[2023-03-17 13:01:51,386] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,386] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,386] [INFO] DQC Reference Directory: /var/lib/cwl/stgd80897fd-38ec-40e2-ad3d-fd0b758d95dd/dqc_reference
[2023-03-17 13:01:52,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,651] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,651] [INFO] Running command: cat /var/lib/cwl/stg41c00fca-2f48-4786-b764-6b389b75700b/OceanDNA-b23454.fa | prodigal -d OceanDNA-b23454/cds.fna -a OceanDNA-b23454/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:08,465] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:08,465] [INFO] Task started: HMMsearch
[2023-03-17 13:02:08,465] [INFO] Running command: hmmsearch --tblout OceanDNA-b23454/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd80897fd-38ec-40e2-ad3d-fd0b758d95dd/dqc_reference/reference_markers.hmm OceanDNA-b23454/protein.faa > /dev/null
[2023-03-17 13:02:08,694] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:08,695] [INFO] Found 6/6 markers.
[2023-03-17 13:02:08,721] [INFO] Query marker FASTA was written to OceanDNA-b23454/markers.fasta
[2023-03-17 13:02:08,721] [INFO] Task started: Blastn
[2023-03-17 13:02:08,721] [INFO] Running command: blastn -query OceanDNA-b23454/markers.fasta -db /var/lib/cwl/stgd80897fd-38ec-40e2-ad3d-fd0b758d95dd/dqc_reference/reference_markers.fasta -out OceanDNA-b23454/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:09,570] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:09,570] [INFO] Selected 15 target genomes.
[2023-03-17 13:02:09,571] [INFO] Target genome list was writen to OceanDNA-b23454/target_genomes.txt
[2023-03-17 13:02:09,578] [INFO] Task started: fastANI
[2023-03-17 13:02:09,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c00fca-2f48-4786-b764-6b389b75700b/OceanDNA-b23454.fa --refList OceanDNA-b23454/target_genomes.txt --output OceanDNA-b23454/fastani_result.tsv --threads 1
[2023-03-17 13:02:22,910] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:22,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd80897fd-38ec-40e2-ad3d-fd0b758d95dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:22,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd80897fd-38ec-40e2-ad3d-fd0b758d95dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:22,921] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:22,921] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:02:22,921] [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 segnis	strain=TK0059	GCA_003015125.1	88688	88688	type	True	85.2405	610	839	95	below_threshold
Caulobacter segnis	strain=ATCC 21756	GCA_000092285.1	88688	88688	type	True	85.2098	610	839	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	85.1346	540	839	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	83.2283	586	839	95	below_threshold
Caulobacter flavus	strain=RHGG3	GCA_003722335.1	1679497	1679497	type	True	83.0003	572	839	95	below_threshold
Caulobacter zeae	strain=410	GCA_002858925.1	2055137	2055137	type	True	82.9645	552	839	95	below_threshold
Caulobacter radicis	strain=695	GCA_003094615.1	2172650	2172650	type	True	82.9156	574	839	95	below_threshold
Caulobacter endophyticus	strain=774	GCA_003116815.1	2172652	2172652	type	True	82.8732	544	839	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	82.8138	557	839	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	82.7366	558	839	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	82.7287	554	839	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	79.1673	390	839	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	78.356	346	839	95	below_threshold
Brevundimonas vitisensis	strain=GR-TSA-9	GCA_016656965.1	2800818	2800818	type	True	77.4787	172	839	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.1863	123	839	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:02:22,922] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23454/tc_result.tsv
[2023-03-17 13:02:22,922] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:22,922] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:22,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd80897fd-38ec-40e2-ad3d-fd0b758d95dd/dqc_reference/checkm_data
[2023-03-17 13:02:22,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:22,928] [INFO] Task started: CheckM
[2023-03-17 13:02:22,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23454/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23454/checkm_input OceanDNA-b23454/checkm_result
[2023-03-17 13:03:04,282] [INFO] Task succeeded: CheckM
[2023-03-17 13:03:04,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.12%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 13:03:04,285] [INFO] ===== Completeness check finished =====
[2023-03-17 13:03:04,285] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:03:04,286] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23454/markers.fasta)
[2023-03-17 13:03:04,286] [INFO] Task started: Blastn
[2023-03-17 13:03:04,286] [INFO] Running command: blastn -query OceanDNA-b23454/markers.fasta -db /var/lib/cwl/stgd80897fd-38ec-40e2-ad3d-fd0b758d95dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23454/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:03:05,922] [INFO] Task succeeded: Blastn
[2023-03-17 13:03:05,923] [INFO] Selected 15 target genomes.
[2023-03-17 13:03:05,923] [INFO] Target genome list was writen to OceanDNA-b23454/target_genomes_gtdb.txt
[2023-03-17 13:03:06,117] [INFO] Task started: fastANI
[2023-03-17 13:03:06,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg41c00fca-2f48-4786-b764-6b389b75700b/OceanDNA-b23454.fa --refList OceanDNA-b23454/target_genomes_gtdb.txt --output OceanDNA-b23454/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:19,914] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:19,922] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:03:19,923] [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_000372645.1	s__Caulobacter vibrioides_E	98.2921	752	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.89	97.90	0.89	0.86	5	conclusive
GCF_002742635.1	s__Caulobacter sp002742635	87.0142	670	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903900155.1	s__Caulobacter sp903900155	86.1983	614	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.93	99.90	0.95	0.93	3	-
GCF_001556515.1	s__Caulobacter sp001556515	86.141	588	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744445.1	s__Caulobacter sp017744445	86.0255	606	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931565.1	s__Caulobacter sp003931565	85.8115	628	839	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	85.6599	622	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	96.44	96.44	0.92	0.92	3	-
GCA_003243465.1	s__Caulobacter segnis_A	85.5856	593	839	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	85.5835	616	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013181195.1	s__Caulobacter sp013181195	85.3307	632	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092285.1	s__Caulobacter segnis	85.2536	607	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002858865.1	s__Caulobacter vibrioides	85.1147	541	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.80	98.06	0.96	0.95	6	-
GCF_002310375.3	s__Caulobacter vibrioides_D	84.9103	557	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742645.2	s__Caulobacter sp002742645	84.7564	613	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.59	99.58	0.91	0.91	3	-
GCA_002280275.1	s__Caulobacter vibrioides_A	84.2072	473	839	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:19,923] [INFO] GTDB search result was written to OceanDNA-b23454/result_gtdb.tsv
[2023-03-17 13:03:19,923] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:19,925] [INFO] DFAST_QC result json was written to OceanDNA-b23454/dqc_result.json
[2023-03-17 13:03:19,925] [INFO] DFAST_QC completed!
[2023-03-17 13:03:19,925] [INFO] Total running time: 0h1m29s