[2024-01-25 18:00:37,398] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:37,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:37,400] [INFO] DQC Reference Directory: /var/lib/cwl/stga148c5f2-ab34-48bb-a637-c1bbc6a23a7b/dqc_reference
[2024-01-25 18:00:38,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:38,541] [INFO] Task started: Prodigal
[2024-01-25 18:00:38,541] [INFO] Running command: gunzip -c /var/lib/cwl/stg2468e564-0bc2-416d-a050-267d9d87f82e/GCF_003116815.1_ASM311681v1_genomic.fna.gz | prodigal -d GCF_003116815.1_ASM311681v1_genomic.fna/cds.fna -a GCF_003116815.1_ASM311681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:50,780] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:50,780] [INFO] Task started: HMMsearch
[2024-01-25 18:00:50,780] [INFO] Running command: hmmsearch --tblout GCF_003116815.1_ASM311681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga148c5f2-ab34-48bb-a637-c1bbc6a23a7b/dqc_reference/reference_markers.hmm GCF_003116815.1_ASM311681v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:51,085] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:51,086] [INFO] Found 6/6 markers.
[2024-01-25 18:00:51,130] [INFO] Query marker FASTA was written to GCF_003116815.1_ASM311681v1_genomic.fna/markers.fasta
[2024-01-25 18:00:51,130] [INFO] Task started: Blastn
[2024-01-25 18:00:51,130] [INFO] Running command: blastn -query GCF_003116815.1_ASM311681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga148c5f2-ab34-48bb-a637-c1bbc6a23a7b/dqc_reference/reference_markers.fasta -out GCF_003116815.1_ASM311681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:52,047] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:52,050] [INFO] Selected 13 target genomes.
[2024-01-25 18:00:52,050] [INFO] Target genome list was writen to GCF_003116815.1_ASM311681v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:52,062] [INFO] Task started: fastANI
[2024-01-25 18:00:52,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg2468e564-0bc2-416d-a050-267d9d87f82e/GCF_003116815.1_ASM311681v1_genomic.fna.gz --refList GCF_003116815.1_ASM311681v1_genomic.fna/target_genomes.txt --output GCF_003116815.1_ASM311681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:11,490] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:11,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga148c5f2-ab34-48bb-a637-c1bbc6a23a7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:11,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga148c5f2-ab34-48bb-a637-c1bbc6a23a7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:11,499] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:11,499] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:11,499] [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 endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	100.0	1757	1761	95	conclusive
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	92.5668	1446	1761	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	92.5233	1448	1761	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	92.1407	1471	1761	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	92.0484	1481	1761	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	89.4342	1324	1761	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	84.183	1092	1761	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	83.4688	968	1761	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	83.4213	974	1761	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.4287	681	1761	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	79.3002	618	1761	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.0705	263	1761	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.6462	294	1761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:11,501] [INFO] DFAST Taxonomy check result was written to GCF_003116815.1_ASM311681v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:11,501] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:11,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:11,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga148c5f2-ab34-48bb-a637-c1bbc6a23a7b/dqc_reference/checkm_data
[2024-01-25 18:01:11,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:11,552] [INFO] Task started: CheckM
[2024-01-25 18:01:11,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003116815.1_ASM311681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003116815.1_ASM311681v1_genomic.fna/checkm_input GCF_003116815.1_ASM311681v1_genomic.fna/checkm_result
[2024-01-25 18:01:47,486] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:47,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:47,507] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:47,507] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:47,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003116815.1_ASM311681v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:47,507] [INFO] Task started: Blastn
[2024-01-25 18:01:47,507] [INFO] Running command: blastn -query GCF_003116815.1_ASM311681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga148c5f2-ab34-48bb-a637-c1bbc6a23a7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003116815.1_ASM311681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:49,176] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:49,178] [INFO] Selected 10 target genomes.
[2024-01-25 18:01:49,179] [INFO] Target genome list was writen to GCF_003116815.1_ASM311681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:49,189] [INFO] Task started: fastANI
[2024-01-25 18:01:49,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg2468e564-0bc2-416d-a050-267d9d87f82e/GCF_003116815.1_ASM311681v1_genomic.fna.gz --refList GCF_003116815.1_ASM311681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003116815.1_ASM311681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:06,234] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:06,242] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:06,242] [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_003116815.1	s__Caulobacter sp003116815	100.0	1757	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001449105.1	s__Caulobacter vibrioides_C	93.3365	1413	1761	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	92.5784	1446	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0713	N/A	N/A	N/A	N/A	1	-
GCF_003094615.1	s__Caulobacter radicis	92.5215	1448	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0713	96.08	96.08	0.90	0.90	2	-
GCF_011043625.1	s__Caulobacter sp011043625	92.3632	1427	1761	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	92.0364	1482	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003185805.1	s__Caulobacter sp003185805	90.1151	1114	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207215.1	s__Caulobacter sp014207215	84.0307	1045	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799245.1	s__Caulobacter sp000799245	83.6848	1051	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	96.44	96.44	0.92	0.92	3	-
GCF_002742625.1	s__Caulobacter sp002742625	83.6328	1019	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:06,243] [INFO] GTDB search result was written to GCF_003116815.1_ASM311681v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:06,243] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:06,246] [INFO] DFAST_QC result json was written to GCF_003116815.1_ASM311681v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:06,246] [INFO] DFAST_QC completed!
[2024-01-25 18:02:06,246] [INFO] Total running time: 0h1m29s