[2024-01-24 14:05:00,473] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg46c4c83d-6b34-4b6b-b9ba-e3862355c1f1/dqc_reference
[2024-01-24 14:05:01,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:01,637] [INFO] Task started: Prodigal
[2024-01-24 14:05:01,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg99c19a7e-7ae1-4cf5-9dbc-339a27031076/GCF_015751895.1_ASM1575189v1_genomic.fna.gz | prodigal -d GCF_015751895.1_ASM1575189v1_genomic.fna/cds.fna -a GCF_015751895.1_ASM1575189v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:10,456] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:10,457] [INFO] Task started: HMMsearch
[2024-01-24 14:05:10,457] [INFO] Running command: hmmsearch --tblout GCF_015751895.1_ASM1575189v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46c4c83d-6b34-4b6b-b9ba-e3862355c1f1/dqc_reference/reference_markers.hmm GCF_015751895.1_ASM1575189v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:10,646] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:10,647] [INFO] Found 6/6 markers.
[2024-01-24 14:05:10,671] [INFO] Query marker FASTA was written to GCF_015751895.1_ASM1575189v1_genomic.fna/markers.fasta
[2024-01-24 14:05:10,672] [INFO] Task started: Blastn
[2024-01-24 14:05:10,672] [INFO] Running command: blastn -query GCF_015751895.1_ASM1575189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c4c83d-6b34-4b6b-b9ba-e3862355c1f1/dqc_reference/reference_markers.fasta -out GCF_015751895.1_ASM1575189v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:11,651] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:11,654] [INFO] Selected 22 target genomes.
[2024-01-24 14:05:11,654] [INFO] Target genome list was writen to GCF_015751895.1_ASM1575189v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:11,710] [INFO] Task started: fastANI
[2024-01-24 14:05:11,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c19a7e-7ae1-4cf5-9dbc-339a27031076/GCF_015751895.1_ASM1575189v1_genomic.fna.gz --refList GCF_015751895.1_ASM1575189v1_genomic.fna/target_genomes.txt --output GCF_015751895.1_ASM1575189v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:24,366] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:24,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46c4c83d-6b34-4b6b-b9ba-e3862355c1f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:24,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46c4c83d-6b34-4b6b-b9ba-e3862355c1f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:24,383] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:24,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:24,383] [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 flava	strain=DSM 26152	GCA_015751895.1	1285193	1285193	type	True	100.0	962	965	95	conclusive
Zhihengliuella salsuginis	strain=KCTC 19466	GCA_014651715.1	578222	578222	type	True	80.5061	587	965	95	below_threshold
Zhihengliuella halotolerans	strain=DSM 17364	GCA_004217565.1	370736	370736	type	True	79.8305	558	965	95	below_threshold
Paeniglutamicibacter kerguelensis	strain=DSM 15797	GCA_017876535.1	254788	254788	type	True	78.2318	252	965	95	below_threshold
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	78.0929	222	965	95	below_threshold
Paeniglutamicibacter psychrophenolicus	strain=DSM 15454	GCA_017876575.1	257454	257454	type	True	77.907	266	965	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	77.8264	224	965	95	below_threshold
Haematomicrobium sanguinis	strain=DSM 21259	GCA_000688395.1	479106	479106	type	True	77.8007	81	965	95	below_threshold
Galactobacter valiniphilus	strain=JZ R-35	GCA_003575975.1	2676122	2676122	type	True	77.7142	238	965	95	below_threshold
Paeniglutamicibacter gangotriensis	strain=Lz1y	GCA_000348945.1	254787	254787	type	True	77.6866	180	965	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	77.6618	217	965	95	below_threshold
Arthrobacter ruber	strain=MDB1-42	GCA_002954225.1	1258893	1258893	type	True	77.6402	178	965	95	below_threshold
Arthrobacter pullicola	strain=Sa2BUA2	GCA_014836875.1	2762224	2762224	type	True	77.589	166	965	95	below_threshold
Arthrobacter crusticola	strain=SLN-3	GCA_004357995.1	2547960	2547960	type	True	77.4636	170	965	95	below_threshold
Arthrobacter citreus	strain=DSM 20133	GCA_009192745.1	1670	1670	type	True	77.4328	172	965	95	below_threshold
Arthrobacter yangruifuii	strain=785	GCA_009192775.1	2606616	2606616	type	True	77.3975	174	965	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	77.3906	220	965	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	76.6641	115	965	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	76.6602	112	965	95	below_threshold
