[2024-01-24 12:44:43,410] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,412] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,413] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0dd15b0-1226-4d04-847d-ecedaea91472/dqc_reference
[2024-01-24 12:44:44,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:44,800] [INFO] Task started: Prodigal
[2024-01-24 12:44:44,800] [INFO] Running command: gunzip -c /var/lib/cwl/stgc871c502-5d8d-44c7-b662-28fac93f35f7/GCF_014205175.1_ASM1420517v1_genomic.fna.gz | prodigal -d GCF_014205175.1_ASM1420517v1_genomic.fna/cds.fna -a GCF_014205175.1_ASM1420517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:51,873] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:51,873] [INFO] Task started: HMMsearch
[2024-01-24 12:44:51,873] [INFO] Running command: hmmsearch --tblout GCF_014205175.1_ASM1420517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0dd15b0-1226-4d04-847d-ecedaea91472/dqc_reference/reference_markers.hmm GCF_014205175.1_ASM1420517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:52,129] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:52,130] [INFO] Found 6/6 markers.
[2024-01-24 12:44:52,159] [INFO] Query marker FASTA was written to GCF_014205175.1_ASM1420517v1_genomic.fna/markers.fasta
[2024-01-24 12:44:52,159] [INFO] Task started: Blastn
[2024-01-24 12:44:52,159] [INFO] Running command: blastn -query GCF_014205175.1_ASM1420517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0dd15b0-1226-4d04-847d-ecedaea91472/dqc_reference/reference_markers.fasta -out GCF_014205175.1_ASM1420517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:53,313] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:53,317] [INFO] Selected 14 target genomes.
[2024-01-24 12:44:53,317] [INFO] Target genome list was writen to GCF_014205175.1_ASM1420517v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:53,324] [INFO] Task started: fastANI
[2024-01-24 12:44:53,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgc871c502-5d8d-44c7-b662-28fac93f35f7/GCF_014205175.1_ASM1420517v1_genomic.fna.gz --refList GCF_014205175.1_ASM1420517v1_genomic.fna/target_genomes.txt --output GCF_014205175.1_ASM1420517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:00,959] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:00,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0dd15b0-1226-4d04-847d-ecedaea91472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:00,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0dd15b0-1226-4d04-847d-ecedaea91472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:00,971] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:00,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:00,971] [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
Micrococcus cohnii	strain=DSM 23974	GCA_014205175.1	993416	993416	type	True	100.0	757	758	95	conclusive
Micrococcus lylae	strain=NBRC 15355	GCA_001570885.1	1273	1273	type	True	81.5093	470	758	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_008868275.1	1270	1270	type	True	81.4077	409	758	95	below_threshold
Micrococcus endophyticus	strain=DSM 17945	GCA_014205115.1	455343	455343	type	True	81.3672	504	758	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	81.3239	380	758	95	below_threshold
Micrococcus luteus	strain=NCTC2665	GCA_900475555.1	1270	1270	type	True	81.2281	466	758	95	below_threshold
Micrococcus luteus	strain=NCTC 2665	GCA_000023205.1	1270	1270	type	True	81.1756	473	758	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	81.1011	448	758	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_014204815.1	384602	384602	type	True	81.0684	464	758	95	below_threshold
Micrococcus flavus	strain=CGMCC 1.5361	GCA_014644875.1	384602	384602	type	True	80.9792	452	758	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.336	199	758	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.2319	203	758	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.1205	146	758	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.8017	195	758	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:00,973] [INFO] DFAST Taxonomy check result was written to GCF_014205175.1_ASM1420517v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:00,973] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:00,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:00,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0dd15b0-1226-4d04-847d-ecedaea91472/dqc_reference/checkm_data
[2024-01-24 12:45:00,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:01,000] [INFO] Task started: CheckM
[2024-01-24 12:45:01,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205175.1_ASM1420517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205175.1_ASM1420517v1_genomic.fna/checkm_input GCF_014205175.1_ASM1420517v1_genomic.fna/checkm_result
[2024-01-24 12:45:41,718] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:41,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:41,750] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:41,751] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:41,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205175.1_ASM1420517v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:41,752] [INFO] Task started: Blastn
[2024-01-24 12:45:41,752] [INFO] Running command: blastn -query GCF_014205175.1_ASM1420517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0dd15b0-1226-4d04-847d-ecedaea91472/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205175.1_ASM1420517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:43,470] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:43,474] [INFO] Selected 8 target genomes.
[2024-01-24 12:45:43,474] [INFO] Target genome list was writen to GCF_014205175.1_ASM1420517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:43,492] [INFO] Task started: fastANI
[2024-01-24 12:45:43,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgc871c502-5d8d-44c7-b662-28fac93f35f7/GCF_014205175.1_ASM1420517v1_genomic.fna.gz --refList GCF_014205175.1_ASM1420517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205175.1_ASM1420517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:48,314] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:48,321] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:48,321] [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_014205175.1	s__Micrococcus cohnii	100.0	758	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.00	98.97	0.96	0.96	3	conclusive
GCF_001570885.1	s__Micrococcus lylae	81.5196	469	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	98.72	97.35	0.93	0.90	6	-
GCF_014205115.1	s__Micrococcus endophyticus	81.404	498	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.47	97.28	0.90	0.88	4	-
GCF_000023205.1	s__Micrococcus luteus	81.1837	473	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	97.15	95.98	0.88	0.78	124	-
GCF_014204815.1	s__Micrococcus flavus	81.0856	466	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Micrococcus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_900116905.1	s__Citricoccus terreus	79.6485	326	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877055.1	s__Citricoccus sp005877055	79.5295	371	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651715.1	s__Zhihengliuella salsuginis	78.2513	260	758	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:48,323] [INFO] GTDB search result was written to GCF_014205175.1_ASM1420517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:48,324] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:48,328] [INFO] DFAST_QC result json was written to GCF_014205175.1_ASM1420517v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:48,328] [INFO] DFAST_QC completed!
[2024-01-24 12:45:48,328] [INFO] Total running time: 0h1m5s