[2024-01-24 12:22:48,398] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,402] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,402] [INFO] DQC Reference Directory: /var/lib/cwl/stgd38da3b7-dd23-4fae-9cba-d825fa46f2ee/dqc_reference
[2024-01-24 12:22:49,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,689] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,690] [INFO] Running command: gunzip -c /var/lib/cwl/stgd84ce06e-7e28-4113-bc34-ebc834427a6e/GCF_016862275.1_ASM1686227v1_genomic.fna.gz | prodigal -d GCF_016862275.1_ASM1686227v1_genomic.fna/cds.fna -a GCF_016862275.1_ASM1686227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:14,930] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:14,930] [INFO] Task started: HMMsearch
[2024-01-24 12:23:14,930] [INFO] Running command: hmmsearch --tblout GCF_016862275.1_ASM1686227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd38da3b7-dd23-4fae-9cba-d825fa46f2ee/dqc_reference/reference_markers.hmm GCF_016862275.1_ASM1686227v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:15,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:15,320] [INFO] Found 6/6 markers.
[2024-01-24 12:23:15,406] [INFO] Query marker FASTA was written to GCF_016862275.1_ASM1686227v1_genomic.fna/markers.fasta
[2024-01-24 12:23:15,406] [INFO] Task started: Blastn
[2024-01-24 12:23:15,406] [INFO] Running command: blastn -query GCF_016862275.1_ASM1686227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd38da3b7-dd23-4fae-9cba-d825fa46f2ee/dqc_reference/reference_markers.fasta -out GCF_016862275.1_ASM1686227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:16,702] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:16,706] [INFO] Selected 11 target genomes.
[2024-01-24 12:23:16,707] [INFO] Target genome list was writen to GCF_016862275.1_ASM1686227v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:16,711] [INFO] Task started: fastANI
[2024-01-24 12:23:16,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84ce06e-7e28-4113-bc34-ebc834427a6e/GCF_016862275.1_ASM1686227v1_genomic.fna.gz --refList GCF_016862275.1_ASM1686227v1_genomic.fna/target_genomes.txt --output GCF_016862275.1_ASM1686227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:42,357] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:42,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd38da3b7-dd23-4fae-9cba-d825fa46f2ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:42,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd38da3b7-dd23-4fae-9cba-d825fa46f2ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:42,373] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:42,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:42,374] [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 nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	100.0	2916	2926	95	conclusive
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	88.4258	2136	2926	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	85.238	1806	2926	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	85.1829	1853	2926	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	84.5723	1898	2926	95	below_threshold
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	82.8591	1557	2926	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.6642	1522	2926	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.7251	911	2926	95	below_threshold
Micromonospora acroterricola	strain=5R2A7	GCA_003172955.1	2202421	2202421	type	True	79.5978	1075	2926	95	below_threshold
Micromonospora ferruginea	strain=28ISP2-46	GCA_013694245.1	2749844	2749844	type	True	79.5197	1249	2926	95	below_threshold
Micromonospora humida	strain=MMS20-R1-14	GCA_016901255.1	2809018	2809018	type	True	79.3581	1250	2926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:42,375] [INFO] DFAST Taxonomy check result was written to GCF_016862275.1_ASM1686227v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:42,378] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:42,378] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:42,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd38da3b7-dd23-4fae-9cba-d825fa46f2ee/dqc_reference/checkm_data
[2024-01-24 12:23:42,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:42,463] [INFO] Task started: CheckM
[2024-01-24 12:23:42,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862275.1_ASM1686227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862275.1_ASM1686227v1_genomic.fna/checkm_input GCF_016862275.1_ASM1686227v1_genomic.fna/checkm_result
[2024-01-24 12:25:09,582] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:09,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:09,614] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:09,615] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:09,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862275.1_ASM1686227v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:09,616] [INFO] Task started: Blastn
[2024-01-24 12:25:09,616] [INFO] Running command: blastn -query GCF_016862275.1_ASM1686227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd38da3b7-dd23-4fae-9cba-d825fa46f2ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862275.1_ASM1686227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:11,614] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:11,618] [INFO] Selected 10 target genomes.
[2024-01-24 12:25:11,618] [INFO] Target genome list was writen to GCF_016862275.1_ASM1686227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:11,627] [INFO] Task started: fastANI
[2024-01-24 12:25:11,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgd84ce06e-7e28-4113-bc34-ebc834427a6e/GCF_016862275.1_ASM1686227v1_genomic.fna.gz --refList GCF_016862275.1_ASM1686227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862275.1_ASM1686227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:37,157] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:37,175] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:37,176] [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_016862275.1	s__Actinoplanes nipponensis	100.0	2916	2926	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_018332655.1	s__Actinoplanes auranticolor	88.4237	2136	2926	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	85.1915	1851	2926	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	84.5561	1901	2926	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	83.5442	1740	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_016464385.1	s__Actinoplanes sp016464385	83.419	1875	2926	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	83.0623	1572	2926	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	82.3387	1652	2926	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	81.9729	1463	2926	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	81.7425	1394	2926	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 12:25:37,179] [INFO] GTDB search result was written to GCF_016862275.1_ASM1686227v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:37,179] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:37,182] [INFO] DFAST_QC result json was written to GCF_016862275.1_ASM1686227v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:37,183] [INFO] DFAST_QC completed!
[2024-01-24 12:25:37,183] [INFO] Total running time: 0h2m49s