[2024-01-24 15:10:48,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,142] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,143] [INFO] DQC Reference Directory: /var/lib/cwl/stgc194e5ad-4fe0-4ae4-a62c-32621c8dbde6/dqc_reference
[2024-01-24 15:10:51,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:51,749] [INFO] Task started: Prodigal
[2024-01-24 15:10:51,750] [INFO] Running command: gunzip -c /var/lib/cwl/stge37b5c9b-80e0-45a6-bcf6-b1aa29fbc8a6/GCF_014644555.1_ASM1464455v1_genomic.fna.gz | prodigal -d GCF_014644555.1_ASM1464455v1_genomic.fna/cds.fna -a GCF_014644555.1_ASM1464455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:03,842] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:03,843] [INFO] Task started: HMMsearch
[2024-01-24 15:11:03,843] [INFO] Running command: hmmsearch --tblout GCF_014644555.1_ASM1464455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc194e5ad-4fe0-4ae4-a62c-32621c8dbde6/dqc_reference/reference_markers.hmm GCF_014644555.1_ASM1464455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:04,150] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:04,152] [INFO] Found 6/6 markers.
[2024-01-24 15:11:04,187] [INFO] Query marker FASTA was written to GCF_014644555.1_ASM1464455v1_genomic.fna/markers.fasta
[2024-01-24 15:11:04,188] [INFO] Task started: Blastn
[2024-01-24 15:11:04,188] [INFO] Running command: blastn -query GCF_014644555.1_ASM1464455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc194e5ad-4fe0-4ae4-a62c-32621c8dbde6/dqc_reference/reference_markers.fasta -out GCF_014644555.1_ASM1464455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:05,014] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:05,027] [INFO] Selected 16 target genomes.
[2024-01-24 15:11:05,027] [INFO] Target genome list was writen to GCF_014644555.1_ASM1464455v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:05,035] [INFO] Task started: fastANI
[2024-01-24 15:11:05,036] [INFO] Running command: fastANI --query /var/lib/cwl/stge37b5c9b-80e0-45a6-bcf6-b1aa29fbc8a6/GCF_014644555.1_ASM1464455v1_genomic.fna.gz --refList GCF_014644555.1_ASM1464455v1_genomic.fna/target_genomes.txt --output GCF_014644555.1_ASM1464455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:16,256] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:16,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc194e5ad-4fe0-4ae4-a62c-32621c8dbde6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:16,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc194e5ad-4fe0-4ae4-a62c-32621c8dbde6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:16,275] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:16,275] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:16,276] [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
Glutamicibacter ardleyensis	strain=CGMCC 1.3685	GCA_014644555.1	225894	225894	type	True	100.0	1297	1298	95	conclusive
Glutamicibacter arilaitensis	strain=Re117	GCA_000197735.1	256701	256701	type	True	81.0161	506	1298	95	below_threshold
Glutamicibacter nicotianae	strain=NBRC 14234	GCA_006539525.1	37929	37929	type	True	80.3009	491	1298	95	below_threshold
Glutamicibacter mysorens	strain=DSM 12798	GCA_002797775.1	257984	257984	type	True	80.1813	468	1298	95	below_threshold
Glutamicibacter mysorens	strain=NBRC 103060	GCA_001552115.1	257984	257984	type	True	80.16	460	1298	95	below_threshold
Glutamicibacter mishrai	strain=S5-52	GCA_012221945.1	1775880	1775880	type	True	80.027	437	1298	95	below_threshold
Glutamicibacter halophytocola	strain=KLBMP 5180	GCA_001302565.1	1933880	1933880	type	True	79.9255	427	1298	95	below_threshold
Glutamicibacter protophormiae	strain=DSM 20168	GCA_017876615.1	37930	37930	type	True	79.9199	433	1298	95	below_threshold
Glutamicibacter protophormiae	strain=JCM 1973	GCA_014647495.1	37930	37930	type	True	79.8287	441	1298	95	below_threshold
Glutamicibacter uratoxydans	strain=NBRC 15515	GCA_006539925.1	43667	43667	type	True	79.5936	395	1298	95	below_threshold
Paenarthrobacter nicotinovorans	strain=ATCC 49919	GCA_021919345.1	29320	29320	suspected-type	True	77.5917	95	1298	95	below_threshold
Renibacterium salmoninarum	strain=ATCC 33209	GCA_000018885.1	1646	1646	type	True	77.5365	52	1298	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	77.4619	118	1298	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	76.0884	55	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:16,278] [INFO] DFAST Taxonomy check result was written to GCF_014644555.1_ASM1464455v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:16,279] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:16,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:16,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc194e5ad-4fe0-4ae4-a62c-32621c8dbde6/dqc_reference/checkm_data
[2024-01-24 15:11:16,281] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:16,324] [INFO] Task started: CheckM
[2024-01-24 15:11:16,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014644555.1_ASM1464455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014644555.1_ASM1464455v1_genomic.fna/checkm_input GCF_014644555.1_ASM1464455v1_genomic.fna/checkm_result
[2024-01-24 15:11:54,537] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:54,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:54,566] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:54,566] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:54,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014644555.1_ASM1464455v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:54,567] [INFO] Task started: Blastn
[2024-01-24 15:11:54,567] [INFO] Running command: blastn -query GCF_014644555.1_ASM1464455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc194e5ad-4fe0-4ae4-a62c-32621c8dbde6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014644555.1_ASM1464455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:55,738] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:55,742] [INFO] Selected 10 target genomes.
[2024-01-24 15:11:55,742] [INFO] Target genome list was writen to GCF_014644555.1_ASM1464455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:55,751] [INFO] Task started: fastANI
[2024-01-24 15:11:55,751] [INFO] Running command: fastANI --query /var/lib/cwl/stge37b5c9b-80e0-45a6-bcf6-b1aa29fbc8a6/GCF_014644555.1_ASM1464455v1_genomic.fna.gz --refList GCF_014644555.1_ASM1464455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014644555.1_ASM1464455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:04,234] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:04,283] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:04,283] [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_014644555.1	s__Glutamicibacter ardleyensis	100.0	1297	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	97.40	97.39	0.84	0.82	3	conclusive
GCA_003486025.1	s__Glutamicibacter sp003486025	91.9236	650	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979915.1	s__Glutamicibacter sp002979915	91.8286	1021	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002975405.1	s__Glutamicibacter sp002975405	82.399	733	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.44	96.03	0.93	0.84	6	-
GCF_000197735.1	s__Glutamicibacter arilaitensis	81.0421	506	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.79	97.54	0.91	0.83	7	-
GCF_002979865.1	s__Glutamicibacter sp002979865	80.1843	492	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.88	98.56	0.94	0.92	3	-
GCF_012221945.1	s__Glutamicibacter mishrai	80.0234	437	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	97.84	97.11	0.89	0.89	3	-
GCF_001302565.1	s__Glutamicibacter halophytocola	79.922	428	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.28	98.01	0.91	0.89	4	-
GCF_014647495.1	s__Glutamicibacter protophormiae	79.8197	441	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.76	97.53	0.93	0.87	3	-
GCF_003309065.1	s__Glutamicibacter soli	79.5498	476	1298	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Glutamicibacter	95.0	98.33	97.69	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:04,285] [INFO] GTDB search result was written to GCF_014644555.1_ASM1464455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:04,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:04,290] [INFO] DFAST_QC result json was written to GCF_014644555.1_ASM1464455v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:04,290] [INFO] DFAST_QC completed!
[2024-01-24 15:12:04,290] [INFO] Total running time: 0h1m16s