[2024-01-24 13:25:47,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,537] [INFO] DQC Reference Directory: /var/lib/cwl/stg58e83a78-e390-4134-9d84-7da8b2af480e/dqc_reference
[2024-01-24 13:25:48,926] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:48,927] [INFO] Task started: Prodigal
[2024-01-24 13:25:48,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fb6701c-5dca-4d42-bc54-c90289e04c49/GCF_008704995.1_ASM870499v1_genomic.fna.gz | prodigal -d GCF_008704995.1_ASM870499v1_genomic.fna/cds.fna -a GCF_008704995.1_ASM870499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:15,595] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:15,595] [INFO] Task started: HMMsearch
[2024-01-24 13:26:15,595] [INFO] Running command: hmmsearch --tblout GCF_008704995.1_ASM870499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58e83a78-e390-4134-9d84-7da8b2af480e/dqc_reference/reference_markers.hmm GCF_008704995.1_ASM870499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:15,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:15,930] [INFO] Found 6/6 markers.
[2024-01-24 13:26:15,996] [INFO] Query marker FASTA was written to GCF_008704995.1_ASM870499v1_genomic.fna/markers.fasta
[2024-01-24 13:26:15,997] [INFO] Task started: Blastn
[2024-01-24 13:26:15,997] [INFO] Running command: blastn -query GCF_008704995.1_ASM870499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58e83a78-e390-4134-9d84-7da8b2af480e/dqc_reference/reference_markers.fasta -out GCF_008704995.1_ASM870499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:17,305] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:17,311] [INFO] Selected 15 target genomes.
[2024-01-24 13:26:17,311] [INFO] Target genome list was writen to GCF_008704995.1_ASM870499v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:17,325] [INFO] Task started: fastANI
[2024-01-24 13:26:17,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fb6701c-5dca-4d42-bc54-c90289e04c49/GCF_008704995.1_ASM870499v1_genomic.fna.gz --refList GCF_008704995.1_ASM870499v1_genomic.fna/target_genomes.txt --output GCF_008704995.1_ASM870499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:47,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:47,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58e83a78-e390-4134-9d84-7da8b2af480e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:47,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58e83a78-e390-4134-9d84-7da8b2af480e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:47,310] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:26:47,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:47,310] [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_008704995.1	40318	40318	type	True	100.0	2588	2590	95	conclusive
Streptomyces nodosus	strain=DSM 40109	GCA_014205035.1	40318	40318	type	True	99.9985	2589	2590	95	conclusive
Streptomyces nodosus	strain=ATCC 14899	GCA_000819545.1	40318	40318	type	True	99.9716	2560	2590	95	conclusive
Streptomyces colonosanans	strain=MUSC 93	GCA_001866645.1	1428652	1428652	type	True	86.086	1396	2590	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	85.9853	1533	2590	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	84.202	1522	2590	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	83.8773	1437	2590	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	83.8356	1489	2590	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	83.8327	1496	2590	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	83.6478	1626	2590	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	83.4827	1570	2590	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	83.3225	1492	2590	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.2997	1399	2590	95	below_threshold
Streptomyces achromogenes subsp. achromogenes	strain=NRRL B-2120	GCA_000720835.1	67256	67255	type	True	83.2916	1462	2590	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.1067	1561	2590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:47,311] [INFO] DFAST Taxonomy check result was written to GCF_008704995.1_ASM870499v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:47,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:47,312] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:47,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58e83a78-e390-4134-9d84-7da8b2af480e/dqc_reference/checkm_data
[2024-01-24 13:26:47,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:47,383] [INFO] Task started: CheckM
[2024-01-24 13:26:47,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704995.1_ASM870499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704995.1_ASM870499v1_genomic.fna/checkm_input GCF_008704995.1_ASM870499v1_genomic.fna/checkm_result
[2024-01-24 13:29:22,635] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:22,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:29:22,658] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:22,658] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:22,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704995.1_ASM870499v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:22,659] [INFO] Task started: Blastn
[2024-01-24 13:29:22,659] [INFO] Running command: blastn -query GCF_008704995.1_ASM870499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58e83a78-e390-4134-9d84-7da8b2af480e/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704995.1_ASM870499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:24,722] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:24,725] [INFO] Selected 15 target genomes.
[2024-01-24 13:29:24,725] [INFO] Target genome list was writen to GCF_008704995.1_ASM870499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:24,746] [INFO] Task started: fastANI
[2024-01-24 13:29:24,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fb6701c-5dca-4d42-bc54-c90289e04c49/GCF_008704995.1_ASM870499v1_genomic.fna.gz --refList GCF_008704995.1_ASM870499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704995.1_ASM870499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:55,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:55,046] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:55,046] [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	100.0	2588	2590	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	86.647	1618	2590	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	86.0374	1403	2590	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	86.0182	1588	2590	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	85.9529	1536	2590	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	85.675	1711	2590	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	84.8436	1740	2590	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	84.8053	1696	2590	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	84.2215	1517	2590	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	83.8671	1486	2590	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	83.806	1501	2590	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	83.6475	1626	2590	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	83.5101	1565	2590	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	83.3539	1415	2590	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	83.0357	1501	2590	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 13:29:55,048] [INFO] GTDB search result was written to GCF_008704995.1_ASM870499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:55,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:55,052] [INFO] DFAST_QC result json was written to GCF_008704995.1_ASM870499v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:55,052] [INFO] DFAST_QC completed!
[2024-01-24 13:29:55,052] [INFO] Total running time: 0h4m8s