspected-type	True	84.2081	1202	2576	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	83.3211	1358	2576	95	below_threshold
Streptomyces qinzhouensis	strain=SSL-25	GCA_007856155.1	2599401	2599401	type	True	82.9073	1510	2576	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.4547	1290	2576	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.2749	1351	2576	95	below_threshold
Streptomyces kurssanovii	strain=JCM 4388	GCA_014649695.1	67312	67312	type	True	82.2387	1303	2576	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	82.2215	1414	2576	95	below_threshold
Streptomyces lateritius	strain=JCM 4389	GCA_014649715.1	67313	67313	type	True	82.1475	1271	2576	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	82.1461	1105	2576	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	81.9509	1286	2576	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	81.8033	1188	2576	95	below_threshold
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	81.7918	1226	2576	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	81.6141	1180	2576	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	81.5289	1012	2576	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	80.8723	1244	2576	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.7757	1196	2576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:20,616] [INFO] DFAST Taxonomy check result was written to GCF_014651115.1_ASM1465111v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:20,617] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:20,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:20,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c159f59-e580-4828-830c-02044908fab7/dqc_reference/checkm_data
[2024-01-25 19:35:20,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:20,693] [INFO] Task started: CheckM
[2024-01-25 19:35:20,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651115.1_ASM1465111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651115.1_ASM1465111v1_genomic.fna/checkm_input GCF_014651115.1_ASM1465111v1_genomic.fna/checkm_result
[2024-01-25 19:37:12,877] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:12,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:12,907] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:12,907] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:12,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651115.1_ASM1465111v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:12,909] [INFO] Task started: Blastn
[2024-01-25 19:37:12,909] [INFO] Running command: blastn -query GCF_014651115.1_ASM1465111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c159f59-e580-4828-830c-02044908fab7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651115.1_ASM1465111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:14,903] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:14,905] [INFO] Selected 17 target genomes.
[2024-01-25 19:37:14,905] [INFO] Target genome list was writen to GCF_014651115.1_ASM1465111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:14,915] [INFO] Task started: fastANI
[2024-01-25 19:37:14,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg57881641-be83-457d-ba2a-66696a740418/GCF_014651115.1_ASM1465111v1_genomic.fna.gz --refList GCF_014651115.1_ASM1465111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651115.1_ASM1465111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:47,431] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:47,441] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:47,442] [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_014651115.1	s__Streptomyces inusitatus	100.0	2572	2576	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_009600885.1	s__Streptomyces jumonjinensis_A	85.7657	1628	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.98	97.98	0.89	0.89	2	-
GCF_005519465.1	s__Streptomyces clavuligerus	84.4189	1567	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.68	0.97	0.92	18	-
GCF_003054555.1	s__Streptomyces lunaelactis	83.3349	1356	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.21	97.91	0.90	0.85	18	-
GCF_006715635.1	s__Streptomyces sp006715635	83.1717	1286	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614585.1	s__Streptomyces sp018614585	83.0493	1240	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932715.1	s__Streptomyces tsukubensis	82.8952	1514	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	99.99	1.00	1.00	5	-
GCF_007856155.1	s__Streptomyces qinzhouensis	82.8826	1515	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387495.1	s__Streptomyces sp013387495	82.5035	1272	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653515.1	s__Streptomyces sp001653515	82.307	1139	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649695.1	s__Streptomyces kurssanovii	82.266	1298	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489615.1	s__Streptomyces sp014489615	82.245	1356	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919245.1	s__Streptomyces zhihengii	82.2232	1414	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	82.0307	1340	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_014649335.1	s__Streptomyces roseolilacinus	81.7402	1198	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279695.1	s__Streptomyces sp001279695	81.6744	1302	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019855.1	s__Streptomyces antibioticus_B	81.0953	1258	2576	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.20	96.76	0.94	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:47,443] [INFO] GTDB search result was written to GCF_014651115.1_ASM1465111v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:47,443] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:47,447] [INFO] DFAST_QC result json was written to GCF_014651115.1_ASM1465111v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:47,447] [INFO] DFAST_QC completed!
[2024-01-25 19:37:47,447] [INFO] Total running time: 0h3m26s