[2024-01-24 12:06:10,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,397] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc8730df-ef83-40a4-9dcb-cfc4aea84b59/dqc_reference
[2024-01-24 12:06:13,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,261] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,261] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4d6dea7-ed62-492d-970a-4462e39e7753/GCF_007421815.1_ASM742181v1_genomic.fna.gz | prodigal -d GCF_007421815.1_ASM742181v1_genomic.fna/cds.fna -a GCF_007421815.1_ASM742181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:24,592] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:24,593] [INFO] Task started: HMMsearch
[2024-01-24 12:06:24,593] [INFO] Running command: hmmsearch --tblout GCF_007421815.1_ASM742181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc8730df-ef83-40a4-9dcb-cfc4aea84b59/dqc_reference/reference_markers.hmm GCF_007421815.1_ASM742181v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:24,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:24,917] [INFO] Found 6/6 markers.
[2024-01-24 12:06:24,956] [INFO] Query marker FASTA was written to GCF_007421815.1_ASM742181v1_genomic.fna/markers.fasta
[2024-01-24 12:06:24,956] [INFO] Task started: Blastn
[2024-01-24 12:06:24,957] [INFO] Running command: blastn -query GCF_007421815.1_ASM742181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8730df-ef83-40a4-9dcb-cfc4aea84b59/dqc_reference/reference_markers.fasta -out GCF_007421815.1_ASM742181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:26,082] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:26,085] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:26,086] [INFO] Target genome list was writen to GCF_007421815.1_ASM742181v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:26,095] [INFO] Task started: fastANI
[2024-01-24 12:06:26,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4d6dea7-ed62-492d-970a-4462e39e7753/GCF_007421815.1_ASM742181v1_genomic.fna.gz --refList GCF_007421815.1_ASM742181v1_genomic.fna/target_genomes.txt --output GCF_007421815.1_ASM742181v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:39,612] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:39,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc8730df-ef83-40a4-9dcb-cfc4aea84b59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:39,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc8730df-ef83-40a4-9dcb-cfc4aea84b59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:39,631] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:39,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:39,631] [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
Aeromicrobium piscarium	strain=Co35	GCA_007421815.1	2590901	2590901	type	True	100.0	1232	1234	95	conclusive
Aeromicrobium camelliae	strain=YS17T	GCA_003850045.1	1538144	1538144	type	True	80.9455	616	1234	95	below_threshold
Aeromicrobium phragmitis	strain=9W16Y-2	GCA_003674095.1	2478914	2478914	type	True	80.8921	580	1234	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	79.9833	481	1234	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	79.9217	472	1234	95	below_threshold
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	79.7538	451	1234	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	79.6132	469	1234	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	79.2346	393	1234	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	79.0267	456	1234	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	78.9059	391	1234	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	78.8478	460	1234	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	77.9617	319	1234	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	77.7947	312	1234	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	77.702	311	1234	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.4338	326	1234	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	77.1922	268	1234	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	77.0756	271	1234	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	76.3933	239	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:39,633] [INFO] DFAST Taxonomy check result was written to GCF_007421815.1_ASM742181v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:39,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:39,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:39,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc8730df-ef83-40a4-9dcb-cfc4aea84b59/dqc_reference/checkm_data
[2024-01-24 12:06:39,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:39,675] [INFO] Task started: CheckM
[2024-01-24 12:06:39,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007421815.1_ASM742181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007421815.1_ASM742181v1_genomic.fna/checkm_input GCF_007421815.1_ASM742181v1_genomic.fna/checkm_result
[2024-01-24 12:07:19,174] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:19,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:19,202] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:19,202] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:19,202] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007421815.1_ASM742181v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:19,203] [INFO] Task started: Blastn
[2024-01-24 12:07:19,203] [INFO] Running command: blastn -query GCF_007421815.1_ASM742181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc8730df-ef83-40a4-9dcb-cfc4aea84b59/dqc_reference/reference_markers_gtdb.fasta -out GCF_007421815.1_ASM742181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:20,842] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:20,847] [INFO] Selected 12 target genomes.
[2024-01-24 12:07:20,847] [INFO] Target genome list was writen to GCF_007421815.1_ASM742181v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:20,860] [INFO] Task started: fastANI
[2024-01-24 12:07:20,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4d6dea7-ed62-492d-970a-4462e39e7753/GCF_007421815.1_ASM742181v1_genomic.fna.gz --refList GCF_007421815.1_ASM742181v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007421815.1_ASM742181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:29,433] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:29,445] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:29,446] [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_007421815.1	s__Aeromicrobium piscarium	100.0	1232	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.34	97.34	0.85	0.85	2	conclusive
GCF_002174305.1	s__Aeromicrobium sp002174305	87.9578	928	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003850045.1	s__Aeromicrobium camelliae	80.9244	618	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003674095.1	s__Aeromicrobium phragmitis	80.8922	580	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408555.1	s__Aeromicrobium tamlense	80.0011	479	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900167475.1	s__Aeromicrobium choanae	79.6569	465	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334735.1	s__Aeromicrobium sp014334735	79.6005	451	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	99.41	98.82	0.96	0.93	3	-
GCF_014873655.1	s__Aeromicrobium sp014873655	79.3597	387	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506105.1	s__Aeromicrobium sp902506105	78.7788	407	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	77.1827	269	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCA_014763705.1	s__Phycicoccus sp014763705	77.0545	202	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971195.1	s__Demequina soli	76.5498	176	1234	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:29,447] [INFO] GTDB search result was written to GCF_007421815.1_ASM742181v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:29,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:29,452] [INFO] DFAST_QC result json was written to GCF_007421815.1_ASM742181v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:29,452] [INFO] DFAST_QC completed!
[2024-01-24 12:07:29,452] [INFO] Total running time: 0h1m19s