[2024-01-24 11:51:10,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,301] [INFO] DQC Reference Directory: /var/lib/cwl/stgf71689ab-67ef-4b65-8b9e-e87372566900/dqc_reference
[2024-01-24 11:51:11,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,642] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgd316c805-f0dc-4b7b-a645-3b267d955489/GCF_016862395.1_ASM1686239v1_genomic.fna.gz | prodigal -d GCF_016862395.1_ASM1686239v1_genomic.fna/cds.fna -a GCF_016862395.1_ASM1686239v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:33,757] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:33,758] [INFO] Task started: HMMsearch
[2024-01-24 11:51:33,758] [INFO] Running command: hmmsearch --tblout GCF_016862395.1_ASM1686239v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf71689ab-67ef-4b65-8b9e-e87372566900/dqc_reference/reference_markers.hmm GCF_016862395.1_ASM1686239v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:34,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:34,170] [INFO] Found 6/6 markers.
[2024-01-24 11:51:34,228] [INFO] Query marker FASTA was written to GCF_016862395.1_ASM1686239v1_genomic.fna/markers.fasta
[2024-01-24 11:51:34,229] [INFO] Task started: Blastn
[2024-01-24 11:51:34,229] [INFO] Running command: blastn -query GCF_016862395.1_ASM1686239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf71689ab-67ef-4b65-8b9e-e87372566900/dqc_reference/reference_markers.fasta -out GCF_016862395.1_ASM1686239v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:35,430] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:35,434] [INFO] Selected 18 target genomes.
[2024-01-24 11:51:35,434] [INFO] Target genome list was writen to GCF_016862395.1_ASM1686239v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:35,441] [INFO] Task started: fastANI
[2024-01-24 11:51:35,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgd316c805-f0dc-4b7b-a645-3b267d955489/GCF_016862395.1_ASM1686239v1_genomic.fna.gz --refList GCF_016862395.1_ASM1686239v1_genomic.fna/target_genomes.txt --output GCF_016862395.1_ASM1686239v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:13,651] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:13,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf71689ab-67ef-4b65-8b9e-e87372566900/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:13,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf71689ab-67ef-4b65-8b9e-e87372566900/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:13,666] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:13,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:13,666] [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 octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	86.4797	1841	2666	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	86.3979	1915	2666	95	below_threshold
Actinoplanes regularis	strain=NBRC 12514	GCA_016862355.1	52697	52697	type	True	86.3019	1796	2666	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	86.2916	1959	2666	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	86.2642	1788	2666	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	86.2503	1763	2666	95	below_threshold
Actinoplanes regularis	strain=DSM 43151	GCA_900188005.1	52697	52697	type	True	86.2422	1818	2666	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	86.1898	1821	2666	95	below_threshold
Actinoplanes ianthinogenes	strain=JCM 3249	GCA_014648375.1	122358	122358	type	True	86.1366	1892	2666	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	86.0443	1870	2666	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	82.7513	1574	2666	95	below_threshold
Actinoplanes philippinensis	strain=NBRC 13878	GCA_016862335.1	35752	35752	type	True	82.7183	1631	2666	95	below_threshold
Actinoplanes philippinensis	strain=DSM 43019	GCA_900113015.1	35752	35752	type	True	82.6796	1648	2666	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	82.4676	1634	2666	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.5387	791	2666	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.2614	1101	2666	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.2435	892	2666	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.692	886	2666	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:13,668] [INFO] DFAST Taxonomy check result was written to GCF_016862395.1_ASM1686239v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:13,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:13,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:13,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf71689ab-67ef-4b65-8b9e-e87372566900/dqc_reference/checkm_data
[2024-01-24 11:52:13,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:13,743] [INFO] Task started: CheckM
[2024-01-24 11:52:13,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862395.1_ASM1686239v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862395.1_ASM1686239v1_genomic.fna/checkm_input GCF_016862395.1_ASM1686239v1_genomic.fna/checkm_result
[2024-01-24 11:53:24,760] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:24,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:24,788] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:24,789] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:24,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862395.1_ASM1686239v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:24,789] [INFO] Task started: Blastn
[2024-01-24 11:53:24,789] [INFO] Running command: blastn -query GCF_016862395.1_ASM1686239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf71689ab-67ef-4b65-8b9e-e87372566900/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862395.1_ASM1686239v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:26,590] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:26,593] [INFO] Selected 11 target genomes.
[2024-01-24 11:53:26,593] [INFO] Target genome list was writen to GCF_016862395.1_ASM1686239v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:26,601] [INFO] Task started: fastANI
[2024-01-24 11:53:26,601] [INFO] Running command: fastANI --query /var/lib/cwl/stgd316c805-f0dc-4b7b-a645-3b267d955489/GCF_016862395.1_ASM1686239v1_genomic.fna.gz --refList GCF_016862395.1_ASM1686239v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862395.1_ASM1686239v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:53,301] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:53,310] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:53,310] [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_016862395.1	s__Actinoplanes siamensis	100.0	2662	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000715855.1	s__Actinoplanes liguriensis	86.3979	1915	2666	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	86.36	1922	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862095.1	s__Actinoplanes cyaneus	86.2911	1959	2666	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	86.2142	1817	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_900188005.1	s__Actinoplanes regularis	86.1955	1826	2666	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	86.0831	1863	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900119315.1	s__Actinoplanes sp900119315	85.5469	1806	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	3	-
GCF_016862315.1	s__Actinoplanes palleronii	85.4321	1864	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_900113015.1	s__Actinoplanes philippinensis	82.6579	1653	2666	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	82.4177	1644	2666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:53,312] [INFO] GTDB search result was written to GCF_016862395.1_ASM1686239v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:53,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:53,315] [INFO] DFAST_QC result json was written to GCF_016862395.1_ASM1686239v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:53,316] [INFO] DFAST_QC completed!
[2024-01-24 11:53:53,316] [INFO] Total running time: 0h2m43s