[2024-01-24 14:39:44,280] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:44,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:44,283] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a8266ec-52fc-4684-a16a-131a7d79f140/dqc_reference
[2024-01-24 14:39:45,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:45,602] [INFO] Task started: Prodigal
[2024-01-24 14:39:45,602] [INFO] Running command: gunzip -c /var/lib/cwl/stg2014d275-fa35-4a7f-92be-b4dadaa3848c/GCF_004217565.1_ASM421756v1_genomic.fna.gz | prodigal -d GCF_004217565.1_ASM421756v1_genomic.fna/cds.fna -a GCF_004217565.1_ASM421756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:56,189] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:56,189] [INFO] Task started: HMMsearch
[2024-01-24 14:39:56,190] [INFO] Running command: hmmsearch --tblout GCF_004217565.1_ASM421756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a8266ec-52fc-4684-a16a-131a7d79f140/dqc_reference/reference_markers.hmm GCF_004217565.1_ASM421756v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:56,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:56,506] [INFO] Found 6/6 markers.
[2024-01-24 14:39:56,547] [INFO] Query marker FASTA was written to GCF_004217565.1_ASM421756v1_genomic.fna/markers.fasta
[2024-01-24 14:39:56,548] [INFO] Task started: Blastn
[2024-01-24 14:39:56,548] [INFO] Running command: blastn -query GCF_004217565.1_ASM421756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a8266ec-52fc-4684-a16a-131a7d79f140/dqc_reference/reference_markers.fasta -out GCF_004217565.1_ASM421756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:57,824] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:57,827] [INFO] Selected 19 target genomes.
[2024-01-24 14:39:57,828] [INFO] Target genome list was writen to GCF_004217565.1_ASM421756v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:57,836] [INFO] Task started: fastANI
[2024-01-24 14:39:57,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg2014d275-fa35-4a7f-92be-b4dadaa3848c/GCF_004217565.1_ASM421756v1_genomic.fna.gz --refList GCF_004217565.1_ASM421756v1_genomic.fna/target_genomes.txt --output GCF_004217565.1_ASM421756v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:13,631] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:13,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a8266ec-52fc-4684-a16a-131a7d79f140/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:13,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a8266ec-52fc-4684-a16a-131a7d79f140/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:13,659] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:13,660] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:13,660] [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
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	100.0	1193	1194	95	conclusive
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	85.936	906	1194	95	below_threshold
Zhihengliuella flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	80.1777	550	1194	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	79.0418	405	1194	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	78.8884	404	1194	95	below_threshold
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	78.8788	325	1194	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	78.6793	402	1194	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	78.6729	342	1194	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.6213	297	1194	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	78.5915	345	1194	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	78.485	323	1194	95	below_threshold
Arthrobacter ruber	strain=MDB1-42	GCA_002954225.1	1258893	1258893	type	True	78.2858	317	1194	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	78.1784	270	1194	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.1225	349	1194	95	below_threshold
Arthrobacter bussei	strain=KR32	GCA_009377195.2	2594179	2594179	type	True	78.11	297	1194	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	78.0237	226	1194	95	below_threshold
Tersicoccus solisilvae	strain=CGMCC 1.15480	GCA_014643255.1	1882339	1882339	type	True	78.0044	318	1194	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	77.0657	241	1194	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	76.9235	248	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,665] [INFO] DFAST Taxonomy check result was written to GCF_004217565.1_ASM421756v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:13,666] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:13,666] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:13,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a8266ec-52fc-4684-a16a-131a7d79f140/dqc_reference/checkm_data
[2024-01-24 14:40:13,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:13,719] [INFO] Task started: CheckM
[2024-01-24 14:40:13,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217565.1_ASM421756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217565.1_ASM421756v1_genomic.fna/checkm_input GCF_004217565.1_ASM421756v1_genomic.fna/checkm_result
[2024-01-24 14:40:47,890] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:47,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:47,914] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:47,914] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:47,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217565.1_ASM421756v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:47,915] [INFO] Task started: Blastn
[2024-01-24 14:40:47,915] [INFO] Running command: blastn -query GCF_004217565.1_ASM421756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a8266ec-52fc-4684-a16a-131a7d79f140/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217565.1_ASM421756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:49,790] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:49,793] [INFO] Selected 16 target genomes.
[2024-01-24 14:40:49,794] [INFO] Target genome list was writen to GCF_004217565.1_ASM421756v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:49,806] [INFO] Task started: fastANI
[2024-01-24 14:40:49,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg2014d275-fa35-4a7f-92be-b4dadaa3848c/GCF_004217565.1_ASM421756v1_genomic.fna.gz --refList GCF_004217565.1_ASM421756v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217565.1_ASM421756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:01,580] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:01,594] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:01,595] [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_004217565.1	s__Zhihengliuella halotolerans	100.0	1193	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	97.65	97.65	0.89	0.89	2	conclusive
GCF_014651715.1	s__Zhihengliuella salsuginis	85.9361	906	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015751895.1	s__Zhihengliuella flava	80.1477	548	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016892645.1	s__Arthrobacter_H sp016892645	79.3385	438	1194	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_008580665.1	s__Zafaria cholistanensis	79.1571	401	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084045.1	s__Paeniglutamicibacter sp019084045	79.071	381	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003575975.1	s__Galactobacter valiniphilus	78.6721	342	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Galactobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190875.1	s__Paeniglutamicibacter cryotolerans	78.6712	344	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577305.1	s__Sinomonas atrocyanea	78.5924	385	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	-
GCF_006094275.1	s__Glutamicibacter creatinolyticus	78.5892	310	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.17	97.78	0.92	0.89	4	-
GCF_014647495.1	s__Glutamicibacter protophormiae	78.4849	323	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.76	97.53	0.93	0.87	3	-
GCF_005877055.1	s__Citricoccus sp005877055	78.44	348	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Citricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929375.1	s__Arthrobacter_D sp002929375	78.1949	340	1194	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_001968825.1	s__Tersicoccus sp001968825	78.1838	322	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328305.2	s__Arthrobacter_F crystallopoietes_A	78.1154	300	1194	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_900163545.1	s__Arthrobacter_H rhombi	78.013	248	1194	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_H	95.0	99.06	99.06	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:01,604] [INFO] GTDB search result was written to GCF_004217565.1_ASM421756v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:01,606] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:01,612] [INFO] DFAST_QC result json was written to GCF_004217565.1_ASM421756v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:01,612] [INFO] DFAST_QC completed!
[2024-01-24 14:41:01,613] [INFO] Total running time: 0h1m17s