[2024-01-25 19:01:05,768] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:01:05,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:01:05,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg822cfb48-47e4-4a4c-819f-b229b7e9cfe7/dqc_reference
[2024-01-25 19:01:06,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:01:06,939] [INFO] Task started: Prodigal
[2024-01-25 19:01:06,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ed5c772-5890-4246-a4be-8d680f08c751/GCF_011764545.1_ASM1176454v1_genomic.fna.gz | prodigal -d GCF_011764545.1_ASM1176454v1_genomic.fna/cds.fna -a GCF_011764545.1_ASM1176454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:01:40,595] [INFO] Task succeeded: Prodigal
[2024-01-25 19:01:40,595] [INFO] Task started: HMMsearch
[2024-01-25 19:01:40,595] [INFO] Running command: hmmsearch --tblout GCF_011764545.1_ASM1176454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg822cfb48-47e4-4a4c-819f-b229b7e9cfe7/dqc_reference/reference_markers.hmm GCF_011764545.1_ASM1176454v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:01:41,017] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:01:41,018] [INFO] Found 6/6 markers.
[2024-01-25 19:01:41,089] [INFO] Query marker FASTA was written to GCF_011764545.1_ASM1176454v1_genomic.fna/markers.fasta
[2024-01-25 19:01:41,090] [INFO] Task started: Blastn
[2024-01-25 19:01:41,090] [INFO] Running command: blastn -query GCF_011764545.1_ASM1176454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg822cfb48-47e4-4a4c-819f-b229b7e9cfe7/dqc_reference/reference_markers.fasta -out GCF_011764545.1_ASM1176454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:01:42,242] [INFO] Task succeeded: Blastn
[2024-01-25 19:01:42,244] [INFO] Selected 17 target genomes.
[2024-01-25 19:01:42,245] [INFO] Target genome list was writen to GCF_011764545.1_ASM1176454v1_genomic.fna/target_genomes.txt
[2024-01-25 19:01:42,254] [INFO] Task started: fastANI
[2024-01-25 19:01:42,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ed5c772-5890-4246-a4be-8d680f08c751/GCF_011764545.1_ASM1176454v1_genomic.fna.gz --refList GCF_011764545.1_ASM1176454v1_genomic.fna/target_genomes.txt --output GCF_011764545.1_ASM1176454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:18,173] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:18,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg822cfb48-47e4-4a4c-819f-b229b7e9cfe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:18,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg822cfb48-47e4-4a4c-819f-b229b7e9cfe7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:18,188] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:18,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:18,189] [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
Phytohabitans flavus	strain=NBRC 107702	GCA_011764545.1	1076124	1076124	type	True	100.0	3202	3202	95	conclusive
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	88.2058	2125	3202	95	below_threshold
Phytohabitans houttuyneae	strain=NBRC 108639	GCA_011764425.1	1076126	1076126	type	True	87.2723	2143	3202	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	82.668	1736	3202	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	79.8745	1019	3202	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.7542	868	3202	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.523	1011	3202	95	below_threshold
Micromonospora palomenae	strain=DSM 102131	GCA_007829925.1	1461247	1461247	type	True	79.5166	1122	3202	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	79.4862	1151	3202	95	below_threshold
Micromonospora chaiyaphumensis	strain=DSM 45246	GCA_900091435.1	307119	307119	type	True	79.4463	1131	3202	95	below_threshold
Micromonospora viridifaciens	strain=DSM 43909	GCA_900091545.1	1881	1881	type	True	79.362	1069	3202	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.2288	1201	3202	95	below_threshold
Micromonospora phaseoli	strain=NBRC 110907	GCA_016863675.1	1144548	1144548	type	True	79.0587	1021	3202	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	79.0139	1101	3202	95	below_threshold
Actinoplanes subtropicus	strain=NRRL B-24665	GCA_000721705.1	543632	543632	type	True	78.1483	1145	3202	95	below_threshold
Actinoplanes teichomyceticus	strain=ATCC 31121	GCA_003711105.1	1867	1867	type	True	78.1009	1107	3202	95	below_threshold
Actinoplanes teichomyceticus	strain=NBRC 13999	GCA_016862415.1	1867	1867	type	True	78.0732	1082	3202	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:18,204] [INFO] DFAST Taxonomy check result was written to GCF_011764545.1_ASM1176454v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:18,207] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:18,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:18,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg822cfb48-47e4-4a4c-819f-b229b7e9cfe7/dqc_reference/checkm_data
[2024-01-25 19:02:18,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:18,293] [INFO] Task started: CheckM
[2024-01-25 19:02:18,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011764545.1_ASM1176454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011764545.1_ASM1176454v1_genomic.fna/checkm_input GCF_011764545.1_ASM1176454v1_genomic.fna/checkm_result
[2024-01-25 19:04:11,479] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:11,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:11,501] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:11,502] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:11,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011764545.1_ASM1176454v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:11,503] [INFO] Task started: Blastn
[2024-01-25 19:04:11,503] [INFO] Running command: blastn -query GCF_011764545.1_ASM1176454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg822cfb48-47e4-4a4c-819f-b229b7e9cfe7/dqc_reference/reference_markers_gtdb.fasta -out GCF_011764545.1_ASM1176454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:13,235] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:13,239] [INFO] Selected 14 target genomes.
[2024-01-25 19:04:13,239] [INFO] Target genome list was writen to GCF_011764545.1_ASM1176454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:13,255] [INFO] Task started: fastANI
[2024-01-25 19:04:13,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ed5c772-5890-4246-a4be-8d680f08c751/GCF_011764545.1_ASM1176454v1_genomic.fna.gz --refList GCF_011764545.1_ASM1176454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011764545.1_ASM1176454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:45,018] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:45,027] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:45,028] [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_011764545.1	s__Phytohabitans flavus	100.0	3202	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011764565.1	s__Phytohabitans suffuscus	88.2053	2123	3202	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	87.2253	2151	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764445.1	s__Phytohabitans rumicis	82.7256	1723	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107255.1	s__Micromonospora_E pattaloongensis	79.8944	1015	3202	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_900091425.1	s__Micromonospora krabiensis	79.5329	1145	3202	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	79.491	1151	3202	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	79.44	1053	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008868175.1	s__Micromonospora sp008868175	79.4315	1053	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091545.1	s__Micromonospora viridifaciens	79.3725	1064	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188485.1	s__Asanoa hainanensis	79.1767	1180	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721705.1	s__Actinoplanes subtropicus	78.1592	1143	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711105.1	s__Actinoplanes teichomyceticus	78.128	1104	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	99.99	1.00	1.00	4	-
GCF_900113015.1	s__Actinoplanes philippinensis	77.8611	1125	3202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:45,029] [INFO] GTDB search result was written to GCF_011764545.1_ASM1176454v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:45,030] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:45,037] [INFO] DFAST_QC result json was written to GCF_011764545.1_ASM1176454v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:45,037] [INFO] DFAST_QC completed!
[2024-01-25 19:04:45,037] [INFO] Total running time: 0h3m39s