[2024-01-25 17:44:50,534] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:50,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:50,536] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc0715f0-ba49-439e-a156-d78952b436f6/dqc_reference
[2024-01-25 17:44:51,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:51,655] [INFO] Task started: Prodigal
[2024-01-25 17:44:51,655] [INFO] Running command: gunzip -c /var/lib/cwl/stg973e0647-255b-4572-9fc2-ae0f2ff193a0/GCF_000819545.1_ASM81954v1_genomic.fna.gz | prodigal -d GCF_000819545.1_ASM81954v1_genomic.fna/cds.fna -a GCF_000819545.1_ASM81954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:17,569] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:17,569] [INFO] Task started: HMMsearch
[2024-01-25 17:45:17,569] [INFO] Running command: hmmsearch --tblout GCF_000819545.1_ASM81954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc0715f0-ba49-439e-a156-d78952b436f6/dqc_reference/reference_markers.hmm GCF_000819545.1_ASM81954v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:17,856] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:17,857] [INFO] Found 6/6 markers.
[2024-01-25 17:45:17,920] [INFO] Query marker FASTA was written to GCF_000819545.1_ASM81954v1_genomic.fna/markers.fasta
[2024-01-25 17:45:17,920] [INFO] Task started: Blastn
[2024-01-25 17:45:17,920] [INFO] Running command: blastn -query GCF_000819545.1_ASM81954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc0715f0-ba49-439e-a156-d78952b436f6/dqc_reference/reference_markers.fasta -out GCF_000819545.1_ASM81954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:19,142] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:19,144] [INFO] Selected 15 target genomes.
[2024-01-25 17:45:19,145] [INFO] Target genome list was writen to GCF_000819545.1_ASM81954v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:19,195] [INFO] Task started: fastANI
[2024-01-25 17:45:19,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg973e0647-255b-4572-9fc2-ae0f2ff193a0/GCF_000819545.1_ASM81954v1_genomic.fna.gz --refList GCF_000819545.1_ASM81954v1_genomic.fna/target_genomes.txt --output GCF_000819545.1_ASM81954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:53,026] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:53,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc0715f0-ba49-439e-a156-d78952b436f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:53,027] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc0715f0-ba49-439e-a156-d78952b436f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:53,037] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:45:53,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:53,037] [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 nodosus	strain=ATCC 14899	GCA_000819545.1	40318	40318	type	True	100.0	2568	2571	95	conclusive
Streptomyces nodosus	strain=DSM 40109	GCA_014205035.1	40318	40318	type	True	99.972	2562	2571	95	conclusive
Streptomyces nodosus	strain=ATCC 14899	GCA_008704995.1	40318	40318	type	True	99.9691	2562	2571	95	conclusive
Streptomyces colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	86.1123	1385	2571	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	86.0772	1524	2571	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	84.2249	1494	2571	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	83.8852	1441	2571	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	83.8749	1486	2571	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	83.8681	1470	2571	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	83.7901	1573	2571	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	83.4363	1558	2571	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.3792	1465	2571	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.3103	1381	2571	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.1068	1542	2571	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	83.0932	1519	2571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:53,039] [INFO] DFAST Taxonomy check result was written to GCF_000819545.1_ASM81954v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:53,040] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:53,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:53,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc0715f0-ba49-439e-a156-d78952b436f6/dqc_reference/checkm_data
[2024-01-25 17:45:53,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:53,128] [INFO] Task started: CheckM
[2024-01-25 17:45:53,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000819545.1_ASM81954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000819545.1_ASM81954v1_genomic.fna/checkm_input GCF_000819545.1_ASM81954v1_genomic.fna/checkm_result
[2024-01-25 17:48:57,945] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:57,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-25 17:48:57,971] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:57,971] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:57,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000819545.1_ASM81954v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:57,972] [INFO] Task started: Blastn
[2024-01-25 17:48:57,972] [INFO] Running command: blastn -query GCF_000819545.1_ASM81954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc0715f0-ba49-439e-a156-d78952b436f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000819545.1_ASM81954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:00,056] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:00,059] [INFO] Selected 16 target genomes.
[2024-01-25 17:49:00,059] [INFO] Target genome list was writen to GCF_000819545.1_ASM81954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:00,077] [INFO] Task started: fastANI
[2024-01-25 17:49:00,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg973e0647-255b-4572-9fc2-ae0f2ff193a0/GCF_000819545.1_ASM81954v1_genomic.fna.gz --refList GCF_000819545.1_ASM81954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000819545.1_ASM81954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:34,969] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:34,979] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:34,979] [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_008704995.1	s__Streptomyces nodosus	99.9691	2562	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.42	97.72	0.96	0.87	5	conclusive
GCF_001417775.1	s__Streptomyces sp001417775	86.7486	1586	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866645.1	s__Streptomyces colonosanans	86.0831	1388	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905555.1	s__Streptomyces sp014905555	85.9226	1574	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920635.1	s__Streptomyces sp002920635	85.8332	1528	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507435.1	s__Streptomyces sp001507435	85.7199	1686	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.91	96.23	0.91	0.88	3	-
GCF_006540305.1	s__Streptomyces sp006540305	84.8759	1749	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803075.1	s__Streptomyces sp002803075	84.7696	1699	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	84.2493	1490	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650655.1	s__Streptomyces anandii	83.8817	1467	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650575.1	s__Streptomyces naganishii	83.8448	1491	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654675.1	s__Streptomyces spiralis	83.787	1572	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_014647875.1	s__Streptomyces brasiliensis	83.4731	1551	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017526105.1	s__Streptomyces cyanogenus	83.4456	1486	2571	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650035.1	s__Streptomyces lucensis	83.3719	1403	2571	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	82.8471	1536	2571	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 17:49:34,985] [INFO] GTDB search result was written to GCF_000819545.1_ASM81954v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:34,986] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:34,990] [INFO] DFAST_QC result json was written to GCF_000819545.1_ASM81954v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:34,991] [INFO] DFAST_QC completed!
[2024-01-25 17:49:34,991] [INFO] Total running time: 0h4m44s