[2024-01-24 12:22:38,148] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:38,150] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:38,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg961dd48e-f5ec-4ad4-8ccf-ea2103029b0c/dqc_reference
[2024-01-24 12:22:39,508] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:39,509] [INFO] Task started: Prodigal
[2024-01-24 12:22:39,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg37021ff7-d64c-491f-8a39-f5a995426ea8/GCF_013694245.2_ASM1369424v2_genomic.fna.gz | prodigal -d GCF_013694245.2_ASM1369424v2_genomic.fna/cds.fna -a GCF_013694245.2_ASM1369424v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:04,519] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:04,520] [INFO] Task started: HMMsearch
[2024-01-24 12:23:04,520] [INFO] Running command: hmmsearch --tblout GCF_013694245.2_ASM1369424v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg961dd48e-f5ec-4ad4-8ccf-ea2103029b0c/dqc_reference/reference_markers.hmm GCF_013694245.2_ASM1369424v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:04,855] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:04,859] [INFO] Found 6/6 markers.
[2024-01-24 12:23:04,915] [INFO] Query marker FASTA was written to GCF_013694245.2_ASM1369424v2_genomic.fna/markers.fasta
[2024-01-24 12:23:04,915] [INFO] Task started: Blastn
[2024-01-24 12:23:04,915] [INFO] Running command: blastn -query GCF_013694245.2_ASM1369424v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg961dd48e-f5ec-4ad4-8ccf-ea2103029b0c/dqc_reference/reference_markers.fasta -out GCF_013694245.2_ASM1369424v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:06,224] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:06,228] [INFO] Selected 16 target genomes.
[2024-01-24 12:23:06,228] [INFO] Target genome list was writen to GCF_013694245.2_ASM1369424v2_genomic.fna/target_genomes.txt
[2024-01-24 12:23:06,236] [INFO] Task started: fastANI
[2024-01-24 12:23:06,236] [INFO] Running command: fastANI --query /var/lib/cwl/stg37021ff7-d64c-491f-8a39-f5a995426ea8/GCF_013694245.2_ASM1369424v2_genomic.fna.gz --refList GCF_013694245.2_ASM1369424v2_genomic.fna/target_genomes.txt --output GCF_013694245.2_ASM1369424v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:41,137] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:41,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg961dd48e-f5ec-4ad4-8ccf-ea2103029b0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:41,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg961dd48e-f5ec-4ad4-8ccf-ea2103029b0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:41,156] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:41,157] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:41,157] [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 ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	99.9845	2215	2233	95	conclusive
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	93.5556	1877	2233	95	below_threshold
Micromonospora sediminicola	strain=DSM 45794	GCA_900089585.1	946078	946078	type	True	91.0352	1808	2233	95	below_threshold
Micromonospora maritima		GCA_902825405.1	986711	986711	type	True	90.6037	1265	2233	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_000145235.1	47850	47850	type	True	89.4495	1714	2233	95	below_threshold
Micromonospora aurantiaca	strain=ATCC 27029	GCA_003721415.1	47850	47850	type	True	89.4265	1688	2233	95	below_threshold
Micromonospora chalcea	strain=DSM 43026	GCA_002926165.1	1874	1874	type	True	89.3548	1608	2233	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	88.927	1554	2233	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	88.6679	1621	2233	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	88.2328	1615	2233	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	88.1763	1581	2233	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	88.1557	1593	2233	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	85.3708	1085	2233	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	85.0673	1489	2233	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	84.7027	1292	2233	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	83.2675	1349	2233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:41,159] [INFO] DFAST Taxonomy check result was written to GCF_013694245.2_ASM1369424v2_genomic.fna/tc_result.tsv
[2024-01-24 12:23:41,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:41,160] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:41,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg961dd48e-f5ec-4ad4-8ccf-ea2103029b0c/dqc_reference/checkm_data
[2024-01-24 12:23:41,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:41,257] [INFO] Task started: CheckM
[2024-01-24 12:23:41,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013694245.2_ASM1369424v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013694245.2_ASM1369424v2_genomic.fna/checkm_input GCF_013694245.2_ASM1369424v2_genomic.fna/checkm_result
[2024-01-24 12:25:17,693] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:17,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:17,717] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:17,718] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:17,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013694245.2_ASM1369424v2_genomic.fna/markers.fasta)
[2024-01-24 12:25:17,718] [INFO] Task started: Blastn
[2024-01-24 12:25:17,719] [INFO] Running command: blastn -query GCF_013694245.2_ASM1369424v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg961dd48e-f5ec-4ad4-8ccf-ea2103029b0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_013694245.2_ASM1369424v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:19,921] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:19,925] [INFO] Selected 10 target genomes.
[2024-01-24 12:25:19,926] [INFO] Target genome list was writen to GCF_013694245.2_ASM1369424v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:19,932] [INFO] Task started: fastANI
[2024-01-24 12:25:19,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg37021ff7-d64c-491f-8a39-f5a995426ea8/GCF_013694245.2_ASM1369424v2_genomic.fna.gz --refList GCF_013694245.2_ASM1369424v2_genomic.fna/target_genomes_gtdb.txt --output GCF_013694245.2_ASM1369424v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:44,284] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:44,300] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:44,300] [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_013694245.1	s__Micromonospora sp013694245	99.9844	2215	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900090105.1	s__Micromonospora humi	93.5114	1882	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003027925.1	s__Micromonospora sp003027925	91.8211	1806	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900089585.1	s__Micromonospora sediminicola	91.0529	1804	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	98.55	97.81	0.94	0.92	3	-
GCF_002140155.1	s__Micromonospora sp002140155	90.7229	1657	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902825405.1	s__Micromonospora maritima	90.6566	1261	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000145235.1	s__Micromonospora aurantiaca	89.4067	1720	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	98.37	95.58	0.90	0.84	15	-
GCF_002926165.1	s__Micromonospora chalcea	89.3881	1604	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.52	95.31	0.89	0.84	18	-
GCF_014648395.1	s__Micromonospora fulviviridis	88.6609	1622	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	88.267	1611	2233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:44,302] [INFO] GTDB search result was written to GCF_013694245.2_ASM1369424v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:44,302] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:44,306] [INFO] DFAST_QC result json was written to GCF_013694245.2_ASM1369424v2_genomic.fna/dqc_result.json
[2024-01-24 12:25:44,306] [INFO] DFAST_QC completed!
[2024-01-24 12:25:44,306] [INFO] Total running time: 0h3m6s