[2024-01-24 13:39:59,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:39:59,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:39:59,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg50f117a5-82ab-42b7-94b0-2920c93e2d46/dqc_reference
[2024-01-24 13:40:01,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:01,099] [INFO] Task started: Prodigal
[2024-01-24 13:40:01,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg105c19f8-074a-4f1d-b39d-aa6ba046dd85/GCF_002797495.1_ASM279749v1_genomic.fna.gz | prodigal -d GCF_002797495.1_ASM279749v1_genomic.fna/cds.fna -a GCF_002797495.1_ASM279749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:12,726] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:12,727] [INFO] Task started: HMMsearch
[2024-01-24 13:40:12,727] [INFO] Running command: hmmsearch --tblout GCF_002797495.1_ASM279749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50f117a5-82ab-42b7-94b0-2920c93e2d46/dqc_reference/reference_markers.hmm GCF_002797495.1_ASM279749v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:13,012] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:13,013] [INFO] Found 6/6 markers.
[2024-01-24 13:40:13,053] [INFO] Query marker FASTA was written to GCF_002797495.1_ASM279749v1_genomic.fna/markers.fasta
[2024-01-24 13:40:13,054] [INFO] Task started: Blastn
[2024-01-24 13:40:13,054] [INFO] Running command: blastn -query GCF_002797495.1_ASM279749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50f117a5-82ab-42b7-94b0-2920c93e2d46/dqc_reference/reference_markers.fasta -out GCF_002797495.1_ASM279749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:14,216] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:14,219] [INFO] Selected 27 target genomes.
[2024-01-24 13:40:14,219] [INFO] Target genome list was writen to GCF_002797495.1_ASM279749v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:14,235] [INFO] Task started: fastANI
[2024-01-24 13:40:14,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg105c19f8-074a-4f1d-b39d-aa6ba046dd85/GCF_002797495.1_ASM279749v1_genomic.fna.gz --refList GCF_002797495.1_ASM279749v1_genomic.fna/target_genomes.txt --output GCF_002797495.1_ASM279749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:37,684] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:37,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50f117a5-82ab-42b7-94b0-2920c93e2d46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:37,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50f117a5-82ab-42b7-94b0-2920c93e2d46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:37,704] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:37,704] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:37,705] [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
Mumia flava	strain=DSM 27763	GCA_002797495.1	1348852	1348852	type	True	100.0	1463	1463	95	conclusive
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	78.7298	461	1463	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	78.6096	504	1463	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	78.3614	477	1463	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	78.3557	500	1463	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	78.3548	459	1463	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	78.2966	465	1463	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	78.2465	481	1463	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	78.1571	466	1463	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	78.1312	488	1463	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.0323	505	1463	95	below_threshold
Nocardioides rotundus	strain=MCCC 1A10561	GCA_019931675.1	1774216	1774216	type	True	78.0163	386	1463	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	77.9787	433	1463	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	77.968	508	1463	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	77.8258	505	1463	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	77.726	473	1463	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	77.6471	425	1463	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	77.477	514	1463	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	77.4025	504	1463	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	77.3919	486	1463	95	below_threshold
Nocardioides luteus	strain=JCM 3358	GCA_014648595.1	1844	1844	type	True	77.3541	420	1463	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	77.3186	510	1463	95	below_threshold
Thermasporomyces composti	strain=DSM 22891	GCA_003386795.1	696763	696763	type	True	76.7017	267	1463	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	76.5728	299	1463	95	below_threshold
Lentzea nigeriaca	strain=DSM 45680	GCA_016907955.1	1128665	1128665	type	True	76.309	380	1463	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	76.3002	353	1463	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	76.2654	346	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:37,707] [INFO] DFAST Taxonomy check result was written to GCF_002797495.1_ASM279749v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:37,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:37,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:37,708] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50f117a5-82ab-42b7-94b0-2920c93e2d46/dqc_reference/checkm_data
[2024-01-24 13:40:37,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:37,750] [INFO] Task started: CheckM
[2024-01-24 13:40:37,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002797495.1_ASM279749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002797495.1_ASM279749v1_genomic.fna/checkm_input GCF_002797495.1_ASM279749v1_genomic.fna/checkm_result
[2024-01-24 13:41:42,173] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:42,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:42,200] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:42,201] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:42,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002797495.1_ASM279749v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:42,202] [INFO] Task started: Blastn
[2024-01-24 13:41:42,202] [INFO] Running command: blastn -query GCF_002797495.1_ASM279749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50f117a5-82ab-42b7-94b0-2920c93e2d46/dqc_reference/reference_markers_gtdb.fasta -out GCF_002797495.1_ASM279749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:44,153] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:44,156] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:44,157] [INFO] Target genome list was writen to GCF_002797495.1_ASM279749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:44,181] [INFO] Task started: fastANI
[2024-01-24 13:41:44,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg105c19f8-074a-4f1d-b39d-aa6ba046dd85/GCF_002797495.1_ASM279749v1_genomic.fna.gz --refList GCF_002797495.1_ASM279749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002797495.1_ASM279749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:59,429] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:59,451] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:59,451] [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_002797495.1	s__Mumia flava	100.0	1463	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010994095.1	s__Mumia xiangluensis	80.8775	814	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_014127285.1	s__Mumia sp014127285	80.6218	783	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	99.73	99.46	0.99	0.98	3	-
GCF_004336805.1	s__Aeromicrobium sp004336805	78.6039	515	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428805.1	s__Aeromicrobium sp001428805	78.5261	472	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003586285.1	s__Aeromicrobium endophyticum	78.3458	479	1463	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	78.2827	476	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_000471045.1	s__Aeromicrobium sp000471045	78.2743	396	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695785.1	s__JACCZT01 sp013695785	78.1102	272	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JACCZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395785.1	s__Nocardioides_B mesophilus	77.9872	471	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	77.974	530	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014127485.1	s__Nocardioides sp014127485	77.9675	508	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_014644415.1	s__Marmoricola endophyticus	77.7879	451	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194625.1	s__Nocardioides solisilvae	77.6548	424	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648595.1	s__Nocardioides luteus	77.3446	422	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045035.1	s__Nocardioides sp011045035	77.0976	461	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386795.1	s__Thermasporomyces composti	76.6934	269	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Thermasporomyces	95.0	99.77	99.77	0.94	0.94	2	-
GCF_017349075.1	s__Streptomyces triculaminicus_A	76.4331	382	1463	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:59,455] [INFO] GTDB search result was written to GCF_002797495.1_ASM279749v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:59,461] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:59,468] [INFO] DFAST_QC result json was written to GCF_002797495.1_ASM279749v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:59,469] [INFO] DFAST_QC completed!
[2024-01-24 13:41:59,469] [INFO] Total running time: 0h1m60s