[2024-01-25 19:42:05,390] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:05,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:05,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b2dd201-b7eb-4165-a1e1-197bd62c9a5a/dqc_reference
[2024-01-25 19:42:06,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:06,540] [INFO] Task started: Prodigal
[2024-01-25 19:42:06,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg64738f91-8527-4d39-b4d7-205ba7a3f879/GCF_014648375.1_ASM1464837v1_genomic.fna.gz | prodigal -d GCF_014648375.1_ASM1464837v1_genomic.fna/cds.fna -a GCF_014648375.1_ASM1464837v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:32,057] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:32,057] [INFO] Task started: HMMsearch
[2024-01-25 19:42:32,057] [INFO] Running command: hmmsearch --tblout GCF_014648375.1_ASM1464837v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b2dd201-b7eb-4165-a1e1-197bd62c9a5a/dqc_reference/reference_markers.hmm GCF_014648375.1_ASM1464837v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:32,397] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:32,398] [INFO] Found 6/6 markers.
[2024-01-25 19:42:32,469] [INFO] Query marker FASTA was written to GCF_014648375.1_ASM1464837v1_genomic.fna/markers.fasta
[2024-01-25 19:42:32,470] [INFO] Task started: Blastn
[2024-01-25 19:42:32,470] [INFO] Running command: blastn -query GCF_014648375.1_ASM1464837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2dd201-b7eb-4165-a1e1-197bd62c9a5a/dqc_reference/reference_markers.fasta -out GCF_014648375.1_ASM1464837v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:33,568] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:33,571] [INFO] Selected 12 target genomes.
[2024-01-25 19:42:33,571] [INFO] Target genome list was writen to GCF_014648375.1_ASM1464837v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:33,576] [INFO] Task started: fastANI
[2024-01-25 19:42:33,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg64738f91-8527-4d39-b4d7-205ba7a3f879/GCF_014648375.1_ASM1464837v1_genomic.fna.gz --refList GCF_014648375.1_ASM1464837v1_genomic.fna/target_genomes.txt --output GCF_014648375.1_ASM1464837v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:06,812] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:06,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b2dd201-b7eb-4165-a1e1-197bd62c9a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:06,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b2dd201-b7eb-4165-a1e1-197bd62c9a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:06,822] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:43:06,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:06,823] [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 ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	100.0	3334	3335	95	conclusive
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	99.9911	3262	3335	95	conclusive
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	90.0361	2630	3335	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	89.9805	2697	3335	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	85.8751	1969	3335	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	85.2825	2195	3335	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	82.6993	1871	3335	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	82.6634	1868	3335	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.2392	885	3335	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.0905	1241	3335	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.815	1042	3335	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.7288	1222	3335	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:06,824] [INFO] DFAST Taxonomy check result was written to GCF_014648375.1_ASM1464837v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:06,825] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:06,825] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:06,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b2dd201-b7eb-4165-a1e1-197bd62c9a5a/dqc_reference/checkm_data
[2024-01-25 19:43:06,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:06,918] [INFO] Task started: CheckM
[2024-01-25 19:43:06,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648375.1_ASM1464837v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648375.1_ASM1464837v1_genomic.fna/checkm_input GCF_014648375.1_ASM1464837v1_genomic.fna/checkm_result
[2024-01-25 19:44:55,680] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:55,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:55,750] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:55,750] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:55,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648375.1_ASM1464837v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:55,752] [INFO] Task started: Blastn
[2024-01-25 19:44:55,752] [INFO] Running command: blastn -query GCF_014648375.1_ASM1464837v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b2dd201-b7eb-4165-a1e1-197bd62c9a5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648375.1_ASM1464837v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:57,446] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:57,448] [INFO] Selected 12 target genomes.
[2024-01-25 19:44:57,448] [INFO] Target genome list was writen to GCF_014648375.1_ASM1464837v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:57,463] [INFO] Task started: fastANI
[2024-01-25 19:44:57,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg64738f91-8527-4d39-b4d7-205ba7a3f879/GCF_014648375.1_ASM1464837v1_genomic.fna.gz --refList GCF_014648375.1_ASM1464837v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648375.1_ASM1464837v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:33,510] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:33,519] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:33,519] [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_018324205.1	s__Actinoplanes ianthinogenes	99.9911	3262	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_014205225.1	s__Actinoplanes octamycinicus	89.9844	2696	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862395.1	s__Actinoplanes siamensis	86.0332	1895	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	85.869	1970	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_016862315.1	s__Actinoplanes palleronii	85.7664	2285	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_900188005.1	s__Actinoplanes regularis	85.5606	2094	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000715855.1	s__Actinoplanes liguriensis	85.3608	2252	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119315.1	s__Actinoplanes sp900119315	85.2971	2106	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_016862095.1	s__Actinoplanes cyaneus	85.2942	2193	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015704865.1	s__Actinoplanes sp015704865	82.9156	1930	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647795.1	s__Actinoplanes campanulatus	82.6157	1878	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_014205215.1	s__Actinoplanes lobatus	82.6055	1934	3335	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:33,520] [INFO] GTDB search result was written to GCF_014648375.1_ASM1464837v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:33,521] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:33,524] [INFO] DFAST_QC result json was written to GCF_014648375.1_ASM1464837v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:33,524] [INFO] DFAST_QC completed!
[2024-01-25 19:45:33,524] [INFO] Total running time: 0h3m28s