[2023-03-18 20:40:39,435] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c0f1dee-0541-4216-80e4-e05306ef9857/dqc_reference
[2023-03-18 20:40:41,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,208] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,208] [INFO] Running command: cat /var/lib/cwl/stgba234e9d-40e0-42d7-84a4-179eb0a4197d/OceanDNA-b35320.fa | prodigal -d OceanDNA-b35320/cds.fna -a OceanDNA-b35320/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:41:11,002] [INFO] Task succeeded: Prodigal
[2023-03-18 20:41:11,003] [INFO] Task started: HMMsearch
[2023-03-18 20:41:11,003] [INFO] Running command: hmmsearch --tblout OceanDNA-b35320/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c0f1dee-0541-4216-80e4-e05306ef9857/dqc_reference/reference_markers.hmm OceanDNA-b35320/protein.faa > /dev/null
[2023-03-18 20:41:11,355] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:41:11,356] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgba234e9d-40e0-42d7-84a4-179eb0a4197d/OceanDNA-b35320.fa]
[2023-03-18 20:41:11,385] [INFO] Query marker FASTA was written to OceanDNA-b35320/markers.fasta
[2023-03-18 20:41:11,386] [INFO] Task started: Blastn
[2023-03-18 20:41:11,386] [INFO] Running command: blastn -query OceanDNA-b35320/markers.fasta -db /var/lib/cwl/stg4c0f1dee-0541-4216-80e4-e05306ef9857/dqc_reference/reference_markers.fasta -out OceanDNA-b35320/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:12,135] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:12,136] [INFO] Selected 23 target genomes.
[2023-03-18 20:41:12,136] [INFO] Target genome list was writen to OceanDNA-b35320/target_genomes.txt
[2023-03-18 20:41:12,152] [INFO] Task started: fastANI
[2023-03-18 20:41:12,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgba234e9d-40e0-42d7-84a4-179eb0a4197d/OceanDNA-b35320.fa --refList OceanDNA-b35320/target_genomes.txt --output OceanDNA-b35320/fastani_result.tsv --threads 1
[2023-03-18 20:41:29,272] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:29,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c0f1dee-0541-4216-80e4-e05306ef9857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:29,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c0f1dee-0541-4216-80e4-e05306ef9857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:29,285] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:29,286] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:29,286] [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
Vibrio crassostreae	strain=LMG 22240	GCA_024347415.1	246167	246167	type	True	80.2627	421	1713	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_024347335.1	446372	446372	type	True	80.1421	442	1713	95	below_threshold
Vibrio crassostreae	strain=LGP7	GCA_001048535.1	246167	246167	type	True	80.1374	408	1713	95	below_threshold
Vibrio celticus	strain=CECT 7224	GCA_900089965.1	446372	446372	type	True	80.0481	430	1713	95	below_threshold
Vibrio toranzoniae	strain=CECT 7225	GCA_024347655.1	1194427	1194427	type	True	79.9752	386	1713	95	below_threshold
Vibrio kanaloae	strain=LMG 20539	GCA_024347535.1	170673	170673	type	True	79.9682	388	1713	95	below_threshold
Vibrio artabrorum	strain=CECT 7226	GCA_024347295.1	446374	446374	type	True	79.9668	346	1713	95	below_threshold
Vibrio kanaloae	strain=CCUG 56968	GCA_008801285.1	170673	170673	type	True	79.9078	385	1713	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	79.9028	374	1713	95	below_threshold
Vibrio echinoideorum	strain=NFH.MB010	GCA_004764665.1	2100116	2100116	type	True	79.8656	411	1713	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	79.8639	412	1713	95	below_threshold
Vibrio chagasii	strain=CCUG 48643	GCA_008801295.1	170679	170679	suspected-type	True	79.8456	378	1713	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_005281815.1	170679	170679	suspected-type	True	79.7988	371	1713	95	below_threshold
Vibrio gigantis	strain=LMG 22741	GCA_024347515.1	296199	296199	type	True	79.775	431	1713	95	below_threshold
Vibrio gigantis	strain=LGP 13	GCA_002156475.1	296199	296199	type	True	79.766	429	1713	95	below_threshold
Vibrio gallaecicus	strain=DSM 23502	GCA_005281825.1	552386	552386	type	True	79.6575	383	1713	95	below_threshold
Vibrio gallaecicus	strain=VB 8.9	GCA_013416885.1	552386	552386	type	True	79.6504	384	1713	95	below_threshold
Vibrio gallaecicus	strain=CECT 7244	GCA_024347495.1	552386	552386	type	True	79.6454	388	1713	95	below_threshold
Vibrio fortis	strain=LMG 21557	GCA_024347475.1	212667	212667	type	True	79.4443	369	1713	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	79.3812	332	1713	95	below_threshold
Vibrio aquaticus	strain=BEI207	GCA_003970385.1	2496559	2496559	type	True	79.172	384	1713	95	below_threshold
