[2024-01-24 13:58:10,727] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,729] [INFO] DQC Reference Directory: /var/lib/cwl/stgabcf9bce-d482-4658-aba5-ef99e94cfc97/dqc_reference
[2024-01-24 13:58:12,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,168] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg84b5478d-f42c-4f20-a5fb-bc2ec451d8d9/GCF_016834655.1_ASM1683465v1_genomic.fna.gz | prodigal -d GCF_016834655.1_ASM1683465v1_genomic.fna/cds.fna -a GCF_016834655.1_ASM1683465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:47,287] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:47,288] [INFO] Task started: HMMsearch
[2024-01-24 13:58:47,288] [INFO] Running command: hmmsearch --tblout GCF_016834655.1_ASM1683465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabcf9bce-d482-4658-aba5-ef99e94cfc97/dqc_reference/reference_markers.hmm GCF_016834655.1_ASM1683465v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:47,733] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:47,734] [INFO] Found 6/6 markers.
[2024-01-24 13:58:47,825] [INFO] Query marker FASTA was written to GCF_016834655.1_ASM1683465v1_genomic.fna/markers.fasta
[2024-01-24 13:58:47,825] [INFO] Task started: Blastn
[2024-01-24 13:58:47,826] [INFO] Running command: blastn -query GCF_016834655.1_ASM1683465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabcf9bce-d482-4658-aba5-ef99e94cfc97/dqc_reference/reference_markers.fasta -out GCF_016834655.1_ASM1683465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:49,064] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:49,068] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:49,068] [INFO] Target genome list was writen to GCF_016834655.1_ASM1683465v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:49,079] [INFO] Task started: fastANI
[2024-01-24 13:58:49,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg84b5478d-f42c-4f20-a5fb-bc2ec451d8d9/GCF_016834655.1_ASM1683465v1_genomic.fna.gz --refList GCF_016834655.1_ASM1683465v1_genomic.fna/target_genomes.txt --output GCF_016834655.1_ASM1683465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:17,671] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:17,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabcf9bce-d482-4658-aba5-ef99e94cfc97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:17,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabcf9bce-d482-4658-aba5-ef99e94cfc97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:17,690] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:17,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:17,691] [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 ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	100.0	3772	3777	95	conclusive
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	87.4515	2692	3777	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	86.9632	2470	3777	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	86.6315	2597	3777	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	86.362	2329	3777	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	86.3474	2308	3777	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.2171	1623	3777	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.6487	826	3777	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.355	988	3777	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	78.2559	1178	3777	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.3699	1341	3777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,692] [INFO] DFAST Taxonomy check result was written to GCF_016834655.1_ASM1683465v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:17,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:17,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:17,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabcf9bce-d482-4658-aba5-ef99e94cfc97/dqc_reference/checkm_data
[2024-01-24 13:59:17,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:17,796] [INFO] Task started: CheckM
[2024-01-24 13:59:17,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016834655.1_ASM1683465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016834655.1_ASM1683465v1_genomic.fna/checkm_input GCF_016834655.1_ASM1683465v1_genomic.fna/checkm_result
[2024-01-24 14:01:09,609] [INFO] Task succeeded: CheckM
[2024-01-24 14:01:09,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 16.67%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:01:09,634] [INFO] ===== Completeness check finished =====
[2024-01-24 14:01:09,635] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:01:09,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016834655.1_ASM1683465v1_genomic.fna/markers.fasta)
[2024-01-24 14:01:09,636] [INFO] Task started: Blastn
[2024-01-24 14:01:09,636] [INFO] Running command: blastn -query GCF_016834655.1_ASM1683465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabcf9bce-d482-4658-aba5-ef99e94cfc97/dqc_reference/reference_markers_gtdb.fasta -out GCF_016834655.1_ASM1683465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:01:11,627] [INFO] Task succeeded: Blastn
[2024-01-24 14:01:11,631] [INFO] Selected 7 target genomes.
[2024-01-24 14:01:11,631] [INFO] Target genome list was writen to GCF_016834655.1_ASM1683465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:01:11,644] [INFO] Task started: fastANI
[2024-01-24 14:01:11,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg84b5478d-f42c-4f20-a5fb-bc2ec451d8d9/GCF_016834655.1_ASM1683465v1_genomic.fna.gz --refList GCF_016834655.1_ASM1683465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016834655.1_ASM1683465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:33,883] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:33,895] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:01:33,895] [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_016834655.1	s__Actinoplanes sp016834655	100.0	3772	3777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016785085.1	s__Actinoplanes sp016785085	87.4326	2698	3777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	86.9287	2477	3777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018829635.1	s__Actinoplanes bogorensis	86.6223	2600	3777	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	86.3259	2337	3777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003999975.1	s__Actinoplanes sp003999975	84.4523	2122	3777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215205.1	s__Actinoplanes atraurantiacus	82.9293	2196	3777	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 14:01:33,897] [INFO] GTDB search result was written to GCF_016834655.1_ASM1683465v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:33,897] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:33,900] [INFO] DFAST_QC result json was written to GCF_016834655.1_ASM1683465v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:33,900] [INFO] DFAST_QC completed!
[2024-01-24 14:01:33,900] [INFO] Total running time: 0h3m23s