[2024-01-25 19:08:36,034] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:36,036] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:36,036] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0345b5b-4f61-45a0-ad6a-98cdce4ac011/dqc_reference
[2024-01-25 19:08:37,210] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:37,210] [INFO] Task started: Prodigal
[2024-01-25 19:08:37,211] [INFO] Running command: gunzip -c /var/lib/cwl/stge89ede67-ad0a-4d45-bddd-91bbcdadbec1/GCF_000721705.1_ASM72170v1_genomic.fna.gz | prodigal -d GCF_000721705.1_ASM72170v1_genomic.fna/cds.fna -a GCF_000721705.1_ASM72170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:05,290] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:05,290] [INFO] Task started: HMMsearch
[2024-01-25 19:09:05,291] [INFO] Running command: hmmsearch --tblout GCF_000721705.1_ASM72170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0345b5b-4f61-45a0-ad6a-98cdce4ac011/dqc_reference/reference_markers.hmm GCF_000721705.1_ASM72170v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:05,770] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:05,771] [INFO] Found 6/6 markers.
[2024-01-25 19:09:05,863] [INFO] Query marker FASTA was written to GCF_000721705.1_ASM72170v1_genomic.fna/markers.fasta
[2024-01-25 19:09:05,863] [INFO] Task started: Blastn
[2024-01-25 19:09:05,864] [INFO] Running command: blastn -query GCF_000721705.1_ASM72170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0345b5b-4f61-45a0-ad6a-98cdce4ac011/dqc_reference/reference_markers.fasta -out GCF_000721705.1_ASM72170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:07,190] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:07,193] [INFO] Selected 26 target genomes.
[2024-01-25 19:09:07,194] [INFO] Target genome list was writen to GCF_000721705.1_ASM72170v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:07,205] [INFO] Task started: fastANI
[2024-01-25 19:09:07,205] [INFO] Running command: fastANI --query /var/lib/cwl/stge89ede67-ad0a-4d45-bddd-91bbcdadbec1/GCF_000721705.1_ASM72170v1_genomic.fna.gz --refList GCF_000721705.1_ASM72170v1_genomic.fna/target_genomes.txt --output GCF_000721705.1_ASM72170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:05,025] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:05,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0345b5b-4f61-45a0-ad6a-98cdce4ac011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:05,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0345b5b-4f61-45a0-ad6a-98cdce4ac011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:05,047] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:05,048] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:05,048] [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 subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	100.0	3659	3674	95	conclusive
Actinoplanes globisporus	strain=DSM 43857	GCA_000379645.1	113565	113565	type	True	86.208	2351	3674	95	below_threshold
Actinoplanes durhamensis	strain=NBRC 14914	GCA_016862175.1	113563	113563	type	True	83.7457	2075	3674	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	83.5784	2065	3674	95	below_threshold
Actinoplanes toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	83.5446	2042	3674	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	82.7752	1849	3674	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	81.9704	1827	3674	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	81.8548	1827	3674	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	81.2513	1806	3674	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	81.2322	1760	3674	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	81.2008	1525	3674	95	below_threshold
Actinoplanes teichomyceticus	strain=DSM 43866	GCA_007829915.1	1867	1867	type	True	81.1568	1571	3674	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	81.1534	1581	3674	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.5212	1629	3674	95	below_threshold
Actinoplanes derwentensis	strain=NBRC 14935	GCA_016862135.1	113562	113562	type	True	79.911	1500	3674	95	below_threshold
Actinoplanes derwentensis	strain=DSM 43941	GCA_900104725.1	113562	113562	type	True	79.9052	1510	3674	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.8584	1206	3674	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	78.7969	1223	3674	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	78.582	1104	3674	95	below_threshold
Micromonospora rifamycinica	strain=DSM 44983	GCA_900090265.1	291594	291594	type	True	78.5215	1127	3674	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.509	1177	3674	95	below_threshold
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	78.4745	1141	3674	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	78.42	1003	3674	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.2173	786	3674	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	76.129	562	3674	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	75.9584	1034	3674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:05,055] [INFO] DFAST Taxonomy check result was written to GCF_000721705.1_ASM72170v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:05,056] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:05,056] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:05,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0345b5b-4f61-45a0-ad6a-98cdce4ac011/dqc_reference/checkm_data
[2024-01-25 19:10:05,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:05,160] [INFO] Task started: CheckM
[2024-01-25 19:10:05,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000721705.1_ASM72170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000721705.1_ASM72170v1_genomic.fna/checkm_input GCF_000721705.1_ASM72170v1_genomic.fna/checkm_result
[2024-01-25 19:11:54,542] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:54,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:54,571] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:54,571] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:54,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000721705.1_ASM72170v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:54,572] [INFO] Task started: Blastn
[2024-01-25 19:11:54,572] [INFO] Running command: blastn -query GCF_000721705.1_ASM72170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0345b5b-4f61-45a0-ad6a-98cdce4ac011/dqc_reference/reference_markers_gtdb.fasta -out GCF_000721705.1_ASM72170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:56,520] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:56,522] [INFO] Selected 19 target genomes.
[2024-01-25 19:11:56,523] [INFO] Target genome list was writen to GCF_000721705.1_ASM72170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:56,529] [INFO] Task started: fastANI
[2024-01-25 19:11:56,529] [INFO] Running command: fastANI --query /var/lib/cwl/stge89ede67-ad0a-4d45-bddd-91bbcdadbec1/GCF_000721705.1_ASM72170v1_genomic.fna.gz --refList GCF_000721705.1_ASM72170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000721705.1_ASM72170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:43,333] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:43,344] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:43,345] [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_000721705.1	s__Actinoplanes subtropicus	100.0	3659	3674	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_000379645.1	s__Actinoplanes globisporus	86.2938	2334	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862175.1	s__Actinoplanes durhamensis	83.7752	2069	3674	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	83.5992	2030	3674	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	83.5833	2064	3674	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	82.7457	1856	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785085.1	s__Actinoplanes sp016785085	81.8131	1838	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	81.7247	1732	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012933445.1	s__Actinoplanes sp012933445	81.6779	1670	3674	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	81.2508	1808	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862395.1	s__Actinoplanes siamensis	81.1781	1491	3674	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	81.1727	1577	3674	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	80.6243	1700	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	80.3812	1346	3674	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	79.9169	1508	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014646155.1	s__Actinoplanes endophyticus	79.7146	1290	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	79.4987	1287	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089585.1	s__Micromonospora sediminicola	78.7744	1226	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.55	97.81	0.94	0.92	3	-
GCF_900090245.1	s__Micromonospora halophytica	78.5474	1113	3674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:43,346] [INFO] GTDB search result was written to GCF_000721705.1_ASM72170v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:43,346] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:43,350] [INFO] DFAST_QC result json was written to GCF_000721705.1_ASM72170v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:43,351] [INFO] DFAST_QC completed!
[2024-01-25 19:12:43,351] [INFO] Total running time: 0h4m7s