[2024-01-24 10:47:06,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg90c7e13c-5004-4d12-8eca-4ccefe19b96a/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,102] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg436ffce3-cf8f-49d8-8bdd-20a808319f3d/GCF_016862375.1_ASM1686237v1_genomic.fna.gz | prodigal -d GCF_016862375.1_ASM1686237v1_genomic.fna/cds.fna -a GCF_016862375.1_ASM1686237v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:43,735] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:43,735] [INFO] Task started: HMMsearch
[2024-01-24 10:47:43,735] [INFO] Running command: hmmsearch --tblout GCF_016862375.1_ASM1686237v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90c7e13c-5004-4d12-8eca-4ccefe19b96a/dqc_reference/reference_markers.hmm GCF_016862375.1_ASM1686237v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:44,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:44,257] [INFO] Found 6/6 markers.
[2024-01-24 10:47:44,339] [INFO] Query marker FASTA was written to GCF_016862375.1_ASM1686237v1_genomic.fna/markers.fasta
[2024-01-24 10:47:44,339] [INFO] Task started: Blastn
[2024-01-24 10:47:44,340] [INFO] Running command: blastn -query GCF_016862375.1_ASM1686237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90c7e13c-5004-4d12-8eca-4ccefe19b96a/dqc_reference/reference_markers.fasta -out GCF_016862375.1_ASM1686237v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:45,579] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:45,582] [INFO] Selected 26 target genomes.
[2024-01-24 10:47:45,583] [INFO] Target genome list was writen to GCF_016862375.1_ASM1686237v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:45,599] [INFO] Task started: fastANI
[2024-01-24 10:47:45,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg436ffce3-cf8f-49d8-8bdd-20a808319f3d/GCF_016862375.1_ASM1686237v1_genomic.fna.gz --refList GCF_016862375.1_ASM1686237v1_genomic.fna/target_genomes.txt --output GCF_016862375.1_ASM1686237v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:44,621] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:44,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90c7e13c-5004-4d12-8eca-4ccefe19b96a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:44,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90c7e13c-5004-4d12-8eca-4ccefe19b96a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:44,640] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:44,640] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:44,641] [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 rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	100.0	3531	3544	95	conclusive
Actinoplanes durhamensis	strain=NBRC 14914	GCA_016862175.1	113563	113563	type	True	83.0996	1952	3544	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	83.0171	1967	3544	95	below_threshold
Actinoplanes toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	82.9671	1947	3544	95	below_threshold
Actinoplanes globisporus	strain=DSM 43857	GCA_000379645.1	113565	113565	type	True	82.8594	1944	3544	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	82.7091	1918	3544	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	81.9774	1791	3544	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	81.7407	1793	3544	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	81.6682	1772	3544	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	81.6476	1849	3544	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	81.1356	1544	3544	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	81.1279	1497	3544	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	81.0803	1789	3544	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	81.0558	1749	3544	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	81.0519	1559	3544	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.8665	1619	3544	95	below_threshold
Actinoplanes lobatus	strain=NBRC 12513	GCA_016862255.1	113568	113568	type	True	80.7116	1684	3544	95	below_threshold
Actinoplanes lobatus	strain=JCM 3061	GCA_014647815.1	113568	113568	type	True	80.687	1704	3544	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.9533	846	3544	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.8739	1197	3544	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.8228	1021	3544	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	78.7983	1134	3544	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	78.7196	1117	3544	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	78.6803	1151	3544	95	below_threshold
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	78.5734	1124	3544	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.338	751	3544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:44,642] [INFO] DFAST Taxonomy check result was written to GCF_016862375.1_ASM1686237v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:44,643] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:44,643] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:44,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90c7e13c-5004-4d12-8eca-4ccefe19b96a/dqc_reference/checkm_data
[2024-01-24 10:48:44,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:44,738] [INFO] Task started: CheckM
[2024-01-24 10:48:44,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862375.1_ASM1686237v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862375.1_ASM1686237v1_genomic.fna/checkm_input GCF_016862375.1_ASM1686237v1_genomic.fna/checkm_result
[2024-01-24 10:50:15,234] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:15,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:15,254] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:15,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:15,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862375.1_ASM1686237v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:15,255] [INFO] Task started: Blastn
[2024-01-24 10:50:15,255] [INFO] Running command: blastn -query GCF_016862375.1_ASM1686237v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90c7e13c-5004-4d12-8eca-4ccefe19b96a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862375.1_ASM1686237v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:17,135] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:17,139] [INFO] Selected 23 target genomes.
[2024-01-24 10:50:17,140] [INFO] Target genome list was writen to GCF_016862375.1_ASM1686237v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:17,153] [INFO] Task started: fastANI
[2024-01-24 10:50:17,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg436ffce3-cf8f-49d8-8bdd-20a808319f3d/GCF_016862375.1_ASM1686237v1_genomic.fna.gz --refList GCF_016862375.1_ASM1686237v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862375.1_ASM1686237v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:11,456] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:11,473] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:11,473] [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_016862375.1	s__Actinoplanes rishiriensis	100.0	3531	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862175.1	s__Actinoplanes durhamensis	83.0991	1952	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862435.1	s__Actinoplanes tereljensis	82.9792	1974	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332695.1	s__Actinoplanes toevensis	82.9578	1949	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379645.1	s__Actinoplanes globisporus	82.8099	1955	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721705.1	s__Actinoplanes subtropicus	82.7771	1901	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862195.1	s__Actinoplanes ferrugineus	82.398	1715	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	81.9874	1790	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018829635.1	s__Actinoplanes bogorensis	81.7498	1790	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	81.6649	1844	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933445.1	s__Actinoplanes sp012933445	81.4096	1595	3544	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	81.1609	1536	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_018324205.1	s__Actinoplanes ianthinogenes	81.0497	1686	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014205225.1	s__Actinoplanes octamycinicus	81.0455	1797	3544	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	80.838	1667	3544	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	80.7496	1704	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0428	99.99	99.99	1.00	1.00	3	-
GCF_016862315.1	s__Actinoplanes palleronii	80.6168	1781	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	80.4454	1550	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_000389965.1	s__Actinoplanes sp000389965	80.1877	1529	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091515.1	s__Micromonospora purpureochromogenes	78.7287	1115	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.27	95.68	0.85	0.81	4	-
GCF_004217535.1	s__Micromonospora sp004217535	78.6051	1057	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158815.1	s__Micromonospora sp000158815	78.5983	1095	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.02	97.02	0.80	0.80	2	-
GCF_017614955.1	s__Micromonospora echinofusca_A	78.2656	982	3544	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 10:51:11,475] [INFO] GTDB search result was written to GCF_016862375.1_ASM1686237v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:11,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:11,480] [INFO] DFAST_QC result json was written to GCF_016862375.1_ASM1686237v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:11,480] [INFO] DFAST_QC completed!
[2024-01-24 10:51:11,480] [INFO] Total running time: 0h4m5s