[2024-01-25 19:01:20,887] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:20,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:20,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cce5fd6-445c-4023-a3c3-18fd6b001f1a/dqc_reference
[2024-01-25 19:01:22,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:22,080] [INFO] Task started: Prodigal
[2024-01-25 19:01:22,081] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c5d0229-c0d3-4b91-a03c-5618f71528d6/GCF_016862195.1_ASM1686219v1_genomic.fna.gz | prodigal -d GCF_016862195.1_ASM1686219v1_genomic.fna/cds.fna -a GCF_016862195.1_ASM1686219v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:45,104] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:45,104] [INFO] Task started: HMMsearch
[2024-01-25 19:01:45,104] [INFO] Running command: hmmsearch --tblout GCF_016862195.1_ASM1686219v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cce5fd6-445c-4023-a3c3-18fd6b001f1a/dqc_reference/reference_markers.hmm GCF_016862195.1_ASM1686219v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:45,450] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:45,451] [INFO] Found 6/6 markers.
[2024-01-25 19:01:45,524] [INFO] Query marker FASTA was written to GCF_016862195.1_ASM1686219v1_genomic.fna/markers.fasta
[2024-01-25 19:01:45,525] [INFO] Task started: Blastn
[2024-01-25 19:01:45,525] [INFO] Running command: blastn -query GCF_016862195.1_ASM1686219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cce5fd6-445c-4023-a3c3-18fd6b001f1a/dqc_reference/reference_markers.fasta -out GCF_016862195.1_ASM1686219v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:46,774] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:46,777] [INFO] Selected 21 target genomes.
[2024-01-25 19:01:46,778] [INFO] Target genome list was writen to GCF_016862195.1_ASM1686219v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:46,784] [INFO] Task started: fastANI
[2024-01-25 19:01:46,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c5d0229-c0d3-4b91-a03c-5618f71528d6/GCF_016862195.1_ASM1686219v1_genomic.fna.gz --refList GCF_016862195.1_ASM1686219v1_genomic.fna/target_genomes.txt --output GCF_016862195.1_ASM1686219v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:36,810] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:36,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cce5fd6-445c-4023-a3c3-18fd6b001f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:36,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cce5fd6-445c-4023-a3c3-18fd6b001f1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:36,825] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:36,825] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:36,825] [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 ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	100.0	3071	3078	95	conclusive
Actinoplanes durhamensis	strain=NBRC 14914	GCA_016862175.1	113563	113563	type	True	85.6846	2093	3078	95	below_threshold
Actinoplanes toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	85.4228	2098	3078	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	85.3159	2095	3078	95	below_threshold
Actinoplanes globisporus	strain=DSM 43857	GCA_000379645.1	113565	113565	type	True	83.0921	1874	3078	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	83.0116	1783	3078	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	82.0331	1707	3078	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	81.8911	1716	3078	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	81.8842	1735	3078	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	81.7591	1764	3078	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	80.8948	1561	3078	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	80.7472	1580	3078	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.4866	1477	3078	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	80.1337	1230	3078	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	78.5705	1094	3078	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.752	1287	3078	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.5979	1051	3078	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.5946	1199	3078	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.5311	888	3078	95	below_threshold
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	77.2197	962	3078	95	below_threshold
Stackebrandtia nassauensis	strain=DSM 44728	GCA_000024545.1	283811	283811	type	True	76.4236	529	3078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:36,829] [INFO] DFAST Taxonomy check result was written to GCF_016862195.1_ASM1686219v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:36,830] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:36,831] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:36,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cce5fd6-445c-4023-a3c3-18fd6b001f1a/dqc_reference/checkm_data
[2024-01-25 19:02:36,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:36,920] [INFO] Task started: CheckM
[2024-01-25 19:02:36,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862195.1_ASM1686219v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862195.1_ASM1686219v1_genomic.fna/checkm_input GCF_016862195.1_ASM1686219v1_genomic.fna/checkm_result
[2024-01-25 19:04:04,212] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:04,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:04,238] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:04,238] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:04,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862195.1_ASM1686219v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:04,240] [INFO] Task started: Blastn
[2024-01-25 19:04:04,240] [INFO] Running command: blastn -query GCF_016862195.1_ASM1686219v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cce5fd6-445c-4023-a3c3-18fd6b001f1a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862195.1_ASM1686219v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:06,245] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:06,251] [INFO] Selected 18 target genomes.
[2024-01-25 19:04:06,251] [INFO] Target genome list was writen to GCF_016862195.1_ASM1686219v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:06,288] [INFO] Task started: fastANI
[2024-01-25 19:04:06,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c5d0229-c0d3-4b91-a03c-5618f71528d6/GCF_016862195.1_ASM1686219v1_genomic.fna.gz --refList GCF_016862195.1_ASM1686219v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862195.1_ASM1686219v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:49,968] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:49,983] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:49,983] [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_016862195.1	s__Actinoplanes ferrugineus	100.0	3071	3078	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	85.6803	2094	3078	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	85.4076	2102	3078	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	85.2541	2108	3078	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	83.1234	1867	3078	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	82.9891	1786	3078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862375.1	s__Actinoplanes rishiriensis	82.4866	1718	3078	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	81.9436	1704	3078	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	81.8797	1656	3078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016834655.1	s__Actinoplanes sp016834655	81.8455	1746	3078	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	81.7916	1756	3078	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	81.6878	1570	3078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	80.9267	1420	3078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862275.1	s__Actinoplanes nipponensis	80.8826	1564	3078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862315.1	s__Actinoplanes palleronii	80.7915	1628	3078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
GCF_016862095.1	s__Actinoplanes cyaneus	80.6954	1593	3078	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	80.6165	1461	3078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751085.1	s__Micromonospora_E sp003751085	78.1889	985	3078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:49,992] [INFO] GTDB search result was written to GCF_016862195.1_ASM1686219v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:49,994] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:50,000] [INFO] DFAST_QC result json was written to GCF_016862195.1_ASM1686219v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:50,001] [INFO] DFAST_QC completed!
[2024-01-25 19:04:50,001] [INFO] Total running time: 0h3m29s