[2023-03-16 06:03:25,990] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:25,990] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:25,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg87113d0d-f85a-4cde-a313-beb4644ccf37/dqc_reference
[2023-03-16 06:03:27,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:27,090] [INFO] Task started: Prodigal
[2023-03-16 06:03:27,090] [INFO] Running command: cat /var/lib/cwl/stg0b7d57b5-b3d2-4e69-9172-4bc2c36201f0/OceanDNA-b10082.fa | prodigal -d OceanDNA-b10082/cds.fna -a OceanDNA-b10082/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:45,609] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:45,610] [INFO] Task started: HMMsearch
[2023-03-16 06:03:45,610] [INFO] Running command: hmmsearch --tblout OceanDNA-b10082/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87113d0d-f85a-4cde-a313-beb4644ccf37/dqc_reference/reference_markers.hmm OceanDNA-b10082/protein.faa > /dev/null
[2023-03-16 06:03:45,797] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:45,797] [INFO] Found 6/6 markers.
[2023-03-16 06:03:45,819] [INFO] Query marker FASTA was written to OceanDNA-b10082/markers.fasta
[2023-03-16 06:03:45,819] [INFO] Task started: Blastn
[2023-03-16 06:03:45,819] [INFO] Running command: blastn -query OceanDNA-b10082/markers.fasta -db /var/lib/cwl/stg87113d0d-f85a-4cde-a313-beb4644ccf37/dqc_reference/reference_markers.fasta -out OceanDNA-b10082/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:46,453] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:46,453] [INFO] Selected 30 target genomes.
[2023-03-16 06:03:46,454] [INFO] Target genome list was writen to OceanDNA-b10082/target_genomes.txt
[2023-03-16 06:03:46,501] [INFO] Task started: fastANI
[2023-03-16 06:03:46,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b7d57b5-b3d2-4e69-9172-4bc2c36201f0/OceanDNA-b10082.fa --refList OceanDNA-b10082/target_genomes.txt --output OceanDNA-b10082/fastani_result.tsv --threads 1
[2023-03-16 06:04:05,649] [INFO] Task succeeded: fastANI
[2023-03-16 06:04:05,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87113d0d-f85a-4cde-a313-beb4644ccf37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:04:05,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87113d0d-f85a-4cde-a313-beb4644ccf37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:04:05,661] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:04:05,661] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:04:05,661] [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
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	78.502	264	813	95	below_threshold
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	78.2139	293	813	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	77.5366	189	813	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	77.5363	212	813	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	77.1984	175	813	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	77.1533	197	813	95	below_threshold
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	77.0209	183	813	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.9063	177	813	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	76.6324	113	813	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.5079	55	813	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	76.5079	55	813	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	76.3737	74	813	95	below_threshold
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	76.2191	79	813	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.1872	78	813	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	76.1731	105	813	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	76.0777	55	813	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	76.0736	65	813	95	below_threshold
Croceivirga radicis	strain=HSG9	GCA_002072105.2	1929488	1929488	type	True	75.9788	57	813	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	75.835	84	813	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	75.8347	50	813	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	75.7765	53	813	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:04:05,661] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10082/tc_result.tsv
[2023-03-16 06:04:05,661] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:04:05,661] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:04:05,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87113d0d-f85a-4cde-a313-beb4644ccf37/dqc_reference/checkm_data
[2023-03-16 06:04:05,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:04:05,736] [INFO] Task started: CheckM
[2023-03-16 06:04:05,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10082/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10082/checkm_input OceanDNA-b10082/checkm_result
[2023-03-16 06:04:54,286] [INFO] Task succeeded: CheckM
[2023-03-16 06:04:54,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:04:54,307] [INFO] ===== Completeness check finished =====
[2023-03-16 06:04:54,307] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:04:54,307] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10082/markers.fasta)
[2023-03-16 06:04:54,308] [INFO] Task started: Blastn
[2023-03-16 06:04:54,308] [INFO] Running command: blastn -query OceanDNA-b10082/markers.fasta -db /var/lib/cwl/stg87113d0d-f85a-4cde-a313-beb4644ccf37/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10082/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:04:55,159] [INFO] Task succeeded: Blastn
[2023-03-16 06:04:55,169] [INFO] Selected 16 target genomes.
[2023-03-16 06:04:55,169] [INFO] Target genome list was writen to OceanDNA-b10082/target_genomes_gtdb.txt
[2023-03-16 06:04:55,232] [INFO] Task started: fastANI
[2023-03-16 06:04:55,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b7d57b5-b3d2-4e69-9172-4bc2c36201f0/OceanDNA-b10082.fa --refList OceanDNA-b10082/target_genomes_gtdb.txt --output OceanDNA-b10082/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:05:07,827] [INFO] Task succeeded: fastANI
[2023-03-16 06:05:07,837] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:05:07,837] [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_017810075.1	s__Pseudozobellia sp017810075	93.4535	729	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813285.1	s__Pseudozobellia sp002813285	92.3332	715	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855495.1	s__Euzebyella saccharophila	78.502	264	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141855.1	s__Pseudozobellia thermophila	78.4324	263	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855515.1	s__Euzebyella marina	78.2089	294	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	-
GCF_014349235.1	s__Euzebyella sp014349235	77.8423	258	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018728565.1	s__Zobellia russellii	77.552	188	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_015330165.1	s__Zobellia sp015330165	77.5363	212	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_009725985.1	s__Zobellia amurskyensis	77.1533	197	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_015330125.1	s__Zobellia sp015330125	77.0209	183	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCF_018603515.1	s__Zobellia sp018603515	76.9063	177	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100785.1	s__Maribacter sp018100785	76.7132	98	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103215.1	s__Kriegella aquimaris	76.6324	113	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kriegella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153165.2	s__Maribacter_A sp000153165	76.5179	84	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	76.5079	55	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177645.1	s__Arenibacter troitsensis	76.1872	78	813	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:05:07,837] [INFO] GTDB search result was written to OceanDNA-b10082/result_gtdb.tsv
[2023-03-16 06:05:07,837] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:05:07,839] [INFO] DFAST_QC result json was written to OceanDNA-b10082/dqc_result.json
[2023-03-16 06:05:07,839] [INFO] DFAST_QC completed!
[2023-03-16 06:05:07,840] [INFO] Total running time: 0h1m42s