[2024-01-25 18:54:21,129] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:21,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:21,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e4fa7d6-29e3-451d-9099-60ec636d58ff/dqc_reference
[2024-01-25 18:54:22,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:22,376] [INFO] Task started: Prodigal
[2024-01-25 18:54:22,377] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd0505d7-ba16-4fc5-8148-f83ad9cc602d/GCF_014651715.1_ASM1465171v1_genomic.fna.gz | prodigal -d GCF_014651715.1_ASM1465171v1_genomic.fna/cds.fna -a GCF_014651715.1_ASM1465171v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:30,296] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:30,297] [INFO] Task started: HMMsearch
[2024-01-25 18:54:30,297] [INFO] Running command: hmmsearch --tblout GCF_014651715.1_ASM1465171v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e4fa7d6-29e3-451d-9099-60ec636d58ff/dqc_reference/reference_markers.hmm GCF_014651715.1_ASM1465171v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:30,509] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:30,510] [INFO] Found 6/6 markers.
[2024-01-25 18:54:30,537] [INFO] Query marker FASTA was written to GCF_014651715.1_ASM1465171v1_genomic.fna/markers.fasta
[2024-01-25 18:54:30,537] [INFO] Task started: Blastn
[2024-01-25 18:54:30,537] [INFO] Running command: blastn -query GCF_014651715.1_ASM1465171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e4fa7d6-29e3-451d-9099-60ec636d58ff/dqc_reference/reference_markers.fasta -out GCF_014651715.1_ASM1465171v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:31,727] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:31,730] [INFO] Selected 18 target genomes.
[2024-01-25 18:54:31,730] [INFO] Target genome list was writen to GCF_014651715.1_ASM1465171v1_genomic.fna/target_genomes.txt
[2024-01-25 18:54:31,739] [INFO] Task started: fastANI
[2024-01-25 18:54:31,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0505d7-ba16-4fc5-8148-f83ad9cc602d/GCF_014651715.1_ASM1465171v1_genomic.fna.gz --refList GCF_014651715.1_ASM1465171v1_genomic.fna/target_genomes.txt --output GCF_014651715.1_ASM1465171v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:44,334] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:44,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e4fa7d6-29e3-451d-9099-60ec636d58ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:44,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e4fa7d6-29e3-451d-9099-60ec636d58ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:44,345] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:54:44,345] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:44,345] [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 salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	100.0	1104	1107	95	conclusive
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	85.8902	900	1107	95	below_threshold
Zhihengliuella flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	80.4455	593	1107	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	79.1083	432	1107	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	79.1018	391	1107	95	below_threshold
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	79.0247	350	1107	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	78.955	348	1107	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	78.69	369	1107	95	below_threshold
Paeniglutamicibacter cryotolerans	strain=DSM 22826	GCA_014190875.1	670079	670079	type	True	78.5632	354	1107	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.5228	318	1107	95	below_threshold
Arthrobacter ruber	strain=MDB1-42	GCA_002954225.1	1258893	1258893	type	True	78.5047	344	1107	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.3767	377	1107	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	78.2356	370	1107	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	78.1483	300	1107	95	below_threshold
Tersicoccus solisilvae	strain=CGMCC 1.15480	GCA_014643255.1	1882339	1882339	type	True	78.0721	368	1107	95	below_threshold
Arthrobacter cheniae	strain=Hz2	GCA_003602275.1	1258888	1258888	type	True	78.0027	284	1107	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	77.8902	241	1107	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.1222	248	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:44,347] [INFO] DFAST Taxonomy check result was written to GCF_014651715.1_ASM1465171v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:44,348] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:44,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:44,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e4fa7d6-29e3-451d-9099-60ec636d58ff/dqc_reference/checkm_data
[2024-01-25 18:54:44,349] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:44,383] [INFO] Task started: CheckM
[2024-01-25 18:54:44,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651715.1_ASM1465171v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651715.1_ASM1465171v1_genomic.fna/checkm_input GCF_014651715.1_ASM1465171v1_genomic.fna/checkm_result
[2024-01-25 18:55:11,077] [INFO] Task succeeded: CheckM
[2024-01-25 18:55:11,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:55:11,106] [INFO] ===== Completeness check finished =====
[2024-01-25 18:55:11,106] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:55:11,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651715.1_ASM1465171v1_genomic.fna/markers.fasta)
[2024-01-25 18:55:11,106] [INFO] Task started: Blastn
[2024-01-25 18:55:11,106] [INFO] Running command: blastn -query GCF_014651715.1_ASM1465171v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e4fa7d6-29e3-451d-9099-60ec636d58ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651715.1_ASM1465171v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:13,083] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:13,086] [INFO] Selected 15 target genomes.
[2024-01-25 18:55:13,086] [INFO] Target genome list was writen to GCF_014651715.1_ASM1465171v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:55:13,097] [INFO] Task started: fastANI
[2024-01-25 18:55:13,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd0505d7-ba16-4fc5-8148-f83ad9cc602d/GCF_014651715.1_ASM1465171v1_genomic.fna.gz --refList GCF_014651715.1_ASM1465171v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651715.1_ASM1465171v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:55:24,154] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:24,164] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:55:24,164] [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_014651715.1	s__Zhihengliuella salsuginis	100.0	1104	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004217565.1	s__Zhihengliuella halotolerans	85.9159	897	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	97.65	97.65	0.89	0.89	2	-
GCF_015751895.1	s__Zhihengliuella flava	80.4423	594	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008580665.1	s__Zafaria cholistanensis	79.8967	426	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016892645.1	s__Arthrobacter_H sp016892645	79.7308	495	1107	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_001863355.1	s__Paeniglutamicibacter sp001863355	79.1117	441	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	79.0915	392	1107	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	78.9792	395	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	-
GCF_014647495.1	s__Glutamicibacter protophormiae	78.9551	347	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.76	97.53	0.93	0.87	3	-
GCA_900016675.1	s__Arthrobacter_B saudimassiliensis	78.8598	372	1107	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_002927275.1	s__Arthrobacter_D pityocampae	78.6789	332	1107	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_002954225.1	s__Arthrobacter_D ruber	78.5163	343	1107	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_002975405.1	s__Glutamicibacter sp002975405	78.4266	253	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.44	96.03	0.93	0.84	6	-
GCF_001968825.1	s__Tersicoccus sp001968825	78.3874	362	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Tersicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929375.1	s__Arthrobacter_D sp002929375	78.3814	357	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:55:24,165] [INFO] GTDB search result was written to GCF_014651715.1_ASM1465171v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:55:24,166] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:55:24,169] [INFO] DFAST_QC result json was written to GCF_014651715.1_ASM1465171v1_genomic.fna/dqc_result.json
[2024-01-25 18:55:24,169] [INFO] DFAST_QC completed!
[2024-01-25 18:55:24,169] [INFO] Total running time: 0h1m3s