[2024-01-24 13:25:58,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,061] [INFO] DQC Reference Directory: /var/lib/cwl/stgde66145e-703d-40bf-981e-327709d3c2af/dqc_reference
[2024-01-24 13:26:00,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,378] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,380] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd800647-1eef-4c63-b873-bd500ffdc0cf/GCF_001968835.1_ASM196883v1_genomic.fna.gz | prodigal -d GCF_001968835.1_ASM196883v1_genomic.fna/cds.fna -a GCF_001968835.1_ASM196883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:09,495] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:09,496] [INFO] Task started: HMMsearch
[2024-01-24 13:26:09,496] [INFO] Running command: hmmsearch --tblout GCF_001968835.1_ASM196883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde66145e-703d-40bf-981e-327709d3c2af/dqc_reference/reference_markers.hmm GCF_001968835.1_ASM196883v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:09,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:09,790] [INFO] Found 6/6 markers.
[2024-01-24 13:26:09,825] [INFO] Query marker FASTA was written to GCF_001968835.1_ASM196883v1_genomic.fna/markers.fasta
[2024-01-24 13:26:09,826] [INFO] Task started: Blastn
[2024-01-24 13:26:09,826] [INFO] Running command: blastn -query GCF_001968835.1_ASM196883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde66145e-703d-40bf-981e-327709d3c2af/dqc_reference/reference_markers.fasta -out GCF_001968835.1_ASM196883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:11,153] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:11,160] [INFO] Selected 23 target genomes.
[2024-01-24 13:26:11,161] [INFO] Target genome list was writen to GCF_001968835.1_ASM196883v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:11,171] [INFO] Task started: fastANI
[2024-01-24 13:26:11,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd800647-1eef-4c63-b873-bd500ffdc0cf/GCF_001968835.1_ASM196883v1_genomic.fna.gz --refList GCF_001968835.1_ASM196883v1_genomic.fna/target_genomes.txt --output GCF_001968835.1_ASM196883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:27,417] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:27,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde66145e-703d-40bf-981e-327709d3c2af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:27,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde66145e-703d-40bf-981e-327709d3c2af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:27,437] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:27,437] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:27,437] [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
Tersicoccus phoenicis	strain=DSM 30849	GCA_001968835.1	554083	554083	type	True	100.0	1019	1024	95	conclusive
Tersicoccus solisilvae	strain=CGMCC 1.15480	GCA_014643255.1	1882339	1882339	type	True	85.4273	761	1024	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	78.712	374	1024	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	78.35	361	1024	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	78.3417	368	1024	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	78.3325	397	1024	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.2822	350	1024	95	below_threshold
Arthrobacter pityocampae	strain=Tp2	GCA_002927275.1	547334	547334	type	True	78.2763	327	1024	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	78.2065	352	1024	95	below_threshold
Sinomonas atrocyanea	strain=CGMCC 1.1891	GCA_014644475.1	37927	37927	type	True	78.1372	374	1024	95	below_threshold
Arthrobacter woluwensis	strain=DSM 10495	GCA_900105345.1	156980	156980	type	True	78.1226	292	1024	95	below_threshold
Arthrobacter woluwensis	strain=NBRC 107840	GCA_001552095.1	156980	156980	type	True	78.0991	289	1024	95	below_threshold
Micrococcus flavus	strain=CGMCC 1.5361	GCA_014644875.1	384602	384602	type	True	78.0361	270	1024	95	below_threshold
Arthrobacter ruber	strain=MDB1-42	GCA_002954225.1	1258893	1258893	type	True	77.9898	327	1024	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.863	258	1024	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.7699	286	1024	95	below_threshold
Ornithinimicrobium flavum	strain=CPCC 203535	GCA_004526345.1	1288636	1288636	type	True	77.1956	214	1024	95	below_threshold
Occultella gossypii	strain=N2-46	GCA_019947135.1	2800820	2800820	type	True	77.004	267	1024	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.8727	273	1024	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	76.7966	226	1024	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	76.6294	235	1024	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	76.6088	226	1024	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	76.3682	323	1024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:27,440] [INFO] DFAST Taxonomy check result was written to GCF_001968835.1_ASM196883v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:27,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:27,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:27,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde66145e-703d-40bf-981e-327709d3c2af/dqc_reference/checkm_data
[2024-01-24 13:26:27,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:27,492] [INFO] Task started: CheckM
[2024-01-24 13:26:27,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001968835.1_ASM196883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001968835.1_ASM196883v1_genomic.fna/checkm_input GCF_001968835.1_ASM196883v1_genomic.fna/checkm_result
[2024-01-24 13:27:14,219] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:14,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:14,244] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:14,245] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:14,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001968835.1_ASM196883v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:14,246] [INFO] Task started: Blastn
[2024-01-24 13:27:14,246] [INFO] Running command: blastn -query GCF_001968835.1_ASM196883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde66145e-703d-40bf-981e-327709d3c2af/dqc_reference/reference_markers_gtdb.fasta -out GCF_001968835.1_ASM196883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:16,263] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:16,274] [INFO] Selected 16 target genomes.
[2024-01-24 13:27:16,275] [INFO] Target genome list was writen to GCF_001968835.1_ASM196883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:16,289] [INFO] Task started: fastANI
[2024-01-24 13:27:16,290] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd800647-1eef-4c63-b873-bd500ffdc0cf/GCF_001968835.1_ASM196883v1_genomic.fna.gz --refList GCF_001968835.1_ASM196883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001968835.1_ASM196883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:28,303] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:28,321] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:28,322] [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_001968835.1	s__Tersicoccus phoenicis	100.0	1019	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014643255.1	s__Tersicoccus solisilvae	85.4346	760	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001968825.1	s__Tersicoccus sp001968825	85.3053	781	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008580665.1	s__Zafaria cholistanensis	78.5732	290	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877055.1	s__Citricoccus sp005877055	78.3646	342	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	78.348	386	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580365.1	s__Kocuria turfanensis	78.3461	395	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_006094695.1	s__Kocuria rosea	78.3092	370	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_012395835.1	s__Arthrobacter_F mobilis	78.2711	351	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483755.1	s__Kocuria polaris_A	78.2551	352	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016892645.1	s__Arthrobacter_H sp016892645	78.1767	313	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000816565.1	s__Arthrobacter_D sp000816565	78.0828	359	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929295.1	s__Arthrobacter_D sp002929295	77.9598	352	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218545.1	s__Cellulomonas gilvus	76.7669	229	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407765.1	s__Allostreptomyces psammosilenae	76.3285	328	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721495.1	s__Streptomyces sp000721495	76.1877	298	1024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:28,324] [INFO] GTDB search result was written to GCF_001968835.1_ASM196883v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:28,324] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:28,331] [INFO] DFAST_QC result json was written to GCF_001968835.1_ASM196883v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:28,332] [INFO] DFAST_QC completed!
[2024-01-24 13:27:28,332] [INFO] Total running time: 0h1m30s