[2024-01-25 19:53:20,510] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:20,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:20,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg049a7745-0ec2-4d98-b20b-da996ea60b58/dqc_reference
[2024-01-25 19:53:21,627] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:21,628] [INFO] Task started: Prodigal
[2024-01-25 19:53:21,628] [INFO] Running command: gunzip -c /var/lib/cwl/stg07525a85-5d5d-4bf1-9608-95ba731ee56e/GCF_016863615.1_ASM1686361v1_genomic.fna.gz | prodigal -d GCF_016863615.1_ASM1686361v1_genomic.fna/cds.fna -a GCF_016863615.1_ASM1686361v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:52,378] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:52,378] [INFO] Task started: HMMsearch
[2024-01-25 19:53:52,378] [INFO] Running command: hmmsearch --tblout GCF_016863615.1_ASM1686361v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg049a7745-0ec2-4d98-b20b-da996ea60b58/dqc_reference/reference_markers.hmm GCF_016863615.1_ASM1686361v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:52,883] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:52,884] [INFO] Found 6/6 markers.
[2024-01-25 19:53:52,961] [INFO] Query marker FASTA was written to GCF_016863615.1_ASM1686361v1_genomic.fna/markers.fasta
[2024-01-25 19:53:52,961] [INFO] Task started: Blastn
[2024-01-25 19:53:52,961] [INFO] Running command: blastn -query GCF_016863615.1_ASM1686361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg049a7745-0ec2-4d98-b20b-da996ea60b58/dqc_reference/reference_markers.fasta -out GCF_016863615.1_ASM1686361v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:54,141] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:54,144] [INFO] Selected 22 target genomes.
[2024-01-25 19:53:54,144] [INFO] Target genome list was writen to GCF_016863615.1_ASM1686361v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:54,169] [INFO] Task started: fastANI
[2024-01-25 19:53:54,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg07525a85-5d5d-4bf1-9608-95ba731ee56e/GCF_016863615.1_ASM1686361v1_genomic.fna.gz --refList GCF_016863615.1_ASM1686361v1_genomic.fna/target_genomes.txt --output GCF_016863615.1_ASM1686361v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:38,262] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:38,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg049a7745-0ec2-4d98-b20b-da996ea60b58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:38,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg049a7745-0ec2-4d98-b20b-da996ea60b58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:38,275] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:54:38,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:38,276] [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
Virgisporangium aliadipatigenens	strain=NBRC 105644	GCA_016863615.1	741659	741659	type	True	100.0	3367	3374	95	conclusive
Virgisporangium aurantiacum	strain=NBRC 16421	GCA_016863635.1	175570	175570	type	True	78.6809	1612	3374	95	below_threshold
Virgisporangium ochraceum	strain=NBRC 16418	GCA_016863655.1	65505	65505	type	True	78.6676	1560	3374	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	78.1587	871	3374	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	77.9394	901	3374	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	77.9111	1082	3374	95	below_threshold
Micromonospora purpureochromogenes	strain=DSM 43821	GCA_900091515.1	47872	47872	type	True	77.8995	1025	3374	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	77.8955	983	3374	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	77.8725	1080	3374	95	below_threshold
Micromonospora halophytica	strain=DSM 43171	GCA_900090245.1	47864	47864	type	True	77.8658	957	3374	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	77.8559	932	3374	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	77.8379	1028	3374	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	77.8376	1055	3374	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	77.8147	1060	3374	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	77.7976	1415	3374	95	below_threshold
Micromonospora endolithica	strain=JCM 12677	GCA_003626595.1	230091	230091	type	True	77.7014	1007	3374	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	77.6864	1481	3374	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	77.665	1299	3374	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	77.6611	1225	3374	95	below_threshold
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	77.0966	1019	3374	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	76.0655	904	3374	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	75.8849	787	3374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:38,277] [INFO] DFAST Taxonomy check result was written to GCF_016863615.1_ASM1686361v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:38,278] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:38,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:38,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg049a7745-0ec2-4d98-b20b-da996ea60b58/dqc_reference/checkm_data
[2024-01-25 19:54:38,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:38,369] [INFO] Task started: CheckM
[2024-01-25 19:54:38,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863615.1_ASM1686361v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863615.1_ASM1686361v1_genomic.fna/checkm_input GCF_016863615.1_ASM1686361v1_genomic.fna/checkm_result
[2024-01-25 19:56:42,359] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:42,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:42,379] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:42,380] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:42,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863615.1_ASM1686361v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:42,381] [INFO] Task started: Blastn
[2024-01-25 19:56:42,381] [INFO] Running command: blastn -query GCF_016863615.1_ASM1686361v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg049a7745-0ec2-4d98-b20b-da996ea60b58/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863615.1_ASM1686361v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:44,238] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:44,240] [INFO] Selected 18 target genomes.
[2024-01-25 19:56:44,241] [INFO] Target genome list was writen to GCF_016863615.1_ASM1686361v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:44,251] [INFO] Task started: fastANI
[2024-01-25 19:56:44,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg07525a85-5d5d-4bf1-9608-95ba731ee56e/GCF_016863615.1_ASM1686361v1_genomic.fna.gz --refList GCF_016863615.1_ASM1686361v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863615.1_ASM1686361v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:20,107] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:20,118] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:20,118] [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_016863615.1	s__Virgisporangium aliadipatigenens	100.0	3367	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016863635.1	s__Virgisporangium aurantiacum	78.6533	1624	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863655.1	s__Virgisporangium ochraceum	78.6454	1570	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Virgisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	78.2008	861	3374	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_016863255.1	s__Planosporangium mesophilum	78.1873	906	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011947225.1	s__Planosporangium flavigriseum	78.0972	775	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_011947195.1	s__Planosporangium thailandense	77.9363	921	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Planosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090305.1	s__Micromonospora siamensis	77.9172	977	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090245.1	s__Micromonospora halophytica	77.8829	950	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091435.1	s__Micromonospora chaiyaphumensis	77.8587	1024	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.16	95.15	0.86	0.86	3	-
GCF_007830265.1	s__Micromonospora olivasterospora	77.848	936	3374	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	77.8218	1059	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647515.1	s__Dactylosporangium sucinum	77.7922	1418	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	77.6717	1220	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	77.6508	1302	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905095.1	s__Micromonospora sp001905095	77.5346	1046	3374	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	77.5287	1102	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862975.1	s__Rugosimonospora africana	77.115	1009	3374	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Rugosimonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:20,120] [INFO] GTDB search result was written to GCF_016863615.1_ASM1686361v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:20,120] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:20,128] [INFO] DFAST_QC result json was written to GCF_016863615.1_ASM1686361v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:20,129] [INFO] DFAST_QC completed!
[2024-01-25 19:57:20,129] [INFO] Total running time: 0h3m60s