[2024-01-24 13:58:42,544] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:42,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:42,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg89471d31-f850-456e-be2a-d0049435a830/dqc_reference
[2024-01-24 13:58:43,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:43,946] [INFO] Task started: Prodigal
[2024-01-24 13:58:43,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg59702f0d-9082-40a7-894c-2414f9c227ad/GCF_003094615.1_ASM309461v1_genomic.fna.gz | prodigal -d GCF_003094615.1_ASM309461v1_genomic.fna/cds.fna -a GCF_003094615.1_ASM309461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:59,054] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:59,054] [INFO] Task started: HMMsearch
[2024-01-24 13:58:59,054] [INFO] Running command: hmmsearch --tblout GCF_003094615.1_ASM309461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89471d31-f850-456e-be2a-d0049435a830/dqc_reference/reference_markers.hmm GCF_003094615.1_ASM309461v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:59,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:59,359] [INFO] Found 6/6 markers.
[2024-01-24 13:58:59,417] [INFO] Query marker FASTA was written to GCF_003094615.1_ASM309461v1_genomic.fna/markers.fasta
[2024-01-24 13:58:59,417] [INFO] Task started: Blastn
[2024-01-24 13:58:59,417] [INFO] Running command: blastn -query GCF_003094615.1_ASM309461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89471d31-f850-456e-be2a-d0049435a830/dqc_reference/reference_markers.fasta -out GCF_003094615.1_ASM309461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:00,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:00,394] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:00,394] [INFO] Target genome list was writen to GCF_003094615.1_ASM309461v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:00,404] [INFO] Task started: fastANI
[2024-01-24 13:59:00,404] [INFO] Running command: fastANI --query /var/lib/cwl/stg59702f0d-9082-40a7-894c-2414f9c227ad/GCF_003094615.1_ASM309461v1_genomic.fna.gz --refList GCF_003094615.1_ASM309461v1_genomic.fna/target_genomes.txt --output GCF_003094615.1_ASM309461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:20,204] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:20,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89471d31-f850-456e-be2a-d0049435a830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:20,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89471d31-f850-456e-be2a-d0049435a830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:20,230] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:59:20,231] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:59:20,231] [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 radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	100.0	1831	1834	95	inconclusive
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	95.0816	1588	1834	95	inconclusive
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	92.8258	1543	1834	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	92.7792	1516	1834	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	92.5424	1458	1834	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	90.0587	1365	1834	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	84.3107	1151	1834	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	84.2776	1155	1834	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	83.4129	912	1834	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.4503	721	1834	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.38	635	1834	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.673	564	1834	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.0502	291	1834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:20,233] [INFO] DFAST Taxonomy check result was written to GCF_003094615.1_ASM309461v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:20,233] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:20,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:20,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89471d31-f850-456e-be2a-d0049435a830/dqc_reference/checkm_data
[2024-01-24 13:59:20,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:20,292] [INFO] Task started: CheckM
[2024-01-24 13:59:20,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003094615.1_ASM309461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003094615.1_ASM309461v1_genomic.fna/checkm_input GCF_003094615.1_ASM309461v1_genomic.fna/checkm_result
[2024-01-24 14:00:02,948] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:02,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:02,979] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:02,980] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:02,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003094615.1_ASM309461v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:02,981] [INFO] Task started: Blastn
[2024-01-24 14:00:02,981] [INFO] Running command: blastn -query GCF_003094615.1_ASM309461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89471d31-f850-456e-be2a-d0049435a830/dqc_reference/reference_markers_gtdb.fasta -out GCF_003094615.1_ASM309461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:04,691] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:04,695] [INFO] Selected 7 target genomes.
[2024-01-24 14:00:04,695] [INFO] Target genome list was writen to GCF_003094615.1_ASM309461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:04,704] [INFO] Task started: fastANI
[2024-01-24 14:00:04,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg59702f0d-9082-40a7-894c-2414f9c227ad/GCF_003094615.1_ASM309461v1_genomic.fna.gz --refList GCF_003094615.1_ASM309461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003094615.1_ASM309461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:21,365] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:21,378] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:21,378] [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_003094615.1	s__Caulobacter radicis	100.0	1831	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0713	96.08	96.08	0.90	0.90	2	conclusive
GCF_002858925.1	s__Caulobacter zeae	95.0658	1590	1834	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	93.2741	1515	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001449105.1	s__Caulobacter vibrioides_C	93.263	1467	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003722335.1	s__Caulobacter flavus	92.814	1544	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003116815.1	s__Caulobacter sp003116815	92.5549	1456	1834	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	90.5917	1156	1834	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 14:00:21,380] [INFO] GTDB search result was written to GCF_003094615.1_ASM309461v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:21,380] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:21,383] [INFO] DFAST_QC result json was written to GCF_003094615.1_ASM309461v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:21,384] [INFO] DFAST_QC completed!
[2024-01-24 14:00:21,384] [INFO] Total running time: 0h1m39s