[2024-01-25 19:31:51,523] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg92078e5a-84b7-427f-8769-5ea0d68ef760/dqc_reference
[2024-01-25 19:31:52,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,682] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ef80746-7c24-4a47-8b57-5b06b3089dc5/GCF_014643255.1_ASM1464325v1_genomic.fna.gz | prodigal -d GCF_014643255.1_ASM1464325v1_genomic.fna/cds.fna -a GCF_014643255.1_ASM1464325v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:00,679] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:00,680] [INFO] Task started: HMMsearch
[2024-01-25 19:32:00,680] [INFO] Running command: hmmsearch --tblout GCF_014643255.1_ASM1464325v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92078e5a-84b7-427f-8769-5ea0d68ef760/dqc_reference/reference_markers.hmm GCF_014643255.1_ASM1464325v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:00,890] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:00,891] [INFO] Found 6/6 markers.
[2024-01-25 19:32:00,918] [INFO] Query marker FASTA was written to GCF_014643255.1_ASM1464325v1_genomic.fna/markers.fasta
[2024-01-25 19:32:00,919] [INFO] Task started: Blastn
[2024-01-25 19:32:00,919] [INFO] Running command: blastn -query GCF_014643255.1_ASM1464325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92078e5a-84b7-427f-8769-5ea0d68ef760/dqc_reference/reference_markers.fasta -out GCF_014643255.1_ASM1464325v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:02,076] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:02,078] [INFO] Selected 20 target genomes.
[2024-01-25 19:32:02,079] [INFO] Target genome list was writen to GCF_014643255.1_ASM1464325v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:02,084] [INFO] Task started: fastANI
[2024-01-25 19:32:02,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ef80746-7c24-4a47-8b57-5b06b3089dc5/GCF_014643255.1_ASM1464325v1_genomic.fna.gz --refList GCF_014643255.1_ASM1464325v1_genomic.fna/target_genomes.txt --output GCF_014643255.1_ASM1464325v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:17,138] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:17,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92078e5a-84b7-427f-8769-5ea0d68ef760/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:17,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92078e5a-84b7-427f-8769-5ea0d68ef760/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:17,150] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:17,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:17,151] [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 solisilvae	strain=CGMCC 1.15480	GCA_014643255.1	1882339	1882339	type	True	100.0	1069	1072	95	conclusive
Tersicoccus phoenicis	strain=DSM 30849	GCA_001968835.1	554083	554083	type	True	85.3433	761	1072	95	below_threshold
Sinomonas atrocyanea	strain=NBRC 12956	GCA_006539205.1	37927	37927	type	True	78.9533	421	1072	95	below_threshold
Sinomonas atrocyanea	strain=CGMCC 1.1891	GCA_014644475.1	37927	37927	type	True	78.8837	416	1072	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	78.6092	419	1072	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.6081	394	1072	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	78.5529	421	1072	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	78.5191	387	1072	95	below_threshold
Arthrobacter ruber	strain=MDB1-42	GCA_002954225.1	1258893	1258893	type	True	78.5131	359	1072	95	below_threshold
Kocuria varians	strain=NBRC 15358	GCA_006539885.1	1272	1272	type	True	78.4486	294	1072	95	below_threshold
Arthrobacter pityocampae	strain=Tp2	GCA_002927275.1	547334	547334	type	True	78.3755	386	1072	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.1956	343	1072	95	below_threshold
Kocuria tytonicola	strain=DSM 104133	GCA_003687455.1	2055946	2055946	type	True	78.1505	290	1072	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	78.1501	300	1072	95	below_threshold
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	78.1152	365	1072	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.9242	300	1072	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.8156	312	1072	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	77.701	271	1072	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.7133	312	1072	95	below_threshold
Peterkaempfera griseoplana	strain=NRRL B-3064	GCA_001418575.1	66896	66896	type	True	76.3038	322	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:17,153] [INFO] DFAST Taxonomy check result was written to GCF_014643255.1_ASM1464325v1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:17,153] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:17,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:17,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92078e5a-84b7-427f-8769-5ea0d68ef760/dqc_reference/checkm_data
[2024-01-25 19:32:17,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:17,188] [INFO] Task started: CheckM
[2024-01-25 19:32:17,188] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014643255.1_ASM1464325v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014643255.1_ASM1464325v1_genomic.fna/checkm_input GCF_014643255.1_ASM1464325v1_genomic.fna/checkm_result
[2024-01-25 19:33:01,607] [INFO] Task succeeded: CheckM
[2024-01-25 19:33:01,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:33:01,627] [INFO] ===== Completeness check finished =====
[2024-01-25 19:33:01,628] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:33:01,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014643255.1_ASM1464325v1_genomic.fna/markers.fasta)
[2024-01-25 19:33:01,629] [INFO] Task started: Blastn
[2024-01-25 19:33:01,629] [INFO] Running command: blastn -query GCF_014643255.1_ASM1464325v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92078e5a-84b7-427f-8769-5ea0d68ef760/dqc_reference/reference_markers_gtdb.fasta -out GCF_014643255.1_ASM1464325v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:03,530] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:03,537] [INFO] Selected 15 target genomes.
[2024-01-25 19:33:03,537] [INFO] Target genome list was writen to GCF_014643255.1_ASM1464325v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:33:03,571] [INFO] Task started: fastANI
[2024-01-25 19:33:03,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ef80746-7c24-4a47-8b57-5b06b3089dc5/GCF_014643255.1_ASM1464325v1_genomic.fna.gz --refList GCF_014643255.1_ASM1464325v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014643255.1_ASM1464325v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:33:15,027] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:15,037] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:33:15,037] [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_014643255.1	s__Tersicoccus solisilvae	100.0	1069	1072	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_001968825.1	s__Tersicoccus sp001968825	87.2201	906	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001968835.1	s__Tersicoccus phoenicis	85.3433	761	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577305.1	s__Sinomonas atrocyanea	78.9641	422	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	78.8988	408	1072	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_000816565.1	s__Arthrobacter_D sp000816565	78.6284	365	1072	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_012395835.1	s__Arthrobacter_F mobilis	78.6038	395	1072	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_001580365.1	s__Kocuria turfanensis	78.5585	421	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_001483755.1	s__Kocuria polaris_A	78.5145	400	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929375.1	s__Arthrobacter_D sp002929375	78.5121	390	1072	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_001999765.1	s__Sinomonas mesophila	78.4989	389	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539885.1	s__Kocuria varians	78.435	295	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.47	99.47	0.94	0.94	2	-
GCF_900116905.1	s__Citricoccus terreus	78.2951	293	1072	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	78.0866	368	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418575.1	s__Streptomyces_D griseoplanus	76.3215	319	1072	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:33:15,038] [INFO] GTDB search result was written to GCF_014643255.1_ASM1464325v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:33:15,040] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:33:15,043] [INFO] DFAST_QC result json was written to GCF_014643255.1_ASM1464325v1_genomic.fna/dqc_result.json
[2024-01-25 19:33:15,044] [INFO] DFAST_QC completed!
[2024-01-25 19:33:15,044] [INFO] Total running time: 0h1m24s