[2024-01-25 19:36:35,581] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:35,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:35,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg4378f8b4-7bce-441d-890c-d760b6040e47/dqc_reference
[2024-01-25 19:36:36,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:36,825] [INFO] Task started: Prodigal
[2024-01-25 19:36:36,825] [INFO] Running command: gunzip -c /var/lib/cwl/stg469f576a-c522-4e07-9ea5-83b7e9020ed8/GCF_030709675.1_ASM3070967v1_genomic.fna.gz | prodigal -d GCF_030709675.1_ASM3070967v1_genomic.fna/cds.fna -a GCF_030709675.1_ASM3070967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:02,977] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:02,978] [INFO] Task started: HMMsearch
[2024-01-25 19:37:02,978] [INFO] Running command: hmmsearch --tblout GCF_030709675.1_ASM3070967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4378f8b4-7bce-441d-890c-d760b6040e47/dqc_reference/reference_markers.hmm GCF_030709675.1_ASM3070967v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:03,346] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:03,347] [INFO] Found 6/6 markers.
[2024-01-25 19:37:03,418] [INFO] Query marker FASTA was written to GCF_030709675.1_ASM3070967v1_genomic.fna/markers.fasta
[2024-01-25 19:37:03,418] [INFO] Task started: Blastn
[2024-01-25 19:37:03,418] [INFO] Running command: blastn -query GCF_030709675.1_ASM3070967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4378f8b4-7bce-441d-890c-d760b6040e47/dqc_reference/reference_markers.fasta -out GCF_030709675.1_ASM3070967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:04,615] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:04,618] [INFO] Selected 21 target genomes.
[2024-01-25 19:37:04,618] [INFO] Target genome list was writen to GCF_030709675.1_ASM3070967v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:04,644] [INFO] Task started: fastANI
[2024-01-25 19:37:04,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg469f576a-c522-4e07-9ea5-83b7e9020ed8/GCF_030709675.1_ASM3070967v1_genomic.fna.gz --refList GCF_030709675.1_ASM3070967v1_genomic.fna/target_genomes.txt --output GCF_030709675.1_ASM3070967v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:50,992] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:50,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4378f8b4-7bce-441d-890c-d760b6040e47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:50,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4378f8b4-7bce-441d-890c-d760b6040e47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:51,005] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:37:51,006] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:37:51,006] [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	81.9605	1283	2976	95	below_threshold
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	81.8739	1825	2976	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	81.8083	1403	2976	95	below_threshold
Actinoplanes consettensis	strain=NBRC 14913	GCA_018332715.1	113560	113560	type	True	81.7457	1853	2976	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	81.6558	1630	2976	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	81.5118	1675	2976	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	81.4178	1687	2976	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	81.3155	1549	2976	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	81.3148	1574	2976	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	80.6978	1623	2976	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	80.6553	1526	2976	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	80.544	1662	2976	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	80.526	1641	2976	95	below_threshold
Actinoplanes bogorensis	strain=NBRC 110975	GCA_018829635.1	1610840	1610840	type	True	80.4125	1572	2976	95	below_threshold
Actinoplanes toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	80.2007	1525	2976	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	80.0091	1576	2976	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	79.681	1385	2976	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.4602	927	2976	95	below_threshold
Dactylosporangium aurantiacum	strain=NRRL B-8018	GCA_025264705.1	35754	35754	type	True	77.4185	1320	2976	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.3563	1202	2976	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.3358	1095	2976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:51,007] [INFO] DFAST Taxonomy check result was written to GCF_030709675.1_ASM3070967v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:51,008] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:51,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:51,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4378f8b4-7bce-441d-890c-d760b6040e47/dqc_reference/checkm_data
[2024-01-25 19:37:51,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:51,087] [INFO] Task started: CheckM
[2024-01-25 19:37:51,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030709675.1_ASM3070967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030709675.1_ASM3070967v1_genomic.fna/checkm_input GCF_030709675.1_ASM3070967v1_genomic.fna/checkm_result
[2024-01-25 19:40:07,732] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:07,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:07,763] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:07,763] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:07,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030709675.1_ASM3070967v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:07,764] [INFO] Task started: Blastn
[2024-01-25 19:40:07,764] [INFO] Running command: blastn -query GCF_030709675.1_ASM3070967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4378f8b4-7bce-441d-890c-d760b6040e47/dqc_reference/reference_markers_gtdb.fasta -out GCF_030709675.1_ASM3070967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:09,683] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:09,685] [INFO] Selected 16 target genomes.
[2024-01-25 19:40:09,686] [INFO] Target genome list was writen to GCF_030709675.1_ASM3070967v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:09,696] [INFO] Task started: fastANI
[2024-01-25 19:40:09,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg469f576a-c522-4e07-9ea5-83b7e9020ed8/GCF_030709675.1_ASM3070967v1_genomic.fna.gz --refList GCF_030709675.1_ASM3070967v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030709675.1_ASM3070967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:49,672] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:49,682] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:40:49,682] [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_016464385.1	s__Actinoplanes sp016464385	82.3099	1689	2976	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	82.2954	1776	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	82.2267	1642	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_014648355.1	s__Actinoplanes azureus	82.0655	1414	2976	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	82.0058	1535	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862215.1	s__Actinoplanes humidus	81.8946	1820	2976	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	81.7867	1408	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_018332715.1	s__Actinoplanes consettensis	81.7507	1852	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862275.1	s__Actinoplanes nipponensis	81.6194	1638	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000494755.1	s__Actinoplanes friuliensis	81.4062	1690	2976	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	81.3129	1572	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016862115.1	s__Actinoplanes deccanensis	80.6916	1626	2976	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	80.527	1643	2976	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	80.4149	1571	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332695.1	s__Actinoplanes toevensis	80.1821	1530	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862435.1	s__Actinoplanes tereljensis	80.0077	1577	2976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:49,683] [INFO] GTDB search result was written to GCF_030709675.1_ASM3070967v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:49,684] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:49,687] [INFO] DFAST_QC result json was written to GCF_030709675.1_ASM3070967v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:49,688] [INFO] DFAST_QC completed!
[2024-01-25 19:40:49,688] [INFO] Total running time: 0h4m14s