[2024-01-24 15:10:49,792] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:49,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:49,795] [INFO] DQC Reference Directory: /var/lib/cwl/stgc26faeee-6f5d-455f-9670-cabc3897e3ba/dqc_reference
[2024-01-24 15:10:51,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:51,018] [INFO] Task started: Prodigal
[2024-01-24 15:10:51,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg2130de08-bd55-42a0-9b4a-3e18659af6a4/GCF_014204895.1_ASM1420489v1_genomic.fna.gz | prodigal -d GCF_014204895.1_ASM1420489v1_genomic.fna/cds.fna -a GCF_014204895.1_ASM1420489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:20,908] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:20,909] [INFO] Task started: HMMsearch
[2024-01-24 15:11:20,909] [INFO] Running command: hmmsearch --tblout GCF_014204895.1_ASM1420489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc26faeee-6f5d-455f-9670-cabc3897e3ba/dqc_reference/reference_markers.hmm GCF_014204895.1_ASM1420489v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:21,365] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:21,366] [INFO] Found 6/6 markers.
[2024-01-24 15:11:21,448] [INFO] Query marker FASTA was written to GCF_014204895.1_ASM1420489v1_genomic.fna/markers.fasta
[2024-01-24 15:11:21,449] [INFO] Task started: Blastn
[2024-01-24 15:11:21,449] [INFO] Running command: blastn -query GCF_014204895.1_ASM1420489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26faeee-6f5d-455f-9670-cabc3897e3ba/dqc_reference/reference_markers.fasta -out GCF_014204895.1_ASM1420489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:22,765] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:22,768] [INFO] Selected 11 target genomes.
[2024-01-24 15:11:22,769] [INFO] Target genome list was writen to GCF_014204895.1_ASM1420489v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:22,776] [INFO] Task started: fastANI
[2024-01-24 15:11:22,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg2130de08-bd55-42a0-9b4a-3e18659af6a4/GCF_014204895.1_ASM1420489v1_genomic.fna.gz --refList GCF_014204895.1_ASM1420489v1_genomic.fna/target_genomes.txt --output GCF_014204895.1_ASM1420489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:51,239] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:51,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc26faeee-6f5d-455f-9670-cabc3897e3ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:51,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc26faeee-6f5d-455f-9670-cabc3897e3ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:51,251] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:51,251] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:51,251] [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	100.0	3110	3110	95	conclusive
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	90.6635	2671	3110	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	87.8623	2217	3110	95	below_threshold
Actinoplanes brasiliensis	strain=DSM 43805	GCA_004362215.1	52695	52695	type	True	87.7977	2258	3110	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	87.0916	2473	3110	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	83.1228	1946	3110	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.5527	1491	3110	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	78.7854	811	3110	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	78.6402	930	3110	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.6699	1360	3110	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.6576	921	3110	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:51,253] [INFO] DFAST Taxonomy check result was written to GCF_014204895.1_ASM1420489v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:51,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:51,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:51,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc26faeee-6f5d-455f-9670-cabc3897e3ba/dqc_reference/checkm_data
[2024-01-24 15:11:51,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:51,347] [INFO] Task started: CheckM
[2024-01-24 15:11:51,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204895.1_ASM1420489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204895.1_ASM1420489v1_genomic.fna/checkm_input GCF_014204895.1_ASM1420489v1_genomic.fna/checkm_result
[2024-01-24 15:13:30,485] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:30,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:13:30,516] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:30,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:30,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204895.1_ASM1420489v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:30,518] [INFO] Task started: Blastn
[2024-01-24 15:13:30,518] [INFO] Running command: blastn -query GCF_014204895.1_ASM1420489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26faeee-6f5d-455f-9670-cabc3897e3ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204895.1_ASM1420489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:32,408] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:32,411] [INFO] Selected 8 target genomes.
[2024-01-24 15:13:32,412] [INFO] Target genome list was writen to GCF_014204895.1_ASM1420489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:32,419] [INFO] Task started: fastANI
[2024-01-24 15:13:32,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg2130de08-bd55-42a0-9b4a-3e18659af6a4/GCF_014204895.1_ASM1420489v1_genomic.fna.gz --refList GCF_014204895.1_ASM1420489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204895.1_ASM1420489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:55,223] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:55,233] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:55,234] [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	100.0	3110	3110	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	90.6454	2674	3110	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	87.7391	2266	3110	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	87.0641	2479	3110	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	86.1486	2263	3110	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	84.4024	2003	3110	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	83.1118	1948	3110	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	80.5769	1307	3110	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 15:13:55,235] [INFO] GTDB search result was written to GCF_014204895.1_ASM1420489v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:55,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:55,239] [INFO] DFAST_QC result json was written to GCF_014204895.1_ASM1420489v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:55,239] [INFO] DFAST_QC completed!
[2024-01-24 15:13:55,239] [INFO] Total running time: 0h3m5s