[2024-01-24 15:02:18,778] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg1acf06e2-87ba-4159-a339-af87b33fcd96/dqc_reference
[2024-01-24 15:02:20,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,834] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,834] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd7168fd-ba63-4030-a687-fa9f5475aa0b/GCF_014205335.1_ASM1420533v1_genomic.fna.gz | prodigal -d GCF_014205335.1_ASM1420533v1_genomic.fna/cds.fna -a GCF_014205335.1_ASM1420533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:49,486] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:49,486] [INFO] Task started: HMMsearch
[2024-01-24 15:02:49,486] [INFO] Running command: hmmsearch --tblout GCF_014205335.1_ASM1420533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1acf06e2-87ba-4159-a339-af87b33fcd96/dqc_reference/reference_markers.hmm GCF_014205335.1_ASM1420533v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:49,882] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:49,884] [INFO] Found 6/6 markers.
[2024-01-24 15:02:49,962] [INFO] Query marker FASTA was written to GCF_014205335.1_ASM1420533v1_genomic.fna/markers.fasta
[2024-01-24 15:02:49,962] [INFO] Task started: Blastn
[2024-01-24 15:02:49,963] [INFO] Running command: blastn -query GCF_014205335.1_ASM1420533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1acf06e2-87ba-4159-a339-af87b33fcd96/dqc_reference/reference_markers.fasta -out GCF_014205335.1_ASM1420533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:51,201] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:51,205] [INFO] Selected 11 target genomes.
[2024-01-24 15:02:51,205] [INFO] Target genome list was writen to GCF_014205335.1_ASM1420533v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:51,213] [INFO] Task started: fastANI
[2024-01-24 15:02:51,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd7168fd-ba63-4030-a687-fa9f5475aa0b/GCF_014205335.1_ASM1420533v1_genomic.fna.gz --refList GCF_014205335.1_ASM1420533v1_genomic.fna/target_genomes.txt --output GCF_014205335.1_ASM1420533v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:19,739] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:19,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1acf06e2-87ba-4159-a339-af87b33fcd96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:19,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1acf06e2-87ba-4159-a339-af87b33fcd96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:19,750] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:19,750] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:19,750] [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
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	100.0	3041	3042	95	conclusive
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	99.9681	2946	3042	95	conclusive
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	85.1467	1866	3042	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	85.103	1880	3042	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	84.9445	1845	3042	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	82.6761	1568	3042	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.6056	1584	3042	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.4128	1041	3042	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.4013	1180	3042	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.8981	1195	3042	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.8766	1008	3042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:19,752] [INFO] DFAST Taxonomy check result was written to GCF_014205335.1_ASM1420533v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:19,753] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:19,753] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:19,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1acf06e2-87ba-4159-a339-af87b33fcd96/dqc_reference/checkm_data
[2024-01-24 15:03:19,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:19,846] [INFO] Task started: CheckM
[2024-01-24 15:03:19,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205335.1_ASM1420533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205335.1_ASM1420533v1_genomic.fna/checkm_input GCF_014205335.1_ASM1420533v1_genomic.fna/checkm_result
[2024-01-24 15:05:00,342] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:00,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:00,371] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:00,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:00,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205335.1_ASM1420533v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:00,372] [INFO] Task started: Blastn
[2024-01-24 15:05:00,373] [INFO] Running command: blastn -query GCF_014205335.1_ASM1420533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1acf06e2-87ba-4159-a339-af87b33fcd96/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205335.1_ASM1420533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:02,268] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:02,271] [INFO] Selected 10 target genomes.
[2024-01-24 15:05:02,271] [INFO] Target genome list was writen to GCF_014205335.1_ASM1420533v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:02,279] [INFO] Task started: fastANI
[2024-01-24 15:05:02,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd7168fd-ba63-4030-a687-fa9f5475aa0b/GCF_014205335.1_ASM1420533v1_genomic.fna.gz --refList GCF_014205335.1_ASM1420533v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205335.1_ASM1420533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:27,389] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:27,402] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:27,402] [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_014205335.1	s__Actinoplanes digitatis	100.0	3041	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016862275.1	s__Actinoplanes nipponensis	85.1278	1874	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000494755.1	s__Actinoplanes friuliensis	85.0989	1872	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332655.1	s__Actinoplanes auranticolor	84.8969	1854	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	83.0333	1703	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_014648355.1	s__Actinoplanes azureus	82.8694	1538	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464385.1	s__Actinoplanes sp016464385	82.831	1728	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	81.7123	1417	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	81.6292	1580	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553785.1	s__Actinoplanes sp001553785	81.4643	1379	3042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:27,404] [INFO] GTDB search result was written to GCF_014205335.1_ASM1420533v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:27,405] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:27,408] [INFO] DFAST_QC result json was written to GCF_014205335.1_ASM1420533v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:27,408] [INFO] DFAST_QC completed!
[2024-01-24 15:05:27,408] [INFO] Total running time: 0h3m9s