[2024-01-24 12:06:18,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:18,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:18,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg05b2cb71-6bfa-4e35-91f2-dca59665e869/dqc_reference
[2024-01-24 12:06:20,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:20,166] [INFO] Task started: Prodigal
[2024-01-24 12:06:20,166] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ffd24d2-ed37-4ef3-a1df-0be5a468d14c/GCF_016925615.1_ASM1692561v1_genomic.fna.gz | prodigal -d GCF_016925615.1_ASM1692561v1_genomic.fna/cds.fna -a GCF_016925615.1_ASM1692561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:37,104] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:37,105] [INFO] Task started: HMMsearch
[2024-01-24 12:06:37,105] [INFO] Running command: hmmsearch --tblout GCF_016925615.1_ASM1692561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05b2cb71-6bfa-4e35-91f2-dca59665e869/dqc_reference/reference_markers.hmm GCF_016925615.1_ASM1692561v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:37,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:37,417] [INFO] Found 6/6 markers.
[2024-01-24 12:06:37,469] [INFO] Query marker FASTA was written to GCF_016925615.1_ASM1692561v1_genomic.fna/markers.fasta
[2024-01-24 12:06:37,470] [INFO] Task started: Blastn
[2024-01-24 12:06:37,470] [INFO] Running command: blastn -query GCF_016925615.1_ASM1692561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05b2cb71-6bfa-4e35-91f2-dca59665e869/dqc_reference/reference_markers.fasta -out GCF_016925615.1_ASM1692561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:38,513] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:38,517] [INFO] Selected 22 target genomes.
[2024-01-24 12:06:38,517] [INFO] Target genome list was writen to GCF_016925615.1_ASM1692561v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:38,525] [INFO] Task started: fastANI
[2024-01-24 12:06:38,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ffd24d2-ed37-4ef3-a1df-0be5a468d14c/GCF_016925615.1_ASM1692561v1_genomic.fna.gz --refList GCF_016925615.1_ASM1692561v1_genomic.fna/target_genomes.txt --output GCF_016925615.1_ASM1692561v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:08,081] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:08,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05b2cb71-6bfa-4e35-91f2-dca59665e869/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:08,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05b2cb71-6bfa-4e35-91f2-dca59665e869/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:08,103] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:08,103] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:08,103] [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
Natronosporangium hydrolyticum	strain=DSM 106523	GCA_016925615.1	2811111	2811111	type	True	100.0	1899	1899	95	conclusive
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	77.953	536	1899	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	77.9413	612	1899	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	77.863	679	1899	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	77.84	650	1899	95	below_threshold
Micromonospora yangpuensis	strain=DSM 45577	GCA_900091615.1	683228	683228	type	True	77.7292	634	1899	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	77.692	686	1899	95	below_threshold
Micromonospora yangpuensis	strain=CGMCC 4.5736	GCA_014645775.1	683228	683228	type	True	77.6694	633	1899	95	below_threshold
Micromonospora deserti	strain=13K206	GCA_003236335.1	2070366	2070366	type	True	77.6622	618	1899	95	below_threshold
Micromonospora echinofusca	strain=DSM 43913	GCA_900091445.1	47858	47858	type	True	77.6593	678	1899	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	77.5998	646	1899	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	77.5972	684	1899	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	77.5912	643	1899	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	77.5726	630	1899	95	below_threshold
Micromonospora wenchangensis	strain=CCTCC AA 2012002	GCA_002210435.1	1185415	1185415	type	True	77.5006	691	1899	95	below_threshold
Salinispora cortesiana	strain=CNY-202	GCA_000484695.1	1305843	1305843	type	True	77.4181	471	1899	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	77.2378	727	1899	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	77.026	652	1899	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	76.9865	626	1899	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	76.8742	741	1899	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	76.7686	722	1899	95	below_threshold
Actinoplanes rishiriensis	strain=NBRC 108556	GCA_016862375.1	1050105	1050105	type	True	76.6205	650	1899	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:08,105] [INFO] DFAST Taxonomy check result was written to GCF_016925615.1_ASM1692561v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:08,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:08,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:08,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05b2cb71-6bfa-4e35-91f2-dca59665e869/dqc_reference/checkm_data
[2024-01-24 12:07:08,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:08,164] [INFO] Task started: CheckM
[2024-01-24 12:07:08,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016925615.1_ASM1692561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016925615.1_ASM1692561v1_genomic.fna/checkm_input GCF_016925615.1_ASM1692561v1_genomic.fna/checkm_result
[2024-01-24 12:07:59,626] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:59,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:59,655] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:59,655] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:59,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016925615.1_ASM1692561v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:59,656] [INFO] Task started: Blastn
[2024-01-24 12:07:59,656] [INFO] Running command: blastn -query GCF_016925615.1_ASM1692561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05b2cb71-6bfa-4e35-91f2-dca59665e869/dqc_reference/reference_markers_gtdb.fasta -out GCF_016925615.1_ASM1692561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:01,180] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:01,184] [INFO] Selected 21 target genomes.
[2024-01-24 12:08:01,185] [INFO] Target genome list was writen to GCF_016925615.1_ASM1692561v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:01,201] [INFO] Task started: fastANI
[2024-01-24 12:08:01,202] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ffd24d2-ed37-4ef3-a1df-0be5a468d14c/GCF_016925615.1_ASM1692561v1_genomic.fna.gz --refList GCF_016925615.1_ASM1692561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016925615.1_ASM1692561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:29,978] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:30,007] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:30,007] [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
GCA_016925615.1	s__SLSW01 sp016925615	100.0	1899	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__SLSW01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009377645.1	s__SLSW01 sp009377645	79.0919	714	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__SLSW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130245.1	s__SLSW01 sp007130245	78.6868	555	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__SLSW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091465.1	s__Micromonospora rhizosphaerae	77.9716	606	1899	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	77.8361	627	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.98	99.95	0.98	0.97	4	-
GCF_003751085.1	s__Micromonospora_E sp003751085	77.8031	691	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003172935.1	s__Micromonospora sp003172935	77.7976	627	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.27	99.27	0.87	0.87	2	-
GCF_004217615.1	s__Micromonospora kangleipakensis	77.7643	661	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236305.1	s__Micromonospora endophytica	77.696	570	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	99.96	99.96	0.99	0.98	3	-
GCF_003236335.1	s__Micromonospora deserti	77.6537	619	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091445.1	s__Micromonospora echinofusca	77.6395	682	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	97.23	97.23	0.90	0.90	2	-
GCF_000982955.1	s__Micromonospora sp000982955	77.5938	655	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001567585.1	s__Micromonospora rosaria	77.5862	686	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	77.5355	672	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210435.1	s__Micromonospora wenchangensis	77.5046	690	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.84	95.43	0.85	0.83	5	-
GCF_018324255.1	s__Polymorphospora rubra	77.315	698	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	77.2561	723	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	77.0361	649	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_014205225.1	s__Actinoplanes octamycinicus	76.8806	735	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000284295.1	s__Actinoplanes missouriensis	76.7355	585	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862375.1	s__Actinoplanes rishiriensis	76.5983	657	1899	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:30,009] [INFO] GTDB search result was written to GCF_016925615.1_ASM1692561v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:30,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:30,014] [INFO] DFAST_QC result json was written to GCF_016925615.1_ASM1692561v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:30,014] [INFO] DFAST_QC completed!
[2024-01-24 12:08:30,014] [INFO] Total running time: 0h2m11s