[2024-01-24 12:15:18,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg857d4a95-ef16-4a1f-a962-05f7e1ebd141/dqc_reference
[2024-01-24 12:15:19,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:19,906] [INFO] Task started: Prodigal
[2024-01-24 12:15:19,906] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf915060-e53d-49bf-a42e-9284ede1946b/GCF_004364645.1_ASM436464v1_genomic.fna.gz | prodigal -d GCF_004364645.1_ASM436464v1_genomic.fna/cds.fna -a GCF_004364645.1_ASM436464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:30,873] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:30,873] [INFO] Task started: HMMsearch
[2024-01-24 12:15:30,873] [INFO] Running command: hmmsearch --tblout GCF_004364645.1_ASM436464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg857d4a95-ef16-4a1f-a962-05f7e1ebd141/dqc_reference/reference_markers.hmm GCF_004364645.1_ASM436464v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:31,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:31,103] [INFO] Found 6/6 markers.
[2024-01-24 12:15:31,133] [INFO] Query marker FASTA was written to GCF_004364645.1_ASM436464v1_genomic.fna/markers.fasta
[2024-01-24 12:15:31,134] [INFO] Task started: Blastn
[2024-01-24 12:15:31,134] [INFO] Running command: blastn -query GCF_004364645.1_ASM436464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg857d4a95-ef16-4a1f-a962-05f7e1ebd141/dqc_reference/reference_markers.fasta -out GCF_004364645.1_ASM436464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:32,152] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:32,155] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:32,155] [INFO] Target genome list was writen to GCF_004364645.1_ASM436464v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:32,163] [INFO] Task started: fastANI
[2024-01-24 12:15:32,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf915060-e53d-49bf-a42e-9284ede1946b/GCF_004364645.1_ASM436464v1_genomic.fna.gz --refList GCF_004364645.1_ASM436464v1_genomic.fna/target_genomes.txt --output GCF_004364645.1_ASM436464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:47,815] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:47,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg857d4a95-ef16-4a1f-a962-05f7e1ebd141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:47,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg857d4a95-ef16-4a1f-a962-05f7e1ebd141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:47,831] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:47,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:47,831] [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
Naumannella halotolerans	strain=DSM 24323	GCA_004364645.1	993414	993414	type	True	100.0	1155	1155	95	conclusive
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	79.8896	519	1155	95	below_threshold
Enemella evansiae	strain=NML 020265	GCA_002250705.1	2016499	2016499	type	True	78.394	351	1155	95	below_threshold
Desertihabitans aurantiacus	strain=CPCC 204711	GCA_003344635.1	2282477	2282477	type	True	78.2445	307	1155	95	below_threshold
Enemella dayhoffiae	strain=NML 130396	GCA_002250625.1	2016507	2016507	type	True	78.1621	296	1155	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	78.0478	344	1155	95	below_threshold
Auraticoccus monumenti	strain=MON 2.2	GCA_900101785.1	675864	675864	type	True	78.0177	320	1155	95	below_threshold
Auraticoccus cholistanensis	strain=F435	GCA_009742705.1	2656650	2656650	type	True	77.9669	316	1155	95	below_threshold
Microlunatus kandeliicorticis	strain=DSM 100723	GCA_014137855.1	1759536	1759536	type	True	77.556	314	1155	95	below_threshold
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	77.3622	208	1155	95	below_threshold
Microlunatus antarcticus	strain=DSM 11053	GCA_014193425.1	53388	53388	type	True	77.3065	235	1155	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	76.9845	241	1155	95	below_threshold
Propionibacterium acidifaciens	strain=DSM 21887	GCA_000426605.1	556499	556499	type	True	76.8378	132	1155	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	76.7408	238	1155	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	76.6872	249	1155	95	below_threshold
Propionibacterium australiense	strain=NCTC13651	GCA_900637915.1	119981	119981	type	True	76.6696	143	1155	95	below_threshold
Propionibacterium australiense	strain=NML98A072	GCA_003666605.1	119981	119981	type	True	76.6656	134	1155	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.606	218	1155	95	below_threshold
Nocardioides rubriscoriae	strain=DSM 23986	GCA_008087085.1	642762	642762	type	True	76.4851	216	1155	95	below_threshold
Nocardioides acrostichi	strain=CBS4Y-1	GCA_015319165.1	2784339	2784339	type	True	76.4452	188	1155	95	below_threshold
