[2024-01-24 15:10:53,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:53,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:53,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8786695-fe79-4491-9455-d384a40ed46e/dqc_reference
[2024-01-24 15:10:56,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,634] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,635] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8b471c7-b443-47e9-8b1b-456644c90828/GCF_014647895.1_ASM1464789v1_genomic.fna.gz | prodigal -d GCF_014647895.1_ASM1464789v1_genomic.fna/cds.fna -a GCF_014647895.1_ASM1464789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:10,873] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:10,873] [INFO] Task started: HMMsearch
[2024-01-24 15:11:10,873] [INFO] Running command: hmmsearch --tblout GCF_014647895.1_ASM1464789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8786695-fe79-4491-9455-d384a40ed46e/dqc_reference/reference_markers.hmm GCF_014647895.1_ASM1464789v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:11,159] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:11,161] [INFO] Found 6/6 markers.
[2024-01-24 15:11:11,208] [INFO] Query marker FASTA was written to GCF_014647895.1_ASM1464789v1_genomic.fna/markers.fasta
[2024-01-24 15:11:11,208] [INFO] Task started: Blastn
[2024-01-24 15:11:11,209] [INFO] Running command: blastn -query GCF_014647895.1_ASM1464789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8786695-fe79-4491-9455-d384a40ed46e/dqc_reference/reference_markers.fasta -out GCF_014647895.1_ASM1464789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:12,527] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:12,531] [INFO] Selected 22 target genomes.
[2024-01-24 15:11:12,532] [INFO] Target genome list was writen to GCF_014647895.1_ASM1464789v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:12,550] [INFO] Task started: fastANI
[2024-01-24 15:11:12,551] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b471c7-b443-47e9-8b1b-456644c90828/GCF_014647895.1_ASM1464789v1_genomic.fna.gz --refList GCF_014647895.1_ASM1464789v1_genomic.fna/target_genomes.txt --output GCF_014647895.1_ASM1464789v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:49,481] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:49,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8786695-fe79-4491-9455-d384a40ed46e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:49,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8786695-fe79-4491-9455-d384a40ed46e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:49,505] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:49,505] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:49,506] [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
Pilimelia anulata	strain=JCM 3090	GCA_014647895.1	53371	53371	type	True	100.0	1698	1701	95	conclusive
Pilimelia terevasa	strain=JCM 3091	GCA_014647915.1	53372	53372	type	True	83.9665	1087	1701	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	79.099	840	1701	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	78.9832	762	1701	95	below_threshold
Micromonospora tulbaghiae	strain=DSM 45142	GCA_900091605.1	479978	479978	type	True	78.9769	863	1701	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	78.9311	896	1701	95	below_threshold
Micromonospora haikouensis	strain=DSM 45626	GCA_900091595.1	686309	686309	type	True	78.8708	920	1701	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	78.8118	846	1701	95	below_threshold
Micromonospora radicis	strain=AZ1-13	GCA_003583405.1	1894971	1894971	type	True	78.8047	751	1701	95	below_threshold
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	78.7851	878	1701	95	below_threshold
Micromonospora citrea	strain=DSM 43903	GCA_900090315.1	47855	47855	type	True	78.7832	887	1701	95	below_threshold
Micromonospora peucetia	strain=DSM 43363	GCA_900091625.1	47871	47871	type	True	78.7787	829	1701	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	78.7661	890	1701	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	78.7561	765	1701	95	below_threshold
Micromonospora endolithica	strain=DSM 44398	GCA_007994185.1	230091	230091	type	True	78.7416	851	1701	95	below_threshold
Micromonospora endolithica	strain=JCM 12677	GCA_003626595.1	230091	230091	type	True	78.6771	850	1701	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	78.5194	760	1701	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	78.2851	641	1701	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	78.275	908	1701	95	below_threshold
Salinispora mooreana	strain=DSM 45549	GCA_000379065.1	999545	999545	type	True	78.2022	546	1701	95	below_threshold
Catellatospora methionotrophica	strain=IMSNU 22006	GCA_011297335.1	121620	121620	type	True	77.9088	819	1701	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	77.8996	825	1701	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:49,508] [INFO] DFAST Taxonomy check result was written to GCF_014647895.1_ASM1464789v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:49,508] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:49,508] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:49,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8786695-fe79-4491-9455-d384a40ed46e/dqc_reference/checkm_data
