[2024-01-24 14:14:30,878] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:30,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:30,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c910d2e-30c1-47ca-a2d6-544be4041e7a/dqc_reference
[2024-01-24 14:14:32,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:32,114] [INFO] Task started: Prodigal
[2024-01-24 14:14:32,114] [INFO] Running command: gunzip -c /var/lib/cwl/stgb01d8c94-5b34-4f54-8602-f61398a43ccf/GCF_006151975.2_ASM615197v2_genomic.fna.gz | prodigal -d GCF_006151975.2_ASM615197v2_genomic.fna/cds.fna -a GCF_006151975.2_ASM615197v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:44,855] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:44,856] [INFO] Task started: HMMsearch
[2024-01-24 14:14:44,856] [INFO] Running command: hmmsearch --tblout GCF_006151975.2_ASM615197v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c910d2e-30c1-47ca-a2d6-544be4041e7a/dqc_reference/reference_markers.hmm GCF_006151975.2_ASM615197v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:45,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:45,213] [INFO] Found 6/6 markers.
[2024-01-24 14:14:45,257] [INFO] Query marker FASTA was written to GCF_006151975.2_ASM615197v2_genomic.fna/markers.fasta
[2024-01-24 14:14:45,258] [INFO] Task started: Blastn
[2024-01-24 14:14:45,258] [INFO] Running command: blastn -query GCF_006151975.2_ASM615197v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c910d2e-30c1-47ca-a2d6-544be4041e7a/dqc_reference/reference_markers.fasta -out GCF_006151975.2_ASM615197v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:46,435] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:46,439] [INFO] Selected 26 target genomes.
[2024-01-24 14:14:46,439] [INFO] Target genome list was writen to GCF_006151975.2_ASM615197v2_genomic.fna/target_genomes.txt
[2024-01-24 14:14:46,483] [INFO] Task started: fastANI
[2024-01-24 14:14:46,483] [INFO] Running command: fastANI --query /var/lib/cwl/stgb01d8c94-5b34-4f54-8602-f61398a43ccf/GCF_006151975.2_ASM615197v2_genomic.fna.gz --refList GCF_006151975.2_ASM615197v2_genomic.fna/target_genomes.txt --output GCF_006151975.2_ASM615197v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:07,848] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:07,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c910d2e-30c1-47ca-a2d6-544be4041e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:07,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c910d2e-30c1-47ca-a2d6-544be4041e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:07,873] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:15:07,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:15:07,874] [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	80.8986	818	1536	95	below_threshold
Aeromicrobium massiliense	strain=JC14	GCA_000312105.1	1464554	1464554	type	True	78.9439	530	1536	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	78.9426	452	1536	95	below_threshold
Aeromicrobium chenweiae	strain=592	GCA_003065605.1	2079793	2079793	type	True	78.9407	494	1536	95	below_threshold
Aeromicrobium stalagmiti	strain=YC3-14	GCA_013283745.1	2738988	2738988	type	True	78.9316	507	1536	95	below_threshold
Aeromicrobium yanjiei	strain=MF47	GCA_009649075.1	2662028	2662028	type	True	78.8075	486	1536	95	below_threshold
Aeromicrobium fastidiosum	strain=DSM 10552	GCA_017876595.1	52699	52699	type	True	78.747	501	1536	95	below_threshold
Aeromicrobium ginsengisoli	strain=JCM 14732	GCA_004134905.2	363867	363867	type	True	78.719	502	1536	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	78.7084	499	1536	95	below_threshold
Aeromicrobium tamlense	strain=DSM 19087	GCA_013408555.1	375541	375541	type	True	78.6372	493	1536	95	below_threshold
Aeromicrobium phoceense	strain=Marseille-Q0843	GCA_013868155.1	2754045	2754045	type	True	78.5859	453	1536	95	below_threshold
Aeromicrobium tamlense	strain=SSW1-57	GCA_014672995.1	375541	375541	type	True	78.4968	491	1536	95	below_threshold
Aeromicrobium erythreum	strain=AR18	GCA_001509405.1	2041	2041	type	True	78.4778	500	1536	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	78.3877	522	1536	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	78.1331	495	1536	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	77.994	499	1536	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	77.9704	516	1536	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	77.9384	482	1536	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	77.8466	447	1536	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	77.8393	466	1536	95	below_threshold
Marmoricola solisilvae	strain=KIS18-7	GCA_003725775.1	1542737	1542737	type	True	77.7927	391	1536	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	76.9213	354	1536	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.9192	343	1536	95	below_threshold
Actinopolymorpha cephalotaxi	strain=DSM 45117	GCA_013408535.1	504797	504797	type	True	76.8938	361	1536	95	below_threshold