Streptomyces lonarensis	strain=NCL716	GCA_012033735.1	700599	700599	type	True	76.2588	180	1155	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:47,833] [INFO] DFAST Taxonomy check result was written to GCF_004364645.1_ASM436464v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:47,834] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:47,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:47,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg857d4a95-ef16-4a1f-a962-05f7e1ebd141/dqc_reference/checkm_data
[2024-01-24 12:15:47,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:47,869] [INFO] Task started: CheckM
[2024-01-24 12:15:47,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004364645.1_ASM436464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004364645.1_ASM436464v1_genomic.fna/checkm_input GCF_004364645.1_ASM436464v1_genomic.fna/checkm_result
[2024-01-24 12:16:37,193] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:37,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:37,212] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:37,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:37,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004364645.1_ASM436464v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:37,213] [INFO] Task started: Blastn
[2024-01-24 12:16:37,213] [INFO] Running command: blastn -query GCF_004364645.1_ASM436464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg857d4a95-ef16-4a1f-a962-05f7e1ebd141/dqc_reference/reference_markers_gtdb.fasta -out GCF_004364645.1_ASM436464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:38,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:38,675] [INFO] Selected 17 target genomes.
[2024-01-24 12:16:38,675] [INFO] Target genome list was writen to GCF_004364645.1_ASM436464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:38,684] [INFO] Task started: fastANI
[2024-01-24 12:16:38,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf915060-e53d-49bf-a42e-9284ede1946b/GCF_004364645.1_ASM436464v1_genomic.fna.gz --refList GCF_004364645.1_ASM436464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004364645.1_ASM436464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:49,557] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:49,571] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:49,571] [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_004364645.1	s__Naumannella halotolerans	100.0	1155	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013408305.1	s__Naumannella cuiyingiana	79.9273	515	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344635.1	s__Desertihabitans aurantiacus	78.2444	307	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Desertihabitans	95.0	95.17	95.17	0.87	0.87	2	-
GCF_004362375.1	s__Enemella evansiae	78.1914	363	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Enemella	95.0	98.12	97.98	0.94	0.92	8	-
GCA_002250625.1	s__Enemella sp002250625	78.1608	298	1155	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	78.0186	320	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009742705.1	s__Auraticoccus cholistanensis	77.9941	312	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Auraticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408315.1	s__Microlunatus_A terrae	77.7246	327	1155	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_014137855.1	s__Friedmanniella_A endophytica	77.528	317	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Friedmanniella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423085.1	s__Granulicoccus phenolivorans	77.4758	269	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Granulicoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCA_013693855.1	s__Micropruina sp013693855	77.2712	211	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018055925.1	s__Micropruina sp018055925	76.8623	229	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426605.1	s__Propionibacterium acidifaciens	76.8193	133	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.24	99.02	0.93	0.90	4	-
GCF_000826085.1	s__Nigerium massiliense	76.7983	191	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Nigerium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013361955.1	s__JABFXA01 sp013361955	76.6818	217	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_003666605.1	s__Propionibacterium australiense	76.6666	134	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propionibacterium	95.0	99.91	99.75	0.98	0.97	4	-
GCF_015319165.1	s__Nocardioides acrostichi	76.4449	188	1155	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:49,573] [INFO] GTDB search result was written to GCF_004364645.1_ASM436464v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:49,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:49,578] [INFO] DFAST_QC result json was written to GCF_004364645.1_ASM436464v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:49,578] [INFO] DFAST_QC completed!
[2024-01-24 12:16:49,579] [INFO] Total running time: 0h1m31s