[2024-01-24 11:26:54,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,322] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa3b359d-adb8-40cd-a3c3-6fed0d4e3a67/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,223] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d708edf-c6f8-4714-8e49-7cd55487045e/GCF_002858845.1_ASM285884v1_genomic.fna.gz | prodigal -d GCF_002858845.1_ASM285884v1_genomic.fna/cds.fna -a GCF_002858845.1_ASM285884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:13,101] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:13,101] [INFO] Task started: HMMsearch
[2024-01-24 11:27:13,101] [INFO] Running command: hmmsearch --tblout GCF_002858845.1_ASM285884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa3b359d-adb8-40cd-a3c3-6fed0d4e3a67/dqc_reference/reference_markers.hmm GCF_002858845.1_ASM285884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:13,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:13,433] [INFO] Found 6/6 markers.
[2024-01-24 11:27:13,482] [INFO] Query marker FASTA was written to GCF_002858845.1_ASM285884v1_genomic.fna/markers.fasta
[2024-01-24 11:27:13,482] [INFO] Task started: Blastn
[2024-01-24 11:27:13,482] [INFO] Running command: blastn -query GCF_002858845.1_ASM285884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa3b359d-adb8-40cd-a3c3-6fed0d4e3a67/dqc_reference/reference_markers.fasta -out GCF_002858845.1_ASM285884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:14,467] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:14,471] [INFO] Selected 14 target genomes.
[2024-01-24 11:27:14,471] [INFO] Target genome list was writen to GCF_002858845.1_ASM285884v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:14,476] [INFO] Task started: fastANI
[2024-01-24 11:27:14,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d708edf-c6f8-4714-8e49-7cd55487045e/GCF_002858845.1_ASM285884v1_genomic.fna.gz --refList GCF_002858845.1_ASM285884v1_genomic.fna/target_genomes.txt --output GCF_002858845.1_ASM285884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:34,238] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:34,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa3b359d-adb8-40cd-a3c3-6fed0d4e3a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:34,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa3b359d-adb8-40cd-a3c3-6fed0d4e3a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:34,252] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:34,252] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:34,252] [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=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	99.9999	1910	1915	95	conclusive
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	99.9848	1849	1915	95	conclusive
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	92.7308	1526	1915	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	92.638	1508	1915	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	92.1255	1487	1915	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	89.7654	1375	1915	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	84.3593	1139	1915	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	83.5684	1001	1915	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	83.4855	1014	1915	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	83.335	901	1915	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.4122	729	1915	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.0709	655	1915	95	below_threshold
Brevundimonas albigilva	strain=KEME 9005-016	GCA_023503965.1	1312364	1312364	type	True	78.5899	563	1915	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	77.787	352	1915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:34,254] [INFO] DFAST Taxonomy check result was written to GCF_002858845.1_ASM285884v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:34,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:34,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:34,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa3b359d-adb8-40cd-a3c3-6fed0d4e3a67/dqc_reference/checkm_data
[2024-01-24 11:27:34,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:34,310] [INFO] Task started: CheckM
[2024-01-24 11:27:34,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002858845.1_ASM285884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002858845.1_ASM285884v1_genomic.fna/checkm_input GCF_002858845.1_ASM285884v1_genomic.fna/checkm_result
[2024-01-24 11:28:18,067] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:18,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:18,092] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:18,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:18,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002858845.1_ASM285884v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:18,094] [INFO] Task started: Blastn
[2024-01-24 11:28:18,094] [INFO] Running command: blastn -query GCF_002858845.1_ASM285884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa3b359d-adb8-40cd-a3c3-6fed0d4e3a67/dqc_reference/reference_markers_gtdb.fasta -out GCF_002858845.1_ASM285884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:19,814] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:19,818] [INFO] Selected 10 target genomes.
[2024-01-24 11:28:19,818] [INFO] Target genome list was writen to GCF_002858845.1_ASM285884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:19,822] [INFO] Task started: fastANI
[2024-01-24 11:28:19,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d708edf-c6f8-4714-8e49-7cd55487045e/GCF_002858845.1_ASM285884v1_genomic.fna.gz --refList GCF_002858845.1_ASM285884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002858845.1_ASM285884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:37,132] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:37,141] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:37,141] [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	99.9848	1849	1915	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_001449105.1	s__Caulobacter vibrioides_C	92.7623	1443	1915	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003094615.1	s__Caulobacter radicis	92.753	1524	1915	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0713	96.08	96.08	0.90	0.90	2	-
GCF_002858925.1	s__Caulobacter zeae	92.614	1510	1915	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	92.5399	1487	1915	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	92.1373	1486	1915	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	90.2939	1159	1915	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742625.1	s__Caulobacter sp002742625	83.8602	1070	1915	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742635.1	s__Caulobacter sp002742635	83.8409	1034	1915	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002737755.1	s__Caulobacter sp002737755	83.2662	939	1915	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 11:28:37,143] [INFO] GTDB search result was written to GCF_002858845.1_ASM285884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:37,143] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:37,147] [INFO] DFAST_QC result json was written to GCF_002858845.1_ASM285884v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:37,148] [INFO] DFAST_QC completed!
[2024-01-24 11:28:37,148] [INFO] Total running time: 0h1m43s