[2024-01-24 13:49:45,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,558] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e221e36-ef21-4e73-8311-702a05a9b61e/dqc_reference
[2024-01-24 13:49:47,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:47,064] [INFO] Task started: Prodigal
[2024-01-24 13:49:47,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg31ced6b9-e94b-4394-a08d-594d7e76b915/GCF_003752415.1_ASM375241v1_genomic.fna.gz | prodigal -d GCF_003752415.1_ASM375241v1_genomic.fna/cds.fna -a GCF_003752415.1_ASM375241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:59,490] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:59,490] [INFO] Task started: HMMsearch
[2024-01-24 13:49:59,490] [INFO] Running command: hmmsearch --tblout GCF_003752415.1_ASM375241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e221e36-ef21-4e73-8311-702a05a9b61e/dqc_reference/reference_markers.hmm GCF_003752415.1_ASM375241v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:59,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:59,789] [INFO] Found 6/6 markers.
[2024-01-24 13:49:59,824] [INFO] Query marker FASTA was written to GCF_003752415.1_ASM375241v1_genomic.fna/markers.fasta
[2024-01-24 13:49:59,825] [INFO] Task started: Blastn
[2024-01-24 13:49:59,825] [INFO] Running command: blastn -query GCF_003752415.1_ASM375241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e221e36-ef21-4e73-8311-702a05a9b61e/dqc_reference/reference_markers.fasta -out GCF_003752415.1_ASM375241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:01,069] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:01,072] [INFO] Selected 24 target genomes.
[2024-01-24 13:50:01,073] [INFO] Target genome list was writen to GCF_003752415.1_ASM375241v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:01,082] [INFO] Task started: fastANI
[2024-01-24 13:50:01,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ced6b9-e94b-4394-a08d-594d7e76b915/GCF_003752415.1_ASM375241v1_genomic.fna.gz --refList GCF_003752415.1_ASM375241v1_genomic.fna/target_genomes.txt --output GCF_003752415.1_ASM375241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:16,718] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:16,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e221e36-ef21-4e73-8311-702a05a9b61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:16,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e221e36-ef21-4e73-8311-702a05a9b61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:16,741] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:16,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:16,742] [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
Luteococcus japonicus	strain=DSM 10546	GCA_003752415.1	33984	33984	type	True	100.0	1148	1150	95	conclusive
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	78.9755	331	1150	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	78.2978	289	1150	95	below_threshold
Tessaracoccus rhinocerotis	strain=YIM 101269	GCA_007197885.1	1689449	1689449	type	True	78.1279	267	1150	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	78.0295	310	1150	95	below_threshold
Tessaracoccus aquimaris	strain=NSG39	GCA_001997345.1	1332264	1332264	type	True	77.9552	279	1150	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.8511	299	1150	95	below_threshold
Acidipropionibacterium acidipropionici	strain=CGMCC 1.2230	GCA_001441165.1	1748	1748	type	True	77.8177	284	1150	95	below_threshold
Propionibacterium freudenreichii subsp. freudenreichii	strain=DSM 20271	GCA_000940845.1	66712	1744	type	True	77.8174	209	1150	95	below_threshold
Raineyella fluvialis	strain=CBA3103	GCA_009646095.1	2662261	2662261	type	True	77.7591	244	1150	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.7393	289	1150	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.735	213	1150	95	below_threshold
Acidipropionibacterium acidipropionici	strain=DSM 4900	GCA_000427845.1	1748	1748	type	True	77.6625	273	1150	95	below_threshold
Propionibacterium acidifaciens	strain=DSM 21887	GCA_000426605.1	556499	556499	type	True	77.6542	235	1150	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	77.5449	278	1150	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_900182665.1	433330	433330	type	True	77.5326	224	1150	95	below_threshold
Granulicoccus phenolivorans	strain=NBRC 107789	GCA_001552335.1	266854	266854	type	True	77.3988	214	1150	95	below_threshold
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	77.3047	220	1150	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	77.2481	251	1150	95	below_threshold
Microlunatus elymi	strain=KUDC0627	GCA_007362775.1	2596828	2596828	type	True	77.2026	196	1150	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	77.1807	205	1150	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.1448	208	1150	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	76.722	187	1150	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	76.6163	169	1150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:16,744] [INFO] DFAST Taxonomy check result was written to GCF_003752415.1_ASM375241v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:16,745] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:16,745] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:16,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e221e36-ef21-4e73-8311-702a05a9b61e/dqc_reference/checkm_data
