[2024-01-25 18:02:05,637] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:05,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:05,639] [INFO] DQC Reference Directory: /var/lib/cwl/stgc816a96c-f6b0-4ec5-a8c4-ab27451e0bfc/dqc_reference
[2024-01-25 18:02:06,896] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:06,896] [INFO] Task started: Prodigal
[2024-01-25 18:02:06,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgc39b5aa1-5b34-4871-86c9-9e56da072f8a/GCF_003850045.1_ASM385004v1_genomic.fna.gz | prodigal -d GCF_003850045.1_ASM385004v1_genomic.fna/cds.fna -a GCF_003850045.1_ASM385004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:14,618] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:14,619] [INFO] Task started: HMMsearch
[2024-01-25 18:02:14,619] [INFO] Running command: hmmsearch --tblout GCF_003850045.1_ASM385004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc816a96c-f6b0-4ec5-a8c4-ab27451e0bfc/dqc_reference/reference_markers.hmm GCF_003850045.1_ASM385004v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:14,826] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:14,827] [INFO] Found 6/6 markers.
[2024-01-25 18:02:14,861] [INFO] Query marker FASTA was written to GCF_003850045.1_ASM385004v1_genomic.fna/markers.fasta
[2024-01-25 18:02:14,861] [INFO] Task started: Blastn
[2024-01-25 18:02:14,861] [INFO] Running command: blastn -query GCF_003850045.1_ASM385004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc816a96c-f6b0-4ec5-a8c4-ab27451e0bfc/dqc_reference/reference_markers.fasta -out GCF_003850045.1_ASM385004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:15,906] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:15,908] [INFO] Selected 17 target genomes.
[2024-01-25 18:02:15,909] [INFO] Target genome list was writen to GCF_003850045.1_ASM385004v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:15,918] [INFO] Task started: fastANI
[2024-01-25 18:02:15,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgc39b5aa1-5b34-4871-86c9-9e56da072f8a/GCF_003850045.1_ASM385004v1_genomic.fna.gz --refList GCF_003850045.1_ASM385004v1_genomic.fna/target_genomes.txt --output GCF_003850045.1_ASM385004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:28,684] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:28,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc816a96c-f6b0-4ec5-a8c4-ab27451e0bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:28,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc816a96c-f6b0-4ec5-a8c4-ab27451e0bfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:28,695] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:28,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:28,696] [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 camelliae	strain=YS17T	GCA_003850045.1	1538144	1538144	type	True	100.0	1001	1002	95	conclusive
Aeromicrobium phragmitis	strain=9W16Y-2	GCA_003674095.1	2478914	2478914	type	True	87.6404	787	1002	95	below_threshold
Aeromicrobium piscarium	strain=Co35	GCA_007421815.1	2590901	2590901	type	True	80.9246	616	1002	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	80.6168	493	1002	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	80.3966	473	1002	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	80.3933	508	1002	95	below_threshold
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	80.1049	485	1002	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	79.966	437	1002	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	79.8171	460	1002	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	78.3363	303	1002	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	78.071	274	1002	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	78.0622	300	1002	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	77.8896	343	1002	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.8418	342	1002	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	77.5523	298	1002	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	77.1928	294	1002	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	77.1073	263	1002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:28,697] [INFO] DFAST Taxonomy check result was written to GCF_003850045.1_ASM385004v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:28,698] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:28,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:28,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc816a96c-f6b0-4ec5-a8c4-ab27451e0bfc/dqc_reference/checkm_data
[2024-01-25 18:02:28,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:28,744] [INFO] Task started: CheckM
[2024-01-25 18:02:28,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003850045.1_ASM385004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003850045.1_ASM385004v1_genomic.fna/checkm_input GCF_003850045.1_ASM385004v1_genomic.fna/checkm_result
[2024-01-25 18:03:10,910] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:10,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:10,931] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:10,931] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:10,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003850045.1_ASM385004v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:10,932] [INFO] Task started: Blastn
[2024-01-25 18:03:10,932] [INFO] Running command: blastn -query GCF_003850045.1_ASM385004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc816a96c-f6b0-4ec5-a8c4-ab27451e0bfc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003850045.1_ASM385004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:12,661] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:12,664] [INFO] Selected 14 target genomes.
[2024-01-25 18:03:12,664] [INFO] Target genome list was writen to GCF_003850045.1_ASM385004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:12,678] [INFO] Task started: fastANI
[2024-01-25 18:03:12,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgc39b5aa1-5b34-4871-86c9-9e56da072f8a/GCF_003850045.1_ASM385004v1_genomic.fna.gz --refList GCF_003850045.1_ASM385004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003850045.1_ASM385004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:23,597] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:23,607] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:23,607] [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_003850045.1	s__Aeromicrobium camelliae	100.0	1001	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003674095.1	s__Aeromicrobium phragmitis	87.6404	787	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007421815.1	s__Aeromicrobium piscarium	80.9598	612	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.34	97.34	0.85	0.85	2	-
GCF_002174305.1	s__Aeromicrobium sp002174305	80.7246	565	1002	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	80.5509	499	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007992115.1	s__Aeromicrobium flavum	80.5006	466	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167475.1	s__Aeromicrobium choanae	80.3966	473	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873655.1	s__Aeromicrobium sp014873655	80.1884	415	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868155.1	s__Aeromicrobium phoceense	80.0933	485	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.64	97.64	0.92	0.92	2	-
GCF_004336805.1	s__Aeromicrobium sp004336805	80.0416	465	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000471045.1	s__Aeromicrobium sp000471045	79.8713	438	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	77.9151	358	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494815.1	s__Nocardioides sambongensis	77.5307	300	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349065.1	s__Jiangella asiatica	77.0874	264	1002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:23,608] [INFO] GTDB search result was written to GCF_003850045.1_ASM385004v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:23,609] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:23,624] [INFO] DFAST_QC result json was written to GCF_003850045.1_ASM385004v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:23,624] [INFO] DFAST_QC completed!
[2024-01-25 18:03:23,624] [INFO] Total running time: 0h1m18s