[2024-01-24 12:15:21,103] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:21,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:21,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg430b5723-2e48-4200-8c6e-7c0fc1273d87/dqc_reference
[2024-01-24 12:15:22,422] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,425] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,426] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c37a214-e5c5-4cf2-8370-70df60abf49d/GCF_003001815.1_ASM300181v1_genomic.fna.gz | prodigal -d GCF_003001815.1_ASM300181v1_genomic.fna/cds.fna -a GCF_003001815.1_ASM300181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:55,066] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:55,066] [INFO] Task started: HMMsearch
[2024-01-24 12:15:55,067] [INFO] Running command: hmmsearch --tblout GCF_003001815.1_ASM300181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg430b5723-2e48-4200-8c6e-7c0fc1273d87/dqc_reference/reference_markers.hmm GCF_003001815.1_ASM300181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:55,487] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:55,489] [INFO] Found 6/6 markers.
[2024-01-24 12:15:55,571] [INFO] Query marker FASTA was written to GCF_003001815.1_ASM300181v1_genomic.fna/markers.fasta
[2024-01-24 12:15:55,571] [INFO] Task started: Blastn
[2024-01-24 12:15:55,571] [INFO] Running command: blastn -query GCF_003001815.1_ASM300181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg430b5723-2e48-4200-8c6e-7c0fc1273d87/dqc_reference/reference_markers.fasta -out GCF_003001815.1_ASM300181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:56,814] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:56,817] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:56,818] [INFO] Target genome list was writen to GCF_003001815.1_ASM300181v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:56,823] [INFO] Task started: fastANI
[2024-01-24 12:15:56,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c37a214-e5c5-4cf2-8370-70df60abf49d/GCF_003001815.1_ASM300181v1_genomic.fna.gz --refList GCF_003001815.1_ASM300181v1_genomic.fna/target_genomes.txt --output GCF_003001815.1_ASM300181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:39,550] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:39,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg430b5723-2e48-4200-8c6e-7c0fc1273d87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:39,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg430b5723-2e48-4200-8c6e-7c0fc1273d87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:39,567] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:16:39,567] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:39,568] [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 italicus	strain=DSM 43146	GCA_003001815.1	113567	113567	type	True	100.0	3678	3681	95	conclusive
Actinoplanes italicus	strain=NBRC 13911	GCA_016862235.1	113567	113567	type	True	99.9712	3538	3681	95	conclusive
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	86.2388	2403	3681	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	86.193	2487	3681	95	below_threshold
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	86.1408	2454	3681	95	below_threshold
Actinoplanes capillaceus	strain=NBRC 16408	GCA_016862055.1	76756	76756	type	True	85.0094	2137	3681	95	below_threshold
Actinoplanes campanulatus	strain=JCM 3059	GCA_014647795.1	113559	113559	type	True	84.9909	2184	3681	95	below_threshold
Actinoplanes campanulatus	strain=NBRC 12511	GCA_016862035.1	113559	113559	type	True	84.8889	2209	3681	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	84.843	2166	3681	95	below_threshold
Actinoplanes utahensis	strain=NBRC 13244	GCA_016862455.1	1869	1869	type	True	84.7836	2136	3681	95	below_threshold
Actinoplanes derwentensis	strain=NBRC 14935	GCA_016862135.1	113562	113562	type	True	83.7593	2055	3681	95	below_threshold
Actinoplanes derwentensis	strain=DSM 43941	GCA_900104725.1	113562	113562	type	True	83.7174	2098	3681	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	81.8435	1862	3681	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.4065	1457	3681	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.3167	1168	3681	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	76.5331	714	3681	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	76.0884	725	3681	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:39,569] [INFO] DFAST Taxonomy check result was written to GCF_003001815.1_ASM300181v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:39,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:39,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:39,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg430b5723-2e48-4200-8c6e-7c0fc1273d87/dqc_reference/checkm_data
[2024-01-24 12:16:39,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:39,671] [INFO] Task started: CheckM
[2024-01-24 12:16:39,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003001815.1_ASM300181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003001815.1_ASM300181v1_genomic.fna/checkm_input GCF_003001815.1_ASM300181v1_genomic.fna/checkm_result
[2024-01-24 12:18:29,818] [INFO] Task succeeded: CheckM
[2024-01-24 12:18:29,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:18:29,848] [INFO] ===== Completeness check finished =====
[2024-01-24 12:18:29,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:18:29,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003001815.1_ASM300181v1_genomic.fna/markers.fasta)
[2024-01-24 12:18:29,849] [INFO] Task started: Blastn
[2024-01-24 12:18:29,850] [INFO] Running command: blastn -query GCF_003001815.1_ASM300181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg430b5723-2e48-4200-8c6e-7c0fc1273d87/dqc_reference/reference_markers_gtdb.fasta -out GCF_003001815.1_ASM300181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:18:31,675] [INFO] Task succeeded: Blastn
[2024-01-24 12:18:31,680] [INFO] Selected 14 target genomes.
[2024-01-24 12:18:31,680] [INFO] Target genome list was writen to GCF_003001815.1_ASM300181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:18:31,693] [INFO] Task started: fastANI
[2024-01-24 12:18:31,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c37a214-e5c5-4cf2-8370-70df60abf49d/GCF_003001815.1_ASM300181v1_genomic.fna.gz --refList GCF_003001815.1_ASM300181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003001815.1_ASM300181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:19:08,123] [INFO] Task succeeded: fastANI
[2024-01-24 12:19:08,138] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:19:08,138] [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_003001815.1	s__Actinoplanes italicus	100.0	3678	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003148685.1	s__Actinoplanes xinjiangensis	86.1964	2486	3681	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	86.1631	2450	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647795.1	s__Actinoplanes campanulatus	85.0035	2182	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	98.93	96.79	0.95	0.87	4	-
GCF_016862455.1	s__Actinoplanes utahensis	84.7702	2141	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016862075.1	s__Actinoplanes couchii	83.7954	2173	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104725.1	s__Actinoplanes derwentensis	83.6842	2106	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015704865.1	s__Actinoplanes sp015704865	82.8555	2069	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284295.1	s__Actinoplanes missouriensis	82.7923	1908	3681	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	82.726	1915	3681	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	82.3277	1712	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_016862095.1	s__Actinoplanes cyaneus	81.8323	1865	3681	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	81.7814	1698	3681	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003999975.1	s__Actinoplanes sp003999975	80.1226	1640	3681	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 12:19:08,140] [INFO] GTDB search result was written to GCF_003001815.1_ASM300181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:19:08,140] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:19:08,144] [INFO] DFAST_QC result json was written to GCF_003001815.1_ASM300181v1_genomic.fna/dqc_result.json
[2024-01-24 12:19:08,145] [INFO] DFAST_QC completed!
[2024-01-24 12:19:08,145] [INFO] Total running time: 0h3m47s