Ruania suaedae	strain=LR1S40	GCA_021049265.1	2897774	2897774	type	True	76.6453	111	965	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	76.6452	114	965	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	76.5658	118	965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:24,385] [INFO] DFAST Taxonomy check result was written to GCF_015751895.1_ASM1575189v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:24,386] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:24,386] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:24,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46c4c83d-6b34-4b6b-b9ba-e3862355c1f1/dqc_reference/checkm_data
[2024-01-24 14:05:24,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:24,415] [INFO] Task started: CheckM
[2024-01-24 14:05:24,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015751895.1_ASM1575189v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015751895.1_ASM1575189v1_genomic.fna/checkm_input GCF_015751895.1_ASM1575189v1_genomic.fna/checkm_result
[2024-01-24 14:05:54,962] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:54,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:54,994] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:54,995] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:54,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015751895.1_ASM1575189v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:54,995] [INFO] Task started: Blastn
[2024-01-24 14:05:54,995] [INFO] Running command: blastn -query GCF_015751895.1_ASM1575189v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c4c83d-6b34-4b6b-b9ba-e3862355c1f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_015751895.1_ASM1575189v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:56,653] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:56,657] [INFO] Selected 15 target genomes.
[2024-01-24 14:05:56,657] [INFO] Target genome list was writen to GCF_015751895.1_ASM1575189v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:56,673] [INFO] Task started: fastANI
[2024-01-24 14:05:56,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c19a7e-7ae1-4cf5-9dbc-339a27031076/GCF_015751895.1_ASM1575189v1_genomic.fna.gz --refList GCF_015751895.1_ASM1575189v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015751895.1_ASM1575189v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:07,200] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,213] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:07,213] [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_015751895.1	s__Zhihengliuella flava	100.0	963	965	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_014651715.1	s__Zhihengliuella salsuginis	80.4998	588	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217565.1	s__Zhihengliuella halotolerans	79.8396	558	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zhihengliuella	95.0	97.65	97.65	0.89	0.89	2	-
GCF_008580665.1	s__Zafaria cholistanensis	78.3817	286	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Zafaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876535.1	s__Paeniglutamicibacter kerguelensis	78.1909	252	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016892645.1	s__Arthrobacter_H sp016892645	78.1353	276	965	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_001577305.1	s__Sinomonas atrocyanea	78.0814	237	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Sinomonas	95.0	99.98	99.98	1.00	1.00	3	-
GCF_900116905.1	s__Citricoccus terreus	77.9364	179	965	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	77.8846	226	965	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_001863355.1	s__Paeniglutamicibacter sp001863355	77.8072	262	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688395.1	s__Haematomicrobium sanguinis	77.8007	81	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Haematomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287975.1	s__Paeniglutamicibacter sp003287975	77.7692	246	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Paeniglutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047635.1	s__Arthrobacter_F sp005047635	77.7322	192	965	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_002975405.1	s__Glutamicibacter sp002975405	77.7116	174	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.44	96.03	0.93	0.84	6	-
GCF_014647495.1	s__Glutamicibacter protophormiae	77.6427	217	965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.76	97.53	0.93	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,215] [INFO] GTDB search result was written to GCF_015751895.1_ASM1575189v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:07,215] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:07,219] [INFO] DFAST_QC result json was written to GCF_015751895.1_ASM1575189v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:07,220] [INFO] DFAST_QC completed!
[2024-01-24 14:06:07,220] [INFO] Total running time: 0h1m7s