[2023-03-16 02:38:04,922] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg33bbce7c-4e4c-40c4-8763-3c7c83550ff3/dqc_reference
[2023-03-16 02:38:06,259] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,259] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,259] [INFO] Running command: cat /var/lib/cwl/stg08c15c01-28df-4939-be74-88caaedbc4eb/OceanDNA-b23453.fa | prodigal -d OceanDNA-b23453/cds.fna -a OceanDNA-b23453/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:20,910] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:20,911] [INFO] Task started: HMMsearch
[2023-03-16 02:38:20,911] [INFO] Running command: hmmsearch --tblout OceanDNA-b23453/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33bbce7c-4e4c-40c4-8763-3c7c83550ff3/dqc_reference/reference_markers.hmm OceanDNA-b23453/protein.faa > /dev/null
[2023-03-16 02:38:21,173] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:21,173] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg08c15c01-28df-4939-be74-88caaedbc4eb/OceanDNA-b23453.fa]
[2023-03-16 02:38:21,197] [INFO] Query marker FASTA was written to OceanDNA-b23453/markers.fasta
[2023-03-16 02:38:21,197] [INFO] Task started: Blastn
[2023-03-16 02:38:21,197] [INFO] Running command: blastn -query OceanDNA-b23453/markers.fasta -db /var/lib/cwl/stg33bbce7c-4e4c-40c4-8763-3c7c83550ff3/dqc_reference/reference_markers.fasta -out OceanDNA-b23453/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:21,902] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:21,902] [INFO] Selected 16 target genomes.
[2023-03-16 02:38:21,903] [INFO] Target genome list was writen to OceanDNA-b23453/target_genomes.txt
[2023-03-16 02:38:21,913] [INFO] Task started: fastANI
[2023-03-16 02:38:21,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg08c15c01-28df-4939-be74-88caaedbc4eb/OceanDNA-b23453.fa --refList OceanDNA-b23453/target_genomes.txt --output OceanDNA-b23453/fastani_result.tsv --threads 1
[2023-03-16 02:38:36,327] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:36,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33bbce7c-4e4c-40c4-8763-3c7c83550ff3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:36,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33bbce7c-4e4c-40c4-8763-3c7c83550ff3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:36,337] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:36,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 02:38:36,337] [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 henricii	strain=CB4	GCA_001414055.1	69395	69395	type	True	84.4994	528	780	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	83.352	518	780	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	83.0362	510	780	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	82.9019	517	780	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	82.8994	487	780	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	82.7064	495	780	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	82.6374	483	780	95	below_threshold
Caulobacter segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	82.6268	499	780	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	82.5829	479	780	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	82.5417	488	780	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	82.4641	491	780	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	82.3118	482	780	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.1884	367	780	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	78.6174	320	780	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	77.981	192	780	95	below_threshold
Brevundimonas pishanensis	strain=CHPC 1.3453	GCA_022750635.1	2896315	2896315	type	True	76.9056	104	780	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:36,338] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23453/tc_result.tsv
[2023-03-16 02:38:36,338] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:36,338] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:36,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33bbce7c-4e4c-40c4-8763-3c7c83550ff3/dqc_reference/checkm_data
[2023-03-16 02:38:36,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:36,344] [INFO] Task started: CheckM
[2023-03-16 02:38:36,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23453/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23453/checkm_input OceanDNA-b23453/checkm_result
[2023-03-16 02:39:15,452] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:15,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.30%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:15,455] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:15,455] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:15,456] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23453/markers.fasta)
[2023-03-16 02:39:15,456] [INFO] Task started: Blastn
[2023-03-16 02:39:15,456] [INFO] Running command: blastn -query OceanDNA-b23453/markers.fasta -db /var/lib/cwl/stg33bbce7c-4e4c-40c4-8763-3c7c83550ff3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23453/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:16,701] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:16,701] [INFO] Selected 14 target genomes.
[2023-03-16 02:39:16,702] [INFO] Target genome list was writen to OceanDNA-b23453/target_genomes_gtdb.txt
[2023-03-16 02:39:16,992] [INFO] Task started: fastANI
[2023-03-16 02:39:16,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg08c15c01-28df-4939-be74-88caaedbc4eb/OceanDNA-b23453.fa --refList OceanDNA-b23453/target_genomes_gtdb.txt --output OceanDNA-b23453/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:28,854] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:28,862] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 02:39:28,862] [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
GCA_018895795.1	s__Caulobacter sp018895795	91.9356	547	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744465.1	s__Caulobacter henricii_A	86.4304	553	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280875.1	s__Caulobacter sp002280875	85.6044	543	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.61	99.61	0.91	0.91	2	-
GCF_001414055.1	s__Caulobacter henricii	84.5176	527	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002737765.1	s__Caulobacter sp002737765	84.0976	329	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060965.1	s__Caulobacter sp003060965	83.8387	509	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.90	99.90	0.96	0.96	2	-
GCF_000281955.1	s__Caulobacter sp000281955	83.7812	507	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427665.1	s__Caulobacter sp001427665	83.7713	501	780	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	83.6947	536	780	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	83.4298	514	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	96.44	96.44	0.92	0.92	3	-
GCF_007828975.1	s__Caulobacter henricii_D	83.33	511	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.81	99.81	0.94	0.94	2	-
GCF_004342605.1	s__Caulobacter sp004342605	83.0954	500	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016135805.1	s__Caulobacter hibisci	82.9038	487	780	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	82.6979	459	780	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:28,862] [INFO] GTDB search result was written to OceanDNA-b23453/result_gtdb.tsv
[2023-03-16 02:39:28,862] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:28,864] [INFO] DFAST_QC result json was written to OceanDNA-b23453/dqc_result.json
[2023-03-16 02:39:28,864] [INFO] DFAST_QC completed!
[2023-03-16 02:39:28,864] [INFO] Total running time: 0h1m24s