[2023-03-15 11:09:10,836] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,836] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ff5a19f-4544-4c7d-b4aa-ce6febf19b78/dqc_reference
[2023-03-15 11:09:12,111] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,111] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,111] [INFO] Running command: cat /var/lib/cwl/stg77185c2e-2a71-4ba8-a207-c62862ce9493/OceanDNA-b23487.fa | prodigal -d OceanDNA-b23487/cds.fna -a OceanDNA-b23487/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:39,932] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:39,932] [INFO] Task started: HMMsearch
[2023-03-15 11:09:39,932] [INFO] Running command: hmmsearch --tblout OceanDNA-b23487/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ff5a19f-4544-4c7d-b4aa-ce6febf19b78/dqc_reference/reference_markers.hmm OceanDNA-b23487/protein.faa > /dev/null
[2023-03-15 11:09:40,224] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:40,224] [INFO] Found 6/6 markers.
[2023-03-15 11:09:40,251] [INFO] Query marker FASTA was written to OceanDNA-b23487/markers.fasta
[2023-03-15 11:09:40,251] [INFO] Task started: Blastn
[2023-03-15 11:09:40,251] [INFO] Running command: blastn -query OceanDNA-b23487/markers.fasta -db /var/lib/cwl/stg1ff5a19f-4544-4c7d-b4aa-ce6febf19b78/dqc_reference/reference_markers.fasta -out OceanDNA-b23487/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:40,935] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:40,936] [INFO] Selected 26 target genomes.
[2023-03-15 11:09:40,936] [INFO] Target genome list was writen to OceanDNA-b23487/target_genomes.txt
[2023-03-15 11:09:40,954] [INFO] Task started: fastANI
[2023-03-15 11:09:40,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg77185c2e-2a71-4ba8-a207-c62862ce9493/OceanDNA-b23487.fa --refList OceanDNA-b23487/target_genomes.txt --output OceanDNA-b23487/fastani_result.tsv --threads 1
[2023-03-15 11:09:55,880] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:55,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ff5a19f-4544-4c7d-b4aa-ce6febf19b78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:55,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ff5a19f-4544-4c7d-b4aa-ce6febf19b78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:55,889] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:55,889] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:55,889] [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
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	77.7217	60	1465	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	77.3106	74	1465	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.4968	65	1465	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	76.173	63	1465	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	76.0678	60	1465	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	76.0657	55	1465	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	75.9943	58	1465	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	75.9775	64	1465	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	75.9725	73	1465	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	75.956	65	1465	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	75.9523	65	1465	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	75.512	52	1465	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:55,889] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23487/tc_result.tsv
[2023-03-15 11:09:55,889] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:55,889] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:55,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ff5a19f-4544-4c7d-b4aa-ce6febf19b78/dqc_reference/checkm_data
[2023-03-15 11:09:55,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:55,976] [INFO] Task started: CheckM
[2023-03-15 11:09:55,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23487/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23487/checkm_input OceanDNA-b23487/checkm_result
[2023-03-15 11:11:04,566] [INFO] Task succeeded: CheckM
[2023-03-15 11:11:04,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:11:04,569] [INFO] ===== Completeness check finished =====
[2023-03-15 11:11:04,569] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:11:04,569] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23487/markers.fasta)
[2023-03-15 11:11:04,570] [INFO] Task started: Blastn
[2023-03-15 11:11:04,570] [INFO] Running command: blastn -query OceanDNA-b23487/markers.fasta -db /var/lib/cwl/stg1ff5a19f-4544-4c7d-b4aa-ce6febf19b78/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23487/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:11:05,619] [INFO] Task succeeded: Blastn
[2023-03-15 11:11:05,620] [INFO] Selected 30 target genomes.
[2023-03-15 11:11:05,620] [INFO] Target genome list was writen to OceanDNA-b23487/target_genomes_gtdb.txt
[2023-03-15 11:11:05,642] [INFO] Task started: fastANI
[2023-03-15 11:11:05,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg77185c2e-2a71-4ba8-a207-c62862ce9493/OceanDNA-b23487.fa --refList OceanDNA-b23487/target_genomes_gtdb.txt --output OceanDNA-b23487/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:11:22,796] [INFO] Task succeeded: fastANI
[2023-03-15 11:11:22,808] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:11:22,808] [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_000682715.1	s__Hyphomonas atlantica	77.7778	59	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCF_000682675.1	s__Hyphomonas pacifica	77.3106	74	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCA_018222605.1	s__Hyphomonas sp002695785	77.0398	71	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCA_017792385.1	s__Hyphomonas sp017792385	76.8042	72	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700305.1	s__Hyphomonas sp002700305	76.6377	67	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	-
GCF_003576245.1	s__Henriciella algicola	76.5282	64	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961795.1	s__Hyphomonas sp000961795	76.3525	51	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414505.1	s__Hyphomonas sp002414505	76.2406	50	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	-
GCF_000682735.1	s__Hyphomonas sp000682735	76.2376	65	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCA_002338565.1	s__Ponticaulis sp002338565	76.2272	52	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.94	99.86	0.98	0.96	4	-
GCA_013213785.1	s__Henriciella sp013213785	76.1579	57	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682775.1	s__Hyphomonas sp000682775	76.1488	61	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	-
GCF_000685235.1	s__Hyphomonas adhaerens	76.1267	53	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	97.03	96.92	0.83	0.82	4	-
GCA_017642885.1	s__Henriciella sp017642885	76.0848	63	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.99	99.99	0.96	0.96	2	-
GCA_018827375.1	s__Hyphomonas sp018827375	76.0642	51	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
GCF_002088935.1	s__Henriciella litoralis	76.0011	63	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214545.1	s__Henriciella sp013214545	75.9952	80	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	75.9949	72	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088945.1	s__Henriciella pelagia	75.9523	65	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014763715.1	s__Hyphomonas sp014763715	75.6337	63	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	75.5336	51	1465	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:11:22,809] [INFO] GTDB search result was written to OceanDNA-b23487/result_gtdb.tsv
[2023-03-15 11:11:22,809] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:11:22,811] [INFO] DFAST_QC result json was written to OceanDNA-b23487/dqc_result.json
[2023-03-15 11:11:22,811] [INFO] DFAST_QC completed!
[2023-03-15 11:11:22,811] [INFO] Total running time: 0h2m12s