[2024-01-24 15:02:17,231] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:17,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:17,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c18018e-046d-4b7a-b3e1-eafadea306e4/dqc_reference
[2024-01-24 15:02:18,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:18,621] [INFO] Task started: Prodigal
[2024-01-24 15:02:18,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg42f3fea1-db26-428e-972f-11551cb7e6b7/GCF_016862455.1_ASM1686245v1_genomic.fna.gz | prodigal -d GCF_016862455.1_ASM1686245v1_genomic.fna/cds.fna -a GCF_016862455.1_ASM1686245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:47,317] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:47,317] [INFO] Task started: HMMsearch
[2024-01-24 15:02:47,317] [INFO] Running command: hmmsearch --tblout GCF_016862455.1_ASM1686245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c18018e-046d-4b7a-b3e1-eafadea306e4/dqc_reference/reference_markers.hmm GCF_016862455.1_ASM1686245v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:47,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:47,741] [INFO] Found 6/6 markers.
[2024-01-24 15:02:47,823] [INFO] Query marker FASTA was written to GCF_016862455.1_ASM1686245v1_genomic.fna/markers.fasta
[2024-01-24 15:02:47,824] [INFO] Task started: Blastn
[2024-01-24 15:02:47,824] [INFO] Running command: blastn -query GCF_016862455.1_ASM1686245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c18018e-046d-4b7a-b3e1-eafadea306e4/dqc_reference/reference_markers.fasta -out GCF_016862455.1_ASM1686245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:49,109] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:49,113] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:49,113] [INFO] Target genome list was writen to GCF_016862455.1_ASM1686245v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:49,122] [INFO] Task started: fastANI
[2024-01-24 15:02:49,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg42f3fea1-db26-428e-972f-11551cb7e6b7/GCF_016862455.1_ASM1686245v1_genomic.fna.gz --refList GCF_016862455.1_ASM1686245v1_genomic.fna/target_genomes.txt --output GCF_016862455.1_ASM1686245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:29,782] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:29,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c18018e-046d-4b7a-b3e1-eafadea306e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:29,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c18018e-046d-4b7a-b3e1-eafadea306e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:29,795] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:29,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:29,795] [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 utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	100.0	3050	3056	95	conclusive
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	85.1265	1958	3056	95	below_threshold
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	85.1107	1973	3056	95	below_threshold
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	85.081	2031	3056	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	85.0544	1999	3056	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	85.0347	1958	3056	95	below_threshold
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	85.0275	1981	3056	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	85.0272	1997	3056	95	below_threshold
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	84.9717	2077	3056	95	below_threshold
Actinoplanes lobatus	strain=DSM 43150	GCA_014205215.1	113568	113568	type	True	84.9409	2006	3056	95	below_threshold
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	84.9111	2021	3056	95	below_threshold
Actinoplanes italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	84.8373	2120	3056	95	below_threshold
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	84.8202	2100	3056	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.8458	1102	3056	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8357	943	3056	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.4206	939	3056	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.3452	1081	3056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:29,797] [INFO] DFAST Taxonomy check result was written to GCF_016862455.1_ASM1686245v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:29,798] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:29,798] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:29,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c18018e-046d-4b7a-b3e1-eafadea306e4/dqc_reference/checkm_data
[2024-01-24 15:03:29,800] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:29,917] [INFO] Task started: CheckM
[2024-01-24 15:03:29,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862455.1_ASM1686245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862455.1_ASM1686245v1_genomic.fna/checkm_input GCF_016862455.1_ASM1686245v1_genomic.fna/checkm_result
[2024-01-24 15:05:00,633] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:00,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:00,664] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:00,665] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:00,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862455.1_ASM1686245v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:00,666] [INFO] Task started: Blastn
[2024-01-24 15:05:00,666] [INFO] Running command: blastn -query GCF_016862455.1_ASM1686245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c18018e-046d-4b7a-b3e1-eafadea306e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862455.1_ASM1686245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:02,706] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:02,710] [INFO] Selected 10 target genomes.
[2024-01-24 15:05:02,711] [INFO] Target genome list was writen to GCF_016862455.1_ASM1686245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:02,718] [INFO] Task started: fastANI
[2024-01-24 15:05:02,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg42f3fea1-db26-428e-972f-11551cb7e6b7/GCF_016862455.1_ASM1686245v1_genomic.fna.gz --refList GCF_016862455.1_ASM1686245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862455.1_ASM1686245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:30,385] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:30,396] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:30,396] [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_016862455.1	s__Actinoplanes utahensis	100.0	3050	3056	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_017592555.1	s__Actinoplanes sp017592555	85.0696	1995	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	85.0604	2148	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	84.9986	2074	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014205215.1	s__Actinoplanes lobatus	84.934	2007	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_014647795.1	s__Actinoplanes campanulatus	84.9134	2021	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_003001815.1	s__Actinoplanes italicus	84.7964	2127	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016862075.1	s__Actinoplanes couchii	84.3481	1987	3056	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	83.3863	1902	3056	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	82.2423	1658	3056	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:30,398] [INFO] GTDB search result was written to GCF_016862455.1_ASM1686245v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:30,399] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:30,404] [INFO] DFAST_QC result json was written to GCF_016862455.1_ASM1686245v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:30,405] [INFO] DFAST_QC completed!
[2024-01-24 15:05:30,405] [INFO] Total running time: 0h3m13s