[2024-01-24 13:50:16,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:16,784] [INFO] Task started: CheckM
[2024-01-24 13:50:16,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003752415.1_ASM375241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003752415.1_ASM375241v1_genomic.fna/checkm_input GCF_003752415.1_ASM375241v1_genomic.fna/checkm_result
[2024-01-24 13:51:35,807] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:35,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:35,828] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:35,828] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:35,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003752415.1_ASM375241v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:35,829] [INFO] Task started: Blastn
[2024-01-24 13:51:35,829] [INFO] Running command: blastn -query GCF_003752415.1_ASM375241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e221e36-ef21-4e73-8311-702a05a9b61e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003752415.1_ASM375241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:37,581] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:37,585] [INFO] Selected 20 target genomes.
[2024-01-24 13:51:37,585] [INFO] Target genome list was writen to GCF_003752415.1_ASM375241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:37,645] [INFO] Task started: fastANI
[2024-01-24 13:51:37,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ced6b9-e94b-4394-a08d-594d7e76b915/GCF_003752415.1_ASM375241v1_genomic.fna.gz --refList GCF_003752415.1_ASM375241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003752415.1_ASM375241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:49,770] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:49,793] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:49,793] [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_003752415.1	s__Luteococcus japonicus	100.0	1145	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Luteococcus	95.0	98.56	98.56	0.91	0.91	2	conclusive
GCA_002387005.1	s__Luteococcus avicola	81.0437	407	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Luteococcus	95.0	96.77	96.77	0.82	0.82	2	-
GCF_015352975.1	s__Aestuariimicrobium ganziense	78.9617	331	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355265.1	s__Aestuariimicrobium sp017355265	78.382	271	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Aestuariimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004324755.1	s__Brevilactibacter sinopodophylli	78.2943	289	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197885.1	s__Arachnia rhinocerotis	78.1141	268	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838755.1	s__Brevilactibacter sp012838755	78.0839	249	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101785.1	s__Auraticoccus monumenti	78.0558	310	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900605005.1	s__Cutibacterium timonense	78.012	236	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Cutibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001997345.1	s__Arachnia aquimaris	77.9689	278	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009742705.1	s__Auraticoccus cholistanensis	77.8506	299	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001441165.1	s__Acidipropionibacterium acidipropionici	77.8288	283	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Acidipropionibacterium	95.0	99.00	98.39	0.93	0.89	8	-
GCF_900289195.1	s__Propionibacterium sp900289195	77.7599	224	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.03	99.03	0.94	0.94	2	-
GCA_012837465.1	s__Arachnia sp012837465	77.7422	222	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Arachnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426605.1	s__Propionibacterium acidifaciens	77.6481	235	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.24	99.02	0.93	0.90	4	-
GCF_003344635.1	s__Desertihabitans aurantiacus	77.5672	276	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCA_018055925.1	s__Micropruina sp018055925	77.5003	228	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423085.1	s__Granulicoccus phenolivorans	77.3125	219	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Granulicoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_007362775.1	s__Microlunatus_A sp007362775	77.2049	195	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Microlunatus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720335.1	s__Marmoricola aequoreus	77.1328	208	1150	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:49,795] [INFO] GTDB search result was written to GCF_003752415.1_ASM375241v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:49,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:49,800] [INFO] DFAST_QC result json was written to GCF_003752415.1_ASM375241v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:49,800] [INFO] DFAST_QC completed!
[2024-01-24 13:51:49,800] [INFO] Total running time: 0h2m4s