[2024-01-24 12:14:33,672] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,673] [INFO] DQC Reference Directory: /var/lib/cwl/stg22fdd3fe-8cac-49aa-b481-932a7c19a836/dqc_reference
[2024-01-24 12:14:34,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,989] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,990] [INFO] Running command: gunzip -c /var/lib/cwl/stgf39e2530-bc85-4cd0-a518-b800bc0d0c4f/GCF_003722335.1_ASM372233v1_genomic.fna.gz | prodigal -d GCF_003722335.1_ASM372233v1_genomic.fna/cds.fna -a GCF_003722335.1_ASM372233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:48,208] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:48,208] [INFO] Task started: HMMsearch
[2024-01-24 12:14:48,208] [INFO] Running command: hmmsearch --tblout GCF_003722335.1_ASM372233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22fdd3fe-8cac-49aa-b481-932a7c19a836/dqc_reference/reference_markers.hmm GCF_003722335.1_ASM372233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:48,459] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:48,460] [INFO] Found 6/6 markers.
[2024-01-24 12:14:48,502] [INFO] Query marker FASTA was written to GCF_003722335.1_ASM372233v1_genomic.fna/markers.fasta
[2024-01-24 12:14:48,502] [INFO] Task started: Blastn
[2024-01-24 12:14:48,502] [INFO] Running command: blastn -query GCF_003722335.1_ASM372233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22fdd3fe-8cac-49aa-b481-932a7c19a836/dqc_reference/reference_markers.fasta -out GCF_003722335.1_ASM372233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,492] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,494] [INFO] Selected 12 target genomes.
[2024-01-24 12:14:49,495] [INFO] Target genome list was writen to GCF_003722335.1_ASM372233v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:49,498] [INFO] Task started: fastANI
[2024-01-24 12:14:49,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgf39e2530-bc85-4cd0-a518-b800bc0d0c4f/GCF_003722335.1_ASM372233v1_genomic.fna.gz --refList GCF_003722335.1_ASM372233v1_genomic.fna/target_genomes.txt --output GCF_003722335.1_ASM372233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:07,384] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:07,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22fdd3fe-8cac-49aa-b481-932a7c19a836/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:07,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22fdd3fe-8cac-49aa-b481-932a7c19a836/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:07,393] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:07,393] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:07,393] [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
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	100.0	1885	1886	95	conclusive
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	99.9766	1839	1886	95	conclusive
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	92.8363	1522	1886	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	92.6652	1503	1886	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	92.135	1472	1886	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	89.7679	1375	1886	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	84.4372	1149	1886	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	83.3779	894	1886	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.373	740	1886	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.1104	668	1886	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.7191	579	1886	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	77.9092	364	1886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:07,394] [INFO] DFAST Taxonomy check result was written to GCF_003722335.1_ASM372233v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:07,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:07,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:07,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22fdd3fe-8cac-49aa-b481-932a7c19a836/dqc_reference/checkm_data
[2024-01-24 12:15:07,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:07,448] [INFO] Task started: CheckM
[2024-01-24 12:15:07,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003722335.1_ASM372233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003722335.1_ASM372233v1_genomic.fna/checkm_input GCF_003722335.1_ASM372233v1_genomic.fna/checkm_result
[2024-01-24 12:15:47,930] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:47,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:47,946] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:47,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:47,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003722335.1_ASM372233v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:47,946] [INFO] Task started: Blastn
[2024-01-24 12:15:47,946] [INFO] Running command: blastn -query GCF_003722335.1_ASM372233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22fdd3fe-8cac-49aa-b481-932a7c19a836/dqc_reference/reference_markers_gtdb.fasta -out GCF_003722335.1_ASM372233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:49,952] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:49,955] [INFO] Selected 7 target genomes.
[2024-01-24 12:15:49,955] [INFO] Target genome list was writen to GCF_003722335.1_ASM372233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:49,959] [INFO] Task started: fastANI
[2024-01-24 12:15:49,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgf39e2530-bc85-4cd0-a518-b800bc0d0c4f/GCF_003722335.1_ASM372233v1_genomic.fna.gz --refList GCF_003722335.1_ASM372233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003722335.1_ASM372233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:03,358] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:03,363] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:03,364] [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_003722335.1	s__Caulobacter flavus	100.0	1885	1886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCF_003094615.1	s__Caulobacter radicis	92.824	1523	1886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0713	96.08	96.08	0.90	0.90	2	-
GCF_001449105.1	s__Caulobacter vibrioides_C	92.7691	1469	1886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858925.1	s__Caulobacter zeae	92.6652	1503	1886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0713	N/A	N/A	N/A	N/A	1	-
GCF_011043625.1	s__Caulobacter sp011043625	92.6407	1486	1886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116815.1	s__Caulobacter sp003116815	92.129	1472	1886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003185805.1	s__Caulobacter sp003185805	90.2152	1172	1886	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:03,365] [INFO] GTDB search result was written to GCF_003722335.1_ASM372233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:03,365] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:03,370] [INFO] DFAST_QC result json was written to GCF_003722335.1_ASM372233v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:03,370] [INFO] DFAST_QC completed!
[2024-01-24 12:16:03,370] [INFO] Total running time: 0h1m30s