[2024-01-24 15:03:29,722] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg228ea180-cd29-4ede-933d-951d0bcffcff/dqc_reference
[2024-01-24 15:03:31,094] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:31,108] [INFO] Task started: Prodigal
[2024-01-24 15:03:31,108] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cdfd483-2809-4aac-80c4-e418e8fab77e/GCF_014645055.1_ASM1464505v1_genomic.fna.gz | prodigal -d GCF_014645055.1_ASM1464505v1_genomic.fna/cds.fna -a GCF_014645055.1_ASM1464505v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:46,702] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:46,702] [INFO] Task started: HMMsearch
[2024-01-24 15:03:46,703] [INFO] Running command: hmmsearch --tblout GCF_014645055.1_ASM1464505v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg228ea180-cd29-4ede-933d-951d0bcffcff/dqc_reference/reference_markers.hmm GCF_014645055.1_ASM1464505v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:47,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:47,037] [INFO] Found 6/6 markers.
[2024-01-24 15:03:47,095] [INFO] Query marker FASTA was written to GCF_014645055.1_ASM1464505v1_genomic.fna/markers.fasta
[2024-01-24 15:03:47,096] [INFO] Task started: Blastn
[2024-01-24 15:03:47,096] [INFO] Running command: blastn -query GCF_014645055.1_ASM1464505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg228ea180-cd29-4ede-933d-951d0bcffcff/dqc_reference/reference_markers.fasta -out GCF_014645055.1_ASM1464505v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:48,240] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:48,247] [INFO] Selected 13 target genomes.
[2024-01-24 15:03:48,248] [INFO] Target genome list was writen to GCF_014645055.1_ASM1464505v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:48,254] [INFO] Task started: fastANI
[2024-01-24 15:03:48,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cdfd483-2809-4aac-80c4-e418e8fab77e/GCF_014645055.1_ASM1464505v1_genomic.fna.gz --refList GCF_014645055.1_ASM1464505v1_genomic.fna/target_genomes.txt --output GCF_014645055.1_ASM1464505v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:04:08,093] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:08,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg228ea180-cd29-4ede-933d-951d0bcffcff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:04:08,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg228ea180-cd29-4ede-933d-951d0bcffcff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:04:08,106] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:04:08,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:04:08,107] [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 rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	100.0	1934	1937	95	conclusive
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	99.9986	1935	1937	95	conclusive
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	88.9094	1265	1937	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	84.702	1128	1937	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	84.3377	1137	1937	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	84.3308	1110	1937	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	84.3126	1136	1937	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	84.3015	1131	1937	95	below_threshold
Caulobacter henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	82.5312	846	1937	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.5922	721	1937	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.2038	654	1937	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.7628	510	1937	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	78.6636	424	1937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:04:08,111] [INFO] DFAST Taxonomy check result was written to GCF_014645055.1_ASM1464505v1_genomic.fna/tc_result.tsv
[2024-01-24 15:04:08,111] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:04:08,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:04:08,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg228ea180-cd29-4ede-933d-951d0bcffcff/dqc_reference/checkm_data
[2024-01-24 15:04:08,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:04:08,174] [INFO] Task started: CheckM
[2024-01-24 15:04:08,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645055.1_ASM1464505v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645055.1_ASM1464505v1_genomic.fna/checkm_input GCF_014645055.1_ASM1464505v1_genomic.fna/checkm_result
[2024-01-24 15:04:55,250] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:55,251] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:55,273] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:55,273] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:55,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645055.1_ASM1464505v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:55,274] [INFO] Task started: Blastn
[2024-01-24 15:04:55,274] [INFO] Running command: blastn -query GCF_014645055.1_ASM1464505v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg228ea180-cd29-4ede-933d-951d0bcffcff/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645055.1_ASM1464505v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:57,355] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:57,358] [INFO] Selected 9 target genomes.
[2024-01-24 15:04:57,358] [INFO] Target genome list was writen to GCF_014645055.1_ASM1464505v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:57,365] [INFO] Task started: fastANI
[2024-01-24 15:04:57,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cdfd483-2809-4aac-80c4-e418e8fab77e/GCF_014645055.1_ASM1464505v1_genomic.fna.gz --refList GCF_014645055.1_ASM1464505v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645055.1_ASM1464505v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:15,254] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:15,267] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:15,267] [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_010977555.1	s__Caulobacter rhizosphaerae	99.9986	1935	1937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.18	95.88	0.94	0.91	4	conclusive
GCF_000426025.1	s__Caulobacter sp000426025	92.3322	1454	1937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342605.1	s__Caulobacter sp004342605	92.1235	1444	1937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828975.1	s__Caulobacter henricii_D	92.0758	1480	1937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.81	99.81	0.94	0.94	2	-
GCF_000745545.1	s__Caulobacter henricii_C	91.4766	1523	1937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.38	99.38	0.95	0.95	2	-
GCF_900114015.1	s__Caulobacter sp900114015	90.9968	1413	1937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712075.1	s__Caulobacter sp000712075	89.6696	1275	1937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426905.1	s__Caulobacter sp001426905	89.6634	1260	1937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.12	99.12	0.97	0.97	2	-
GCF_011045195.1	s__Caulobacter soli	88.9418	1261	1937	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 15:05:15,269] [INFO] GTDB search result was written to GCF_014645055.1_ASM1464505v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:15,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:15,274] [INFO] DFAST_QC result json was written to GCF_014645055.1_ASM1464505v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:15,274] [INFO] DFAST_QC completed!
[2024-01-24 15:05:15,274] [INFO] Total running time: 0h1m46s