[2024-01-24 13:45:45,267] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg969f71e2-f91d-4ac3-bde8-0a6ddf63091a/dqc_reference
[2024-01-24 13:45:46,659] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:46,660] [INFO] Task started: Prodigal
[2024-01-24 13:45:46,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg5371d923-f40d-4b7e-9e53-32d2bdb3d767/GCF_014196835.1_ASM1419683v1_genomic.fna.gz | prodigal -d GCF_014196835.1_ASM1419683v1_genomic.fna/cds.fna -a GCF_014196835.1_ASM1419683v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:00,634] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:00,635] [INFO] Task started: HMMsearch
[2024-01-24 13:46:00,635] [INFO] Running command: hmmsearch --tblout GCF_014196835.1_ASM1419683v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg969f71e2-f91d-4ac3-bde8-0a6ddf63091a/dqc_reference/reference_markers.hmm GCF_014196835.1_ASM1419683v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:00,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:00,962] [INFO] Found 6/6 markers.
[2024-01-24 13:46:01,013] [INFO] Query marker FASTA was written to GCF_014196835.1_ASM1419683v1_genomic.fna/markers.fasta
[2024-01-24 13:46:01,013] [INFO] Task started: Blastn
[2024-01-24 13:46:01,013] [INFO] Running command: blastn -query GCF_014196835.1_ASM1419683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg969f71e2-f91d-4ac3-bde8-0a6ddf63091a/dqc_reference/reference_markers.fasta -out GCF_014196835.1_ASM1419683v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:02,090] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:02,094] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:02,094] [INFO] Target genome list was writen to GCF_014196835.1_ASM1419683v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:02,120] [INFO] Task started: fastANI
[2024-01-24 13:46:02,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg5371d923-f40d-4b7e-9e53-32d2bdb3d767/GCF_014196835.1_ASM1419683v1_genomic.fna.gz --refList GCF_014196835.1_ASM1419683v1_genomic.fna/target_genomes.txt --output GCF_014196835.1_ASM1419683v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:20,341] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:20,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg969f71e2-f91d-4ac3-bde8-0a6ddf63091a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:20,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg969f71e2-f91d-4ac3-bde8-0a6ddf63091a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:20,361] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:20,362] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:20,362] [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
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	100.0	1639	1642	95	conclusive
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	82.0004	814	1642	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	81.9925	914	1642	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	81.9761	905	1642	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	81.969	845	1642	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	80.2727	593	1642	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	80.1451	789	1642	95	below_threshold
Aureimonas populi	strain=KCTC 42087	GCA_017815515.1	1701758	1701758	type	True	80.0688	586	1642	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	79.7304	620	1642	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	79.7259	594	1642	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.7142	619	1642	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.3124	662	1642	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.7147	472	1642	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.9173	350	1642	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.9	351	1642	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	75.3248	71	1642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:20,364] [INFO] DFAST Taxonomy check result was written to GCF_014196835.1_ASM1419683v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:20,364] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:20,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:20,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg969f71e2-f91d-4ac3-bde8-0a6ddf63091a/dqc_reference/checkm_data
[2024-01-24 13:46:20,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:20,414] [INFO] Task started: CheckM
[2024-01-24 13:46:20,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196835.1_ASM1419683v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196835.1_ASM1419683v1_genomic.fna/checkm_input GCF_014196835.1_ASM1419683v1_genomic.fna/checkm_result
[2024-01-24 13:47:05,036] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:05,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:05,061] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:05,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:05,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196835.1_ASM1419683v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:05,063] [INFO] Task started: Blastn
[2024-01-24 13:47:05,063] [INFO] Running command: blastn -query GCF_014196835.1_ASM1419683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg969f71e2-f91d-4ac3-bde8-0a6ddf63091a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196835.1_ASM1419683v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:07,050] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:07,055] [INFO] Selected 18 target genomes.
[2024-01-24 13:47:07,056] [INFO] Target genome list was writen to GCF_014196835.1_ASM1419683v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:07,093] [INFO] Task started: fastANI
[2024-01-24 13:47:07,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg5371d923-f40d-4b7e-9e53-32d2bdb3d767/GCF_014196835.1_ASM1419683v1_genomic.fna.gz --refList GCF_014196835.1_ASM1419683v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196835.1_ASM1419683v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:26,032] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:26,102] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:26,102] [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_014196835.1	s__Aureimonas pseudogalii	100.0	1639	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001463705.1	s__Aureimonas sp001463705	85.7537	1090	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423245.1	s__Aureimonas sp001423245	82.0962	863	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442755.1	s__Aureimonas sp001442755	82.0637	908	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	98.47	96.94	0.96	0.92	3	-
GCF_003583935.1	s__Aureimonas flava	82.0118	811	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382705.1	s__Aureimonas ureilytica	81.9536	908	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900113065.1	s__Aureimonas phyllosphaerae	81.9357	858	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001463745.1	s__Aureimonas sp001463745	81.8165	811	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463765.1	s__Aureimonas sp001463765	81.7477	841	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903970965.1	s__Aureimonas sp903970965	81.5756	789	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104035.1	s__Aureimonas jatrophae	81.2054	816	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001425485.1	s__Aureimonas_A sp001425485	81.2053	834	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014643375.1	s__Aureimonas_A glaciei	80.2906	752	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014058705.1	s__Aureimonas mangrovi	80.2887	591	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	79.5099	658	1642	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:26,106] [INFO] GTDB search result was written to GCF_014196835.1_ASM1419683v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:26,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:26,114] [INFO] DFAST_QC result json was written to GCF_014196835.1_ASM1419683v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:26,115] [INFO] DFAST_QC completed!
[2024-01-24 13:47:26,115] [INFO] Total running time: 0h1m41s