[2024-01-24 12:43:54,218] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:43:54,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:43:54,221] [INFO] DQC Reference Directory: /var/lib/cwl/stge505cfa5-8cfb-47f9-bc9e-94327f83aedd/dqc_reference
[2024-01-24 12:43:59,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:43:59,339] [INFO] Task started: Prodigal
[2024-01-24 12:43:59,339] [INFO] Running command: gunzip -c /var/lib/cwl/stge9c49869-c966-4cfc-8de6-0e14c2130fb7/GCF_003002065.1_ASM300206v1_genomic.fna.gz | prodigal -d GCF_003002065.1_ASM300206v1_genomic.fna/cds.fna -a GCF_003002065.1_ASM300206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:23,724] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:23,724] [INFO] Task started: HMMsearch
[2024-01-24 12:44:23,724] [INFO] Running command: hmmsearch --tblout GCF_003002065.1_ASM300206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge505cfa5-8cfb-47f9-bc9e-94327f83aedd/dqc_reference/reference_markers.hmm GCF_003002065.1_ASM300206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:24,084] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:24,085] [INFO] Found 6/6 markers.
[2024-01-24 12:44:24,150] [INFO] Query marker FASTA was written to GCF_003002065.1_ASM300206v1_genomic.fna/markers.fasta
[2024-01-24 12:44:24,150] [INFO] Task started: Blastn
[2024-01-24 12:44:24,150] [INFO] Running command: blastn -query GCF_003002065.1_ASM300206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge505cfa5-8cfb-47f9-bc9e-94327f83aedd/dqc_reference/reference_markers.fasta -out GCF_003002065.1_ASM300206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:25,377] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:25,381] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:25,381] [INFO] Target genome list was writen to GCF_003002065.1_ASM300206v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:25,401] [INFO] Task started: fastANI
[2024-01-24 12:44:25,401] [INFO] Running command: fastANI --query /var/lib/cwl/stge9c49869-c966-4cfc-8de6-0e14c2130fb7/GCF_003002065.1_ASM300206v1_genomic.fna.gz --refList GCF_003002065.1_ASM300206v1_genomic.fna/target_genomes.txt --output GCF_003002065.1_ASM300206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:03,352] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:03,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge505cfa5-8cfb-47f9-bc9e-94327f83aedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:03,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge505cfa5-8cfb-47f9-bc9e-94327f83aedd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:03,367] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:03,368] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:03,368] [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
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	84.9422	1451	2840	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	84.8533	1608	2840	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	83.6027	1745	2840	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	83.3597	1765	2840	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	83.0751	1649	2840	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	82.9745	1707	2840	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	82.8297	1781	2840	95	below_threshold
Actinoplanes consettensis	strain=NBRC 14913	GCA_018332715.1	113560	113560	type	True	82.2202	1651	2840	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	80.8829	1610	2840	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	80.6657	1549	2840	95	below_threshold
Actinoplanes ovalisporus	strain=LDG1-06	GCA_016834655.1	2810368	2810368	type	True	80.6151	1557	2840	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.3346	1410	2840	95	below_threshold
Micromonospora olivasterospora	strain=DSM 43868	GCA_007830265.1	1880	1880	type	True	79.0842	1043	2840	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.9204	1391	2840	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.8229	989	2840	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.7529	1119	2840	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.6591	1231	2840	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:03,369] [INFO] DFAST Taxonomy check result was written to GCF_003002065.1_ASM300206v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:03,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:03,370] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:03,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge505cfa5-8cfb-47f9-bc9e-94327f83aedd/dqc_reference/checkm_data
[2024-01-24 12:45:03,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:03,471] [INFO] Task started: CheckM
[2024-01-24 12:45:03,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002065.1_ASM300206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002065.1_ASM300206v1_genomic.fna/checkm_input GCF_003002065.1_ASM300206v1_genomic.fna/checkm_result
[2024-01-24 12:46:29,227] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:29,228] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:29,260] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:29,260] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:29,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002065.1_ASM300206v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:29,261] [INFO] Task started: Blastn
[2024-01-24 12:46:29,261] [INFO] Running command: blastn -query GCF_003002065.1_ASM300206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge505cfa5-8cfb-47f9-bc9e-94327f83aedd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002065.1_ASM300206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:31,085] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:31,090] [INFO] Selected 8 target genomes.
[2024-01-24 12:46:31,090] [INFO] Target genome list was writen to GCF_003002065.1_ASM300206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:31,096] [INFO] Task started: fastANI
[2024-01-24 12:46:31,096] [INFO] Running command: fastANI --query /var/lib/cwl/stge9c49869-c966-4cfc-8de6-0e14c2130fb7/GCF_003002065.1_ASM300206v1_genomic.fna.gz --refList GCF_003002065.1_ASM300206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002065.1_ASM300206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:50,884] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:50,902] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:50,903] [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_003002065.1	s__Actinoplanes ferrugineus_A	100.0	2835	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	conclusive
GCF_016464385.1	s__Actinoplanes sp016464385	85.1667	1893	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648355.1	s__Actinoplanes azureus	85.1198	1582	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751945.1	s__Actinoplanes caeruleus	84.8303	1611	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_016862275.1	s__Actinoplanes nipponensis	83.5844	1748	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205335.1	s__Actinoplanes digitatis	83.0186	1698	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000494755.1	s__Actinoplanes friuliensis	82.8282	1781	2840	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389965.1	s__Actinoplanes sp000389965	82.6969	1665	2840	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 12:46:50,905] [INFO] GTDB search result was written to GCF_003002065.1_ASM300206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:50,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:50,909] [INFO] DFAST_QC result json was written to GCF_003002065.1_ASM300206v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:50,909] [INFO] DFAST_QC completed!
[2024-01-24 12:46:50,909] [INFO] Total running time: 0h2m57s