Vibrio renipiscarius	strain=DCR 1-4-2	GCA_000827885.1	1461322	1461322	type	True	78.9028	301	1713	95	below_threshold
Vibrio gangliei	strain=SZDIS-1	GCA_002934045.1	2077090	2077090	type	True	77.8674	192	1713	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:29,286] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35320/tc_result.tsv
[2023-03-18 20:41:29,286] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:29,286] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:29,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c0f1dee-0541-4216-80e4-e05306ef9857/dqc_reference/checkm_data
[2023-03-18 20:41:29,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:29,388] [INFO] Task started: CheckM
[2023-03-18 20:41:29,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35320/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35320/checkm_input OceanDNA-b35320/checkm_result
[2023-03-18 20:42:41,597] [INFO] Task succeeded: CheckM
[2023-03-18 20:42:41,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.34%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:42:41,600] [INFO] ===== Completeness check finished =====
[2023-03-18 20:42:41,600] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:42:41,600] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35320/markers.fasta)
[2023-03-18 20:42:41,601] [INFO] Task started: Blastn
[2023-03-18 20:42:41,601] [INFO] Running command: blastn -query OceanDNA-b35320/markers.fasta -db /var/lib/cwl/stg4c0f1dee-0541-4216-80e4-e05306ef9857/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35320/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:42:42,571] [INFO] Task succeeded: Blastn
[2023-03-18 20:42:42,572] [INFO] Selected 17 target genomes.
[2023-03-18 20:42:42,572] [INFO] Target genome list was writen to OceanDNA-b35320/target_genomes_gtdb.txt
[2023-03-18 20:42:42,614] [INFO] Task started: fastANI
[2023-03-18 20:42:42,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgba234e9d-40e0-42d7-84a4-179eb0a4197d/OceanDNA-b35320.fa --refList OceanDNA-b35320/target_genomes_gtdb.txt --output OceanDNA-b35320/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:57,204] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:57,214] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:42:57,214] [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_001874155.1	s__Vibrio sp001874155	99.9108	825	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002877365.1	s__Vibrio sp002877365	83.773	1026	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000287055.2	s__Vibrio sp000287055	81.0394	585	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.47	99.16	0.95	0.92	3	-
GCF_000272045.2	s__Vibrio crassostreae_C	80.2666	431	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.007	97.54	97.16	0.89	0.87	25	-
GCF_001048535.1	s__Vibrio crassostreae	80.1286	409	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.86	96.20	0.91	0.83	177	-
GCF_008801285.1	s__Vibrio kanaloae	79.8991	386	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.372	98.50	98.26	0.91	0.88	16	-
GCF_002954585.1	s__Vibrio chagasii_A	79.8706	375	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.42	95.44	0.90	0.87	4	-
GCF_004764665.1	s__Vibrio echinoideorum	79.8543	413	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.83	0.88	0.82	5	-
GCF_005281815.1	s__Vibrio chagasii	79.7909	372	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	96.30	95.30	0.86	0.82	10	-
GCF_001635455.1	s__Vibrio sp001635455	79.6607	362	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281825.1	s__Vibrio gallaecicus	79.6494	384	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000169995.1	s__Vibrio sp000169995	79.5408	358	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000272145.2	s__Vibrio sp000272145	79.2819	322	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.26	98.15	0.92	0.92	4	-
GCF_002873395.1	s__Vibrio sp002873395	79.1582	276	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900233005.1	s__Vibrio tapetis	78.9395	278	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827885.1	s__Vibrio renipiscarius	78.9091	300	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002934045.1	s__Vibrio gangliei	77.8506	193	1713	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:57,214] [INFO] GTDB search result was written to OceanDNA-b35320/result_gtdb.tsv
[2023-03-18 20:42:57,214] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:57,217] [INFO] DFAST_QC result json was written to OceanDNA-b35320/dqc_result.json
[2023-03-18 20:42:57,217] [INFO] DFAST_QC completed!
[2023-03-18 20:42:57,217] [INFO] Total running time: 0h2m18s