[2024-01-24 12:22:48,437] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,439] [INFO] DQC Reference Directory: /var/lib/cwl/stgd80642e6-b6dd-4abc-b073-97bdc150c063/dqc_reference
[2024-01-24 12:22:49,851] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,852] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,852] [INFO] Running command: gunzip -c /var/lib/cwl/stge7b6b846-b1fb-4d6f-908c-59d39989a2f7/GCF_014647795.1_ASM1464779v1_genomic.fna.gz | prodigal -d GCF_014647795.1_ASM1464779v1_genomic.fna/cds.fna -a GCF_014647795.1_ASM1464779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:18,165] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:18,166] [INFO] Task started: HMMsearch
[2024-01-24 12:23:18,166] [INFO] Running command: hmmsearch --tblout GCF_014647795.1_ASM1464779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd80642e6-b6dd-4abc-b073-97bdc150c063/dqc_reference/reference_markers.hmm GCF_014647795.1_ASM1464779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:18,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:18,595] [INFO] Found 6/6 markers.
[2024-01-24 12:23:18,682] [INFO] Query marker FASTA was written to GCF_014647795.1_ASM1464779v1_genomic.fna/markers.fasta
[2024-01-24 12:23:18,683] [INFO] Task started: Blastn
[2024-01-24 12:23:18,683] [INFO] Running command: blastn -query GCF_014647795.1_ASM1464779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd80642e6-b6dd-4abc-b073-97bdc150c063/dqc_reference/reference_markers.fasta -out GCF_014647795.1_ASM1464779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:19,901] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:19,905] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:19,906] [INFO] Target genome list was writen to GCF_014647795.1_ASM1464779v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:19,919] [INFO] Task started: fastANI
[2024-01-24 12:23:19,920] [INFO] Running command: fastANI --query /var/lib/cwl/stge7b6b846-b1fb-4d6f-908c-59d39989a2f7/GCF_014647795.1_ASM1464779v1_genomic.fna.gz --refList GCF_014647795.1_ASM1464779v1_genomic.fna/target_genomes.txt --output GCF_014647795.1_ASM1464779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:56,529] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:56,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd80642e6-b6dd-4abc-b073-97bdc150c063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:56,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd80642e6-b6dd-4abc-b073-97bdc150c063/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:56,543] [INFO] Found 16 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 12:23:56,543] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:23:56,544] [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 campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	100.0	3279	3282	95	inconclusive
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	99.9796	3210	3282	95	inconclusive
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	96.7054	2728	3282	95	inconclusive
Actinoplanes hulinensis	strain=NEAU-M9	GCA_019429605.1	1144547	1144547	type	True	96.3033	2725	3282	95	inconclusive
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	95.0604	2766	3282	95	inconclusive
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	95.0558	2695	3282	95	inconclusive
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	93.9095	2692	3282	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	80.6576	1500	3282	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	80.5857	1547	3282	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	79.8461	1423	3282	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.0519	940	3282	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.7615	1136	3282	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	77.9062	1124	3282	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.4759	914	3282	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.1104	1201	3282	95	below_threshold
Stackebrandtia albiflava	strain=DSM 45044	GCA_007994225.1	406432	406432	type	True	76.3855	489	3282	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:56,545] [INFO] DFAST Taxonomy check result was written to GCF_014647795.1_ASM1464779v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:56,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:56,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:56,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd80642e6-b6dd-4abc-b073-97bdc150c063/dqc_reference/checkm_data
[2024-01-24 12:23:56,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:56,637] [INFO] Task started: CheckM
[2024-01-24 12:23:56,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647795.1_ASM1464779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647795.1_ASM1464779v1_genomic.fna/checkm_input GCF_014647795.1_ASM1464779v1_genomic.fna/checkm_result
[2024-01-24 12:25:29,610] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:29,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:29,639] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:29,639] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:29,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647795.1_ASM1464779v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:29,640] [INFO] Task started: Blastn
[2024-01-24 12:25:29,640] [INFO] Running command: blastn -query GCF_014647795.1_ASM1464779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd80642e6-b6dd-4abc-b073-97bdc150c063/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647795.1_ASM1464779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:31,514] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:31,518] [INFO] Selected 15 target genomes.
[2024-01-24 12:25:31,519] [INFO] Target genome list was writen to GCF_014647795.1_ASM1464779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:31,530] [INFO] Task started: fastANI
[2024-01-24 12:25:31,530] [INFO] Running command: fastANI --query /var/lib/cwl/stge7b6b846-b1fb-4d6f-908c-59d39989a2f7/GCF_014647795.1_ASM1464779v1_genomic.fna.gz --refList GCF_014647795.1_ASM1464779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647795.1_ASM1464779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:09,413] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:09,427] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:09,428] [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_014647795.1	s__Actinoplanes campanulatus	100.0	3279	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	conclusive
GCF_014205215.1	s__Actinoplanes lobatus	95.0126	2788	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_017592555.1	s__Actinoplanes sp017592555	93.9145	2692	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862455.1	s__Actinoplanes utahensis	85.06	1997	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	85.0035	2116	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	85.002	2142	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900104725.1	s__Actinoplanes derwentensis	83.9548	1954	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000284295.1	s__Actinoplanes missouriensis	83.3297	1826	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001265.1	s__Actinoplanes sp004001265	83.0605	1839	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205225.1	s__Actinoplanes octamycinicus	82.905	1907	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	82.7403	1858	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862095.1	s__Actinoplanes cyaneus	82.1343	1743	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	80.3979	1505	3282	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	79.8494	1421	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	79.4702	848	3282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:26:09,432] [INFO] GTDB search result was written to GCF_014647795.1_ASM1464779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:09,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:09,436] [INFO] DFAST_QC result json was written to GCF_014647795.1_ASM1464779v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:09,436] [INFO] DFAST_QC completed!
[2024-01-24 12:26:09,436] [INFO] Total running time: 0h3m21s