[2024-01-24 12:44:52,897] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:52,901] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:52,901] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb937d3a-e132-49fe-ab57-cc81c2eeb135/dqc_reference
[2024-01-24 12:44:54,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:54,294] [INFO] Task started: Prodigal
[2024-01-24 12:44:54,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e3fb556-98c6-4f6c-a358-80a6e35413fb/GCF_016861995.1_ASM1686199v1_genomic.fna.gz | prodigal -d GCF_016861995.1_ASM1686199v1_genomic.fna/cds.fna -a GCF_016861995.1_ASM1686199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:21,790] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:21,791] [INFO] Task started: HMMsearch
[2024-01-24 12:45:21,791] [INFO] Running command: hmmsearch --tblout GCF_016861995.1_ASM1686199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb937d3a-e132-49fe-ab57-cc81c2eeb135/dqc_reference/reference_markers.hmm GCF_016861995.1_ASM1686199v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:22,209] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:22,212] [INFO] Found 6/6 markers.
[2024-01-24 12:45:22,285] [INFO] Query marker FASTA was written to GCF_016861995.1_ASM1686199v1_genomic.fna/markers.fasta
[2024-01-24 12:45:22,286] [INFO] Task started: Blastn
[2024-01-24 12:45:22,286] [INFO] Running command: blastn -query GCF_016861995.1_ASM1686199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb937d3a-e132-49fe-ab57-cc81c2eeb135/dqc_reference/reference_markers.fasta -out GCF_016861995.1_ASM1686199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:23,517] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:23,521] [INFO] Selected 11 target genomes.
[2024-01-24 12:45:23,521] [INFO] Target genome list was writen to GCF_016861995.1_ASM1686199v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:23,529] [INFO] Task started: fastANI
[2024-01-24 12:45:23,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e3fb556-98c6-4f6c-a358-80a6e35413fb/GCF_016861995.1_ASM1686199v1_genomic.fna.gz --refList GCF_016861995.1_ASM1686199v1_genomic.fna/target_genomes.txt --output GCF_016861995.1_ASM1686199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:49,556] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:49,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb937d3a-e132-49fe-ab57-cc81c2eeb135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:49,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb937d3a-e132-49fe-ab57-cc81c2eeb135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:49,573] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:49,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:49,573] [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
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	99.9988	3031	3031	95	conclusive
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	90.7579	2627	3031	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	87.9709	2176	3031	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	87.8753	2217	3031	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	87.1504	2407	3031	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	83.1038	1924	3031	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.4877	1486	3031	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.7992	812	3031	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.5618	957	3031	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.6556	1301	3031	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.4332	921	3031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:49,576] [INFO] DFAST Taxonomy check result was written to GCF_016861995.1_ASM1686199v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:49,577] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:49,577] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:49,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb937d3a-e132-49fe-ab57-cc81c2eeb135/dqc_reference/checkm_data
[2024-01-24 12:45:49,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:49,664] [INFO] Task started: CheckM
[2024-01-24 12:45:49,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016861995.1_ASM1686199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016861995.1_ASM1686199v1_genomic.fna/checkm_input GCF_016861995.1_ASM1686199v1_genomic.fna/checkm_result
[2024-01-24 12:47:14,505] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:14,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:14,541] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:14,542] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:14,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016861995.1_ASM1686199v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:14,543] [INFO] Task started: Blastn
[2024-01-24 12:47:14,543] [INFO] Running command: blastn -query GCF_016861995.1_ASM1686199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb937d3a-e132-49fe-ab57-cc81c2eeb135/dqc_reference/reference_markers_gtdb.fasta -out GCF_016861995.1_ASM1686199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:16,354] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:16,358] [INFO] Selected 8 target genomes.
[2024-01-24 12:47:16,358] [INFO] Target genome list was writen to GCF_016861995.1_ASM1686199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:16,365] [INFO] Task started: fastANI
[2024-01-24 12:47:16,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e3fb556-98c6-4f6c-a358-80a6e35413fb/GCF_016861995.1_ASM1686199v1_genomic.fna.gz --refList GCF_016861995.1_ASM1686199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016861995.1_ASM1686199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:38,393] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:38,401] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:38,401] [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_014204895.1	s__Actinoplanes abujensis	99.9988	3031	3031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016785085.1	s__Actinoplanes sp016785085	90.7631	2626	3031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362215.1	s__Actinoplanes brasiliensis	87.846	2222	3031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016834655.1	s__Actinoplanes sp016834655	87.1364	2410	3031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018829635.1	s__Actinoplanes bogorensis	86.2243	2240	3031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999975.1	s__Actinoplanes sp003999975	84.3356	1993	3031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862115.1	s__Actinoplanes deccanensis	83.155	1913	3031	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553785.1	s__Actinoplanes sp001553785	80.4725	1276	3031	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 12:47:38,405] [INFO] GTDB search result was written to GCF_016861995.1_ASM1686199v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:38,405] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:38,408] [INFO] DFAST_QC result json was written to GCF_016861995.1_ASM1686199v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:38,408] [INFO] DFAST_QC completed!
[2024-01-24 12:47:38,409] [INFO] Total running time: 0h2m46s