[2024-01-24 11:12:53,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:53,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:53,107] [INFO] DQC Reference Directory: /var/lib/cwl/stg43524161-a0a0-4410-9460-b0a548d80f39/dqc_reference
[2024-01-24 11:12:55,436] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:55,437] [INFO] Task started: Prodigal
[2024-01-24 11:12:55,437] [INFO] Running command: gunzip -c /var/lib/cwl/stgce474cfb-3360-4006-9064-481545569e0a/GCF_016862875.1_ASM1686287v1_genomic.fna.gz | prodigal -d GCF_016862875.1_ASM1686287v1_genomic.fna/cds.fna -a GCF_016862875.1_ASM1686287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:12,239] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:12,240] [INFO] Task started: HMMsearch
[2024-01-24 11:13:12,240] [INFO] Running command: hmmsearch --tblout GCF_016862875.1_ASM1686287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43524161-a0a0-4410-9460-b0a548d80f39/dqc_reference/reference_markers.hmm GCF_016862875.1_ASM1686287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:12,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:12,604] [INFO] Found 6/6 markers.
[2024-01-24 11:13:12,649] [INFO] Query marker FASTA was written to GCF_016862875.1_ASM1686287v1_genomic.fna/markers.fasta
[2024-01-24 11:13:12,650] [INFO] Task started: Blastn
[2024-01-24 11:13:12,650] [INFO] Running command: blastn -query GCF_016862875.1_ASM1686287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43524161-a0a0-4410-9460-b0a548d80f39/dqc_reference/reference_markers.fasta -out GCF_016862875.1_ASM1686287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:13,914] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:13,917] [INFO] Selected 31 target genomes.
[2024-01-24 11:13:13,917] [INFO] Target genome list was writen to GCF_016862875.1_ASM1686287v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:13,935] [INFO] Task started: fastANI
[2024-01-24 11:13:13,935] [INFO] Running command: fastANI --query /var/lib/cwl/stgce474cfb-3360-4006-9064-481545569e0a/GCF_016862875.1_ASM1686287v1_genomic.fna.gz --refList GCF_016862875.1_ASM1686287v1_genomic.fna/target_genomes.txt --output GCF_016862875.1_ASM1686287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:55,445] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:55,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43524161-a0a0-4410-9460-b0a548d80f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:55,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43524161-a0a0-4410-9460-b0a548d80f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:55,472] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:55,472] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:55,473] [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 pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	79.5078	777	1836	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	79.0721	749	1836	95	below_threshold
Micromonospora kangleipakensis	strain=DSM 45612	GCA_004217615.1	1077942	1077942	type	True	79.066	762	1836	95	below_threshold
Micromonospora eburnea	strain=DSM 44814	GCA_900090225.1	227316	227316	type	True	79.0227	719	1836	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	78.9535	718	1836	95	below_threshold
Micromonospora terminaliae	strain=DSM 101760	GCA_009671205.1	1914461	1914461	type	True	78.9534	775	1836	95	below_threshold
Micromonospora auratinigra	strain=DSM 44815	GCA_900089595.1	261654	261654	type	True	78.9521	758	1836	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.9505	677	1836	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	78.9281	753	1836	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	78.9036	773	1836	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	78.896	763	1836	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	78.8901	782	1836	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	78.8681	751	1836	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	78.8164	787	1836	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	78.772	809	1836	95	below_threshold
Micromonospora echinospora	strain=ATCC 15837	GCA_002266845.1	1877	1877	type	True	78.7333	693	1836	95	below_threshold
Micromonospora echinospora	strain=DSM 43816	GCA_900091495.1	1877	1877	type	True	78.7333	707	1836	95	below_threshold
Micromonospora musae	strain=MS1-9	GCA_003626635.1	1894970	1894970	type	True	78.6892	687	1836	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	78.6739	784	1836	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	78.6706	750	1836	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	78.6364	839	1836	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.6103	724	1836	95	below_threshold
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	78.6091	660	1836	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	78.5686	822	1836	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	78.3815	782	1836	95	below_threshold
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	78.3035	714	1836	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	78.2553	723	1836	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	78.1971	708	1836	95	below_threshold
Virgisporangium aliadipatigenens	strain=NBRC 105644	GCA_016863615.1	741659	741659	type	True	78.168	750	1836	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	76.9351	443	1836	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	76.3874	561	1836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:55,474] [INFO] DFAST Taxonomy check result was written to GCF_016862875.1_ASM1686287v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:55,475] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:55,475] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:55,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43524161-a0a0-4410-9460-b0a548d80f39/dqc_reference/checkm_data
[2024-01-24 11:13:55,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:55,526] [INFO] Task started: CheckM
[2024-01-24 11:13:55,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862875.1_ASM1686287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862875.1_ASM1686287v1_genomic.fna/checkm_input GCF_016862875.1_ASM1686287v1_genomic.fna/checkm_result
[2024-01-24 11:14:42,622] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:42,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:42,648] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:42,649] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:42,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862875.1_ASM1686287v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:42,649] [INFO] Task started: Blastn
[2024-01-24 11:14:42,650] [INFO] Running command: blastn -query GCF_016862875.1_ASM1686287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43524161-a0a0-4410-9460-b0a548d80f39/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862875.1_ASM1686287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:44,586] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:44,590] [INFO] Selected 16 target genomes.
[2024-01-24 11:14:44,590] [INFO] Target genome list was writen to GCF_016862875.1_ASM1686287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:44,601] [INFO] Task started: fastANI
[2024-01-24 11:14:44,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgce474cfb-3360-4006-9064-481545569e0a/GCF_016862875.1_ASM1686287v1_genomic.fna.gz --refList GCF_016862875.1_ASM1686287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862875.1_ASM1686287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:07,567] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:07,580] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:07,581] [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_011947225.1	s__Planosporangium flavigriseum	99.9924	1832	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_016863255.1	s__Planosporangium mesophilum	84.7495	1271	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011947195.1	s__Planosporangium thailandense	84.2759	1246	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	79.4805	781	1836	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_900090295.1	s__Micromonospora coxensis	79.0328	756	1836	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	79.0131	736	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013694245.1	s__Micromonospora sp013694245	78.9286	758	1836	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	78.8783	761	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091555.1	s__Micromonospora mirobrigensis	78.868	751	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348525.1	s__Micromonospora sp004348525	78.8472	649	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018324255.1	s__Polymorphospora rubra	78.6723	714	1836	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	78.6619	786	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018397995.1	s__NBRC-107566 sp018397995	78.6545	677	1836	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_011764565.1	s__Phytohabitans suffuscus	78.5828	818	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633685.1	s__Micromonospora_G pisi	78.5045	692	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863615.1	s__Virgisporangium aliadipatigenens	78.1392	756	1836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:07,582] [INFO] GTDB search result was written to GCF_016862875.1_ASM1686287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:07,583] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:07,587] [INFO] DFAST_QC result json was written to GCF_016862875.1_ASM1686287v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:07,588] [INFO] DFAST_QC completed!
[2024-01-24 11:15:07,588] [INFO] Total running time: 0h2m14s