[2024-01-25 19:38:20,385] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:20,386] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:20,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg34badca6-cb8e-40f5-9fc7-56e2a0c207bd/dqc_reference
[2024-01-25 19:38:21,492] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:21,492] [INFO] Task started: Prodigal
[2024-01-25 19:38:21,493] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e7cbe1b-0996-4ff9-9437-000bb57d04cd/GCF_018332715.1_ASM1833271v1_genomic.fna.gz | prodigal -d GCF_018332715.1_ASM1833271v1_genomic.fna/cds.fna -a GCF_018332715.1_ASM1833271v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:12,398] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:12,398] [INFO] Task started: HMMsearch
[2024-01-25 19:39:12,398] [INFO] Running command: hmmsearch --tblout GCF_018332715.1_ASM1833271v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34badca6-cb8e-40f5-9fc7-56e2a0c207bd/dqc_reference/reference_markers.hmm GCF_018332715.1_ASM1833271v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:12,771] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:12,772] [INFO] Found 6/6 markers.
[2024-01-25 19:39:12,847] [INFO] Query marker FASTA was written to GCF_018332715.1_ASM1833271v1_genomic.fna/markers.fasta
[2024-01-25 19:39:12,848] [INFO] Task started: Blastn
[2024-01-25 19:39:12,848] [INFO] Running command: blastn -query GCF_018332715.1_ASM1833271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34badca6-cb8e-40f5-9fc7-56e2a0c207bd/dqc_reference/reference_markers.fasta -out GCF_018332715.1_ASM1833271v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:13,978] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:13,981] [INFO] Selected 14 target genomes.
[2024-01-25 19:39:13,981] [INFO] Target genome list was writen to GCF_018332715.1_ASM1833271v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:13,988] [INFO] Task started: fastANI
[2024-01-25 19:39:13,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e7cbe1b-0996-4ff9-9437-000bb57d04cd/GCF_018332715.1_ASM1833271v1_genomic.fna.gz --refList GCF_018332715.1_ASM1833271v1_genomic.fna/target_genomes.txt --output GCF_018332715.1_ASM1833271v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:48,041] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:48,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34badca6-cb8e-40f5-9fc7-56e2a0c207bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:48,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34badca6-cb8e-40f5-9fc7-56e2a0c207bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:48,051] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:39:48,051] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:48,051] [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 consettensis	strain=NBRC 14913	GCA_018332715.1	113560	113560	type	True	100.0	3485	3490	95	conclusive
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	94.8026	2958	3490	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	81.8436	1305	3490	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	81.7534	1420	3490	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	81.6569	1627	3490	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	81.6428	1777	3490	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	81.5001	1695	3490	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	80.0748	1588	3490	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	79.4877	1479	3490	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	79.4547	1338	3490	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.3878	862	3490	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.2975	1281	3490	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.2566	1156	3490	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.2238	1051	3490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:48,053] [INFO] DFAST Taxonomy check result was written to GCF_018332715.1_ASM1833271v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:48,053] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:48,053] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:48,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34badca6-cb8e-40f5-9fc7-56e2a0c207bd/dqc_reference/checkm_data
[2024-01-25 19:39:48,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:48,148] [INFO] Task started: CheckM
[2024-01-25 19:39:48,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018332715.1_ASM1833271v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018332715.1_ASM1833271v1_genomic.fna/checkm_input GCF_018332715.1_ASM1833271v1_genomic.fna/checkm_result
[2024-01-25 19:42:28,957] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:28,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:28,985] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:28,985] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:28,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018332715.1_ASM1833271v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:28,986] [INFO] Task started: Blastn
[2024-01-25 19:42:28,986] [INFO] Running command: blastn -query GCF_018332715.1_ASM1833271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34badca6-cb8e-40f5-9fc7-56e2a0c207bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_018332715.1_ASM1833271v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:30,770] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:30,773] [INFO] Selected 10 target genomes.
[2024-01-25 19:42:30,773] [INFO] Target genome list was writen to GCF_018332715.1_ASM1833271v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:30,785] [INFO] Task started: fastANI
[2024-01-25 19:42:30,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e7cbe1b-0996-4ff9-9437-000bb57d04cd/GCF_018332715.1_ASM1833271v1_genomic.fna.gz --refList GCF_018332715.1_ASM1833271v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018332715.1_ASM1833271v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:56,052] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:56,059] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:56,059] [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_018332715.1	s__Actinoplanes consettensis	100.0	3485	3490	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_016862215.1	s__Actinoplanes humidus	94.8147	2956	3490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	82.7957	1881	3490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553785.1	s__Actinoplanes sp001553785	82.5121	1685	3490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464385.1	s__Actinoplanes sp016464385	82.2155	1720	3490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	82.1934	1652	3490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_014648355.1	s__Actinoplanes azureus	82.0898	1379	3490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751945.1	s__Actinoplanes caeruleus	81.7638	1417	3490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000494755.1	s__Actinoplanes friuliensis	81.6181	1783	3490	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	81.5877	1643	3490	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:56,060] [INFO] GTDB search result was written to GCF_018332715.1_ASM1833271v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:56,061] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:56,065] [INFO] DFAST_QC result json was written to GCF_018332715.1_ASM1833271v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:56,065] [INFO] DFAST_QC completed!
[2024-01-25 19:42:56,066] [INFO] Total running time: 0h4m36s