[2024-01-24 12:31:34,653] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:34,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:34,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a1fe137-f9c5-437e-b2c2-36a7a3d7e7c7/dqc_reference
[2024-01-24 12:31:36,003] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:36,004] [INFO] Task started: Prodigal
[2024-01-24 12:31:36,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a09c76f-c443-4161-8f37-f4457f0edf00/GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/cds.fna -a GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:47,193] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:47,194] [INFO] Task started: HMMsearch
[2024-01-24 12:31:47,194] [INFO] Running command: hmmsearch --tblout GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a1fe137-f9c5-437e-b2c2-36a7a3d7e7c7/dqc_reference/reference_markers.hmm GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:47,478] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:47,480] [INFO] Found 6/6 markers.
[2024-01-24 12:31:47,514] [INFO] Query marker FASTA was written to GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:47,514] [INFO] Task started: Blastn
[2024-01-24 12:31:47,514] [INFO] Running command: blastn -query GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a1fe137-f9c5-437e-b2c2-36a7a3d7e7c7/dqc_reference/reference_markers.fasta -out GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:48,713] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:48,716] [INFO] Selected 17 target genomes.
[2024-01-24 12:31:48,716] [INFO] Target genome list was writen to GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:48,723] [INFO] Task started: fastANI
[2024-01-24 12:31:48,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a09c76f-c443-4161-8f37-f4457f0edf00/GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna.gz --refList GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:01,956] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:01,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a1fe137-f9c5-437e-b2c2-36a7a3d7e7c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:01,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a1fe137-f9c5-437e-b2c2-36a7a3d7e7c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:01,974] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:01,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:01,974] [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
Raineyella antarctica	strain=LZ-22	GCA_900092135.1	1577474	1577474	type	True	100.0	1235	1237	95	conclusive
Raineyella fluvialis	strain=CBA3103	GCA_009646095.1	2662261	2662261	type	True	81.8872	733	1237	95	below_threshold
Granulicoccus phenolivorans	strain=DSM 17626	GCA_000423085.1	266854	266854	type	True	78.0696	338	1237	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.0461	339	1237	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	78.0364	372	1237	95	below_threshold
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	77.9876	337	1237	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	77.9731	310	1237	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	77.8932	371	1237	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	77.8512	365	1237	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	77.7966	393	1237	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	77.7693	333	1237	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	77.2613	301	1237	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.1254	267	1237	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	76.9959	335	1237	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	76.8833	310	1237	95	below_threshold
Streptacidiphilus carbonis	strain=NBRC 100919	GCA_000787775.1	105422	105422	type	True	76.6753	322	1237	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	76.5078	270	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:01,976] [INFO] DFAST Taxonomy check result was written to GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:01,977] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:01,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:01,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a1fe137-f9c5-437e-b2c2-36a7a3d7e7c7/dqc_reference/checkm_data
[2024-01-24 12:32:01,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:02,020] [INFO] Task started: CheckM
[2024-01-24 12:32:02,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/checkm_input GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:32:41,513] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:41,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:41,536] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:41,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:41,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:32:41,537] [INFO] Task started: Blastn
[2024-01-24 12:32:41,537] [INFO] Running command: blastn -query GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a1fe137-f9c5-437e-b2c2-36a7a3d7e7c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:43,334] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:43,339] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:43,339] [INFO] Target genome list was writen to GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:43,352] [INFO] Task started: fastANI
[2024-01-24 12:32:43,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a09c76f-c443-4161-8f37-f4457f0edf00/GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna.gz --refList GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:57,278] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:57,293] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:57,293] [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_900092135.1	s__Raineyella antarctica	100.0	1235	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009646095.1	s__Raineyella sp009646095	81.8997	731	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Raineyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	78.0692	336	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCA_012838755.1	s__Brevilactibacter sp012838755	78.0483	294	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009742705.1	s__Auraticoccus cholistanensis	78.0466	371	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004324755.1	s__Brevilactibacter sinopodophylli	78.0168	306	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826085.1	s__Nigerium massiliense	77.9888	293	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Nigerium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002250625.1	s__Enemella sp002250625	77.9773	338	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.13	98.13	0.89	0.89	2	-
GCF_900101785.1	s__Auraticoccus monumenti	77.9408	365	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876495.1	s__Friedmanniella capsulata	77.7729	407	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362375.1	s__Enemella evansiae	77.7574	374	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCF_013408315.1	s__Microlunatus_A terrae	77.5422	333	1237	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_013408305.1	s__Naumannella cuiyingiana	77.333	310	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104965.1	s__Marmoricola scoriae	77.2151	307	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013624435.2	s__Nocardioides sp013624415	77.0727	300	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	-
GCF_000787775.1	s__Streptacidiphilus carbonis	76.6936	320	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580365.1	s__Kocuria turfanensis	76.5541	264	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_003751325.1	s__Streptacidiphilus sp003751325	76.4753	314	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:57,296] [INFO] GTDB search result was written to GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:57,296] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:57,300] [INFO] DFAST_QC result json was written to GCF_900092135.1_IMG-taxon_2651870304_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:57,300] [INFO] DFAST_QC completed!
[2024-01-24 12:32:57,301] [INFO] Total running time: 0h1m23s