[2024-01-24 15:11:49,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:49,567] [INFO] Task started: CheckM
[2024-01-24 15:11:49,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647895.1_ASM1464789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647895.1_ASM1464789v1_genomic.fna/checkm_input GCF_014647895.1_ASM1464789v1_genomic.fna/checkm_result
[2024-01-24 15:12:34,836] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:34,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:34,863] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:34,863] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:34,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647895.1_ASM1464789v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:34,864] [INFO] Task started: Blastn
[2024-01-24 15:12:34,864] [INFO] Running command: blastn -query GCF_014647895.1_ASM1464789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8786695-fe79-4491-9455-d384a40ed46e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647895.1_ASM1464789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:36,648] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:36,652] [INFO] Selected 22 target genomes.
[2024-01-24 15:12:36,652] [INFO] Target genome list was writen to GCF_014647895.1_ASM1464789v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:36,667] [INFO] Task started: fastANI
[2024-01-24 15:12:36,668] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b471c7-b443-47e9-8b1b-456644c90828/GCF_014647895.1_ASM1464789v1_genomic.fna.gz --refList GCF_014647895.1_ASM1464789v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647895.1_ASM1464789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:11,175] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:11,205] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:11,205] [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_014647895.1	s__Pilimelia anulata	100.0	1698	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014647915.1	s__Pilimelia terevasa	83.9464	1089	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Pilimelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830265.1	s__Micromonospora olivasterospora	79.0794	844	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217615.1	s__Micromonospora kangleipakensis	79.0256	867	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725545.1	s__Micromonospora sp003725545	79.0021	807	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_900091605.1	s__Micromonospora tulbaghiae	78.9759	864	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.1942	97.73	96.20	0.92	0.87	5	-
GCF_900091445.1	s__Micromonospora echinofusca	78.8213	870	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.23	97.23	0.90	0.90	2	-
GCF_018397995.1	s__NBRC-107566 sp018397995	78.8083	771	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__NBRC-107566	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583405.1	s__Micromonospora radicis	78.8054	750	1701	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	78.8054	882	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091585.1	s__Micromonospora nigra	78.7205	772	1701	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	78.6908	846	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004348525.1	s__Micromonospora sp004348525	78.5812	762	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846275.1	s__Plantactinospora sp002846275	78.5628	783	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003030345.1	s__Plantactinospora sp003030345	78.5485	869	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	98.72	98.72	0.95	0.95	2	-
GCF_017614955.1	s__Micromonospora echinofusca_A	78.5463	753	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862915.1	s__Plantactinospora endophytica	78.5294	891	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010560025.1	s__Micromonospora sp010560025	78.4872	746	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.75	99.70	1.00	1.00	3	-
GCF_004217235.1	s__Plantactinospora sp004217235	78.3117	816	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863495.1	s__Micromonospora andamanensis	78.2855	725	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	96.71	95.67	0.86	0.84	3	-
GCF_011297335.1	s__Catellatospora methionotrophica	77.9424	811	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	99.99	99.99	0.99	0.99	2	-
GCA_009377645.1	s__SLSW01 sp009377645	77.7791	641	1701	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__SLSW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:11,207] [INFO] GTDB search result was written to GCF_014647895.1_ASM1464789v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:11,207] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:11,212] [INFO] DFAST_QC result json was written to GCF_014647895.1_ASM1464789v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:11,212] [INFO] DFAST_QC completed!
[2024-01-24 15:13:11,212] [INFO] Total running time: 0h2m17s