[2024-01-24 11:09:50,718] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e95ddf4-bb85-4123-975a-0856a9f8e508/dqc_reference
[2024-01-24 11:09:53,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,303] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg828036c0-3718-48b5-88ae-7223bdf6421d/GCF_007992115.1_ASM799211v1_genomic.fna.gz | prodigal -d GCF_007992115.1_ASM799211v1_genomic.fna/cds.fna -a GCF_007992115.1_ASM799211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:01,829] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:01,829] [INFO] Task started: HMMsearch
[2024-01-24 11:10:01,830] [INFO] Running command: hmmsearch --tblout GCF_007992115.1_ASM799211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e95ddf4-bb85-4123-975a-0856a9f8e508/dqc_reference/reference_markers.hmm GCF_007992115.1_ASM799211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:02,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:02,123] [INFO] Found 6/6 markers.
[2024-01-24 11:10:02,158] [INFO] Query marker FASTA was written to GCF_007992115.1_ASM799211v1_genomic.fna/markers.fasta
[2024-01-24 11:10:02,159] [INFO] Task started: Blastn
[2024-01-24 11:10:02,159] [INFO] Running command: blastn -query GCF_007992115.1_ASM799211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e95ddf4-bb85-4123-975a-0856a9f8e508/dqc_reference/reference_markers.fasta -out GCF_007992115.1_ASM799211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:03,397] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:03,400] [INFO] Selected 15 target genomes.
[2024-01-24 11:10:03,401] [INFO] Target genome list was writen to GCF_007992115.1_ASM799211v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:03,433] [INFO] Task started: fastANI
[2024-01-24 11:10:03,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg828036c0-3718-48b5-88ae-7223bdf6421d/GCF_007992115.1_ASM799211v1_genomic.fna.gz --refList GCF_007992115.1_ASM799211v1_genomic.fna/target_genomes.txt --output GCF_007992115.1_ASM799211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:14,251] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:14,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e95ddf4-bb85-4123-975a-0856a9f8e508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:14,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e95ddf4-bb85-4123-975a-0856a9f8e508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:14,269] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:10:14,269] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:10:14,270] [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 phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	86.9386	794	1016	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	86.8975	776	1016	95	below_threshold
Aeromicrobium choanae	strain=9H-4	GCA_900167475.1	1736691	1736691	type	True	86.8259	780	1016	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	86.7962	790	1016	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	81.0304	534	1016	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	80.9014	468	1016	95	below_threshold
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	80.7726	534	1016	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	80.6085	541	1016	95	below_threshold
Aeromicrobium phragmitis	strain=9W16Y-2	GCA_003674095.1	2478914	2478914	type	True	80.0564	466	1016	95	below_threshold
Aeromicrobium piscarium	strain=Co35	GCA_007421815.1	2590901	2590901	type	True	79.6402	464	1016	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	78.5727	382	1016	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	78.4009	429	1016	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.2703	408	1016	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	78.2554	391	1016	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	78.2431	343	1016	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:14,271] [INFO] DFAST Taxonomy check result was written to GCF_007992115.1_ASM799211v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:14,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:14,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:14,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e95ddf4-bb85-4123-975a-0856a9f8e508/dqc_reference/checkm_data
[2024-01-24 11:10:14,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:14,303] [INFO] Task started: CheckM
[2024-01-24 11:10:14,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992115.1_ASM799211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992115.1_ASM799211v1_genomic.fna/checkm_input GCF_007992115.1_ASM799211v1_genomic.fna/checkm_result
[2024-01-24 11:10:47,898] [INFO] Task succeeded: CheckM
[2024-01-24 11:10:47,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:10:47,922] [INFO] ===== Completeness check finished =====
[2024-01-24 11:10:47,923] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:10:47,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992115.1_ASM799211v1_genomic.fna/markers.fasta)
[2024-01-24 11:10:47,924] [INFO] Task started: Blastn
[2024-01-24 11:10:47,925] [INFO] Running command: blastn -query GCF_007992115.1_ASM799211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e95ddf4-bb85-4123-975a-0856a9f8e508/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992115.1_ASM799211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:49,882] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:49,885] [INFO] Selected 5 target genomes.
[2024-01-24 11:10:49,886] [INFO] Target genome list was writen to GCF_007992115.1_ASM799211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:10:49,897] [INFO] Task started: fastANI
[2024-01-24 11:10:49,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg828036c0-3718-48b5-88ae-7223bdf6421d/GCF_007992115.1_ASM799211v1_genomic.fna.gz --refList GCF_007992115.1_ASM799211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992115.1_ASM799211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:10:54,061] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:54,073] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:10:54,074] [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_007992115.1	s__Aeromicrobium flavum	100.0	1013	1016	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_014334735.1	s__Aeromicrobium sp014334735	87.0264	791	1016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	99.41	98.82	0.96	0.93	3	-
GCF_013868155.1	s__Aeromicrobium phoceense	86.9386	794	1016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.64	97.64	0.92	0.92	2	-
GCF_013408555.1	s__Aeromicrobium tamlense	86.8975	776	1016	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	86.8605	777	1016	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:10:54,076] [INFO] GTDB search result was written to GCF_007992115.1_ASM799211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:10:54,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:10:54,079] [INFO] DFAST_QC result json was written to GCF_007992115.1_ASM799211v1_genomic.fna/dqc_result.json
[2024-01-24 11:10:54,080] [INFO] DFAST_QC completed!
[2024-01-24 11:10:54,080] [INFO] Total running time: 0h1m3s