Actinopolymorpha singaporensis	strain=DSM 22024	GCA_900104745.1	117157	117157	type	True	76.8602	357	1536	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	76.3854	431	1536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:07,875] [INFO] DFAST Taxonomy check result was written to GCF_006151975.2_ASM615197v2_genomic.fna/tc_result.tsv
[2024-01-24 14:15:07,876] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:07,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:07,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c910d2e-30c1-47ca-a2d6-544be4041e7a/dqc_reference/checkm_data
[2024-01-24 14:15:07,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:07,925] [INFO] Task started: CheckM
[2024-01-24 14:15:07,925] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006151975.2_ASM615197v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006151975.2_ASM615197v2_genomic.fna/checkm_input GCF_006151975.2_ASM615197v2_genomic.fna/checkm_result
[2024-01-24 14:16:13,828] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:13,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:13,846] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:13,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:13,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006151975.2_ASM615197v2_genomic.fna/markers.fasta)
[2024-01-24 14:16:13,848] [INFO] Task started: Blastn
[2024-01-24 14:16:13,848] [INFO] Running command: blastn -query GCF_006151975.2_ASM615197v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c910d2e-30c1-47ca-a2d6-544be4041e7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006151975.2_ASM615197v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:16,003] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:16,006] [INFO] Selected 18 target genomes.
[2024-01-24 14:16:16,007] [INFO] Target genome list was writen to GCF_006151975.2_ASM615197v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:16,028] [INFO] Task started: fastANI
[2024-01-24 14:16:16,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgb01d8c94-5b34-4f54-8602-f61398a43ccf/GCF_006151975.2_ASM615197v2_genomic.fna.gz --refList GCF_006151975.2_ASM615197v2_genomic.fna/target_genomes_gtdb.txt --output GCF_006151975.2_ASM615197v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:34,123] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:34,142] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:34,142] [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_010994095.1	s__Mumia xiangluensis	100.0	1516	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCF_014127285.1	s__Mumia sp014127285	83.4466	1057	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	99.73	99.46	0.99	0.98	3	-
GCF_002797495.1	s__Mumia flava	80.9083	817	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Mumia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428805.1	s__Aeromicrobium sp001428805	78.9629	488	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426485.1	s__Aeromicrobium sp001426485	78.9609	519	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	97.44	97.44	0.91	0.91	2	-
GCF_000312105.1	s__Aeromicrobium massiliense	78.956	528	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425755.1	s__Aeromicrobium sp001425755	78.881	478	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336805.1	s__Aeromicrobium sp004336805	78.8752	520	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992115.1	s__Aeromicrobium flavum	78.7604	436	1536	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	78.7112	406	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	99.41	98.82	0.96	0.93	3	-
GCF_013408555.1	s__Aeromicrobium tamlense	78.6294	494	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Aeromicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	78.3907	522	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361955.1	s__JABFXA01 sp013361955	77.9112	449	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_010686755.1	s__Nocardioides zeae	77.8624	452	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725775.1	s__Marmoricola solisilvae	77.777	392	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715835.1	s__Nocardioides sp006715835	77.2351	460	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408535.1	s__Actinopolymorpha cephalotaxi	76.8876	362	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Actinopolymorpha	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016907715.1	s__Tenggerimyces flavus	76.7271	429	1536	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Actinopolymorphaceae;g__Tenggerimyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:34,144] [INFO] GTDB search result was written to GCF_006151975.2_ASM615197v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:34,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:34,149] [INFO] DFAST_QC result json was written to GCF_006151975.2_ASM615197v2_genomic.fna/dqc_result.json
[2024-01-24 14:16:34,149] [INFO] DFAST_QC completed!
[2024-01-24 14:16:34,149] [INFO] Total running time: 0h2m3s