[2024-01-24 15:27:10,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:10,479] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:10,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg6045cb64-0d04-4949-9691-207b3a3d2d65/dqc_reference
[2024-01-24 15:27:11,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:11,822] [INFO] Task started: Prodigal
[2024-01-24 15:27:11,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg1366ea5f-53d1-47ed-b5bf-5e16d4aacf55/GCF_002266845.1_ASM226684v1_genomic.fna.gz | prodigal -d GCF_002266845.1_ASM226684v1_genomic.fna/cds.fna -a GCF_002266845.1_ASM226684v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:36,509] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:36,509] [INFO] Task started: HMMsearch
[2024-01-24 15:27:36,509] [INFO] Running command: hmmsearch --tblout GCF_002266845.1_ASM226684v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6045cb64-0d04-4949-9691-207b3a3d2d65/dqc_reference/reference_markers.hmm GCF_002266845.1_ASM226684v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:36,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:36,871] [INFO] Found 6/6 markers.
[2024-01-24 15:27:36,939] [INFO] Query marker FASTA was written to GCF_002266845.1_ASM226684v1_genomic.fna/markers.fasta
[2024-01-24 15:27:36,940] [INFO] Task started: Blastn
[2024-01-24 15:27:36,940] [INFO] Running command: blastn -query GCF_002266845.1_ASM226684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6045cb64-0d04-4949-9691-207b3a3d2d65/dqc_reference/reference_markers.fasta -out GCF_002266845.1_ASM226684v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:38,257] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:38,260] [INFO] Selected 18 target genomes.
[2024-01-24 15:27:38,261] [INFO] Target genome list was writen to GCF_002266845.1_ASM226684v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:38,267] [INFO] Task started: fastANI
[2024-01-24 15:27:38,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg1366ea5f-53d1-47ed-b5bf-5e16d4aacf55/GCF_002266845.1_ASM226684v1_genomic.fna.gz --refList GCF_002266845.1_ASM226684v1_genomic.fna/target_genomes.txt --output GCF_002266845.1_ASM226684v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:17,088] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:17,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6045cb64-0d04-4949-9691-207b3a3d2d65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:17,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6045cb64-0d04-4949-9691-207b3a3d2d65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:17,104] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:28:17,104] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:17,104] [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
Micromonospora echinospora	strain=ATCC 15837	GCA_002266845.1	1877	1877	type	True	100.0	2522	2530	95	conclusive
Micromonospora echinospora	strain=DSM 43816	GCA_900091495.1	1877	1877	type	True	99.991	2527	2530	95	conclusive
Micromonospora sagamiensis	strain=JCM 3310	GCA_014680085.1	47875	47875	type	True	91.8616	1918	2530	95	below_threshold
Micromonospora sagamiensis	strain=DSM 43912	GCA_007829995.1	47875	47875	type	True	91.8442	1915	2530	95	below_threshold
Micromonospora inyonensis	strain=DSM 46123	GCA_900091415.1	47866	47866	type	True	91.2565	1685	2530	95	below_threshold
Micromonospora pallida	strain=DSM 43817	GCA_900090325.1	145854	145854	type	True	90.5217	1878	2530	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	84.529	1453	2530	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	84.4181	1060	2530	95	below_threshold
Micromonospora inositola	strain=DSM 43819	GCA_900090285.1	47865	47865	type	True	84.3949	1270	2530	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	84.1789	1449	2530	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	84.115	1550	2530	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	84.0604	1350	2530	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	84.0108	1290	2530	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	83.7173	1412	2530	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	83.661	1209	2530	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	83.5934	1409	2530	95	below_threshold
Micromonospora costi	strain=CS1-12	GCA_003626655.1	1530042	1530042	type	True	83.0425	1353	2530	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	82.9327	1252	2530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:17,106] [INFO] DFAST Taxonomy check result was written to GCF_002266845.1_ASM226684v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:17,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:17,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:17,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6045cb64-0d04-4949-9691-207b3a3d2d65/dqc_reference/checkm_data
[2024-01-24 15:28:17,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:17,177] [INFO] Task started: CheckM
[2024-01-24 15:28:17,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002266845.1_ASM226684v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002266845.1_ASM226684v1_genomic.fna/checkm_input GCF_002266845.1_ASM226684v1_genomic.fna/checkm_result
[2024-01-24 15:29:42,645] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:42,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:42,672] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:42,672] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:42,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002266845.1_ASM226684v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:42,673] [INFO] Task started: Blastn
[2024-01-24 15:29:42,673] [INFO] Running command: blastn -query GCF_002266845.1_ASM226684v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6045cb64-0d04-4949-9691-207b3a3d2d65/dqc_reference/reference_markers_gtdb.fasta -out GCF_002266845.1_ASM226684v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:44,516] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:44,520] [INFO] Selected 18 target genomes.
[2024-01-24 15:29:44,521] [INFO] Target genome list was writen to GCF_002266845.1_ASM226684v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:44,576] [INFO] Task started: fastANI
[2024-01-24 15:29:44,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg1366ea5f-53d1-47ed-b5bf-5e16d4aacf55/GCF_002266845.1_ASM226684v1_genomic.fna.gz --refList GCF_002266845.1_ASM226684v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002266845.1_ASM226684v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:21,132] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:21,152] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:21,153] [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_900091495.1	s__Micromonospora echinospora	99.991	2527	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.77	97.55	0.96	0.91	3	conclusive
GCF_900091415.1	s__Micromonospora inyonensis	91.277	1681	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.10	96.06	0.74	0.74	3	-
GCF_900090325.1	s__Micromonospora pallida	90.5522	1875	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	84.5765	1446	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090285.1	s__Micromonospora inositola	84.3981	1270	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090235.1	s__Micromonospora echinaurantiaca	84.3664	1416	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.93	95.22	0.84	0.83	3	-
GCF_003664255.1	s__Micromonospora sp003664255	84.338	1559	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830265.1	s__Micromonospora olivasterospora	84.281	1336	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090315.1	s__Micromonospora citrea	84.1585	1453	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205165.1	s__Micromonospora carbonacea	84.1382	1546	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	99.19	98.38	0.95	0.91	3	-
GCF_004217615.1	s__Micromonospora kangleipakensis	84.0571	1350	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598485.1	s__Micromonospora veneta	84.0346	1287	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091595.1	s__Micromonospora haikouensis	83.9692	1490	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.5545	97.81	97.42	0.87	0.87	3	-
GCF_003172935.1	s__Micromonospora sp003172935	83.8848	1236	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	83.8498	1240	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090305.1	s__Micromonospora siamensis	83.7521	1333	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626595.1	s__Micromonospora endolithica	83.6818	1363	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003626655.1	s__Micromonospora costi	83.0313	1355	2530	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:21,155] [INFO] GTDB search result was written to GCF_002266845.1_ASM226684v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:21,155] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:21,160] [INFO] DFAST_QC result json was written to GCF_002266845.1_ASM226684v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:21,160] [INFO] DFAST_QC completed!
[2024-01-24 15:30:21,161] [INFO] Total running time: 0h3m11s