[2023-03-15 16:14:47,378] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:14:47,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:14:47,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg122ceb0b-2afb-468e-92f2-2a35e40928cd/dqc_reference
[2023-03-15 16:14:49,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:14:49,239] [INFO] Task started: Prodigal
[2023-03-15 16:14:49,240] [INFO] Running command: cat /var/lib/cwl/stgcd775a2f-df09-4200-9817-2c9969966044/OceanDNA-b6190.fa | prodigal -d OceanDNA-b6190/cds.fna -a OceanDNA-b6190/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:15:03,342] [INFO] Task succeeded: Prodigal
[2023-03-15 16:15:03,342] [INFO] Task started: HMMsearch
[2023-03-15 16:15:03,342] [INFO] Running command: hmmsearch --tblout OceanDNA-b6190/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg122ceb0b-2afb-468e-92f2-2a35e40928cd/dqc_reference/reference_markers.hmm OceanDNA-b6190/protein.faa > /dev/null
[2023-03-15 16:15:03,555] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:15:03,556] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcd775a2f-df09-4200-9817-2c9969966044/OceanDNA-b6190.fa]
[2023-03-15 16:15:03,598] [INFO] Query marker FASTA was written to OceanDNA-b6190/markers.fasta
[2023-03-15 16:15:03,599] [INFO] Task started: Blastn
[2023-03-15 16:15:03,599] [INFO] Running command: blastn -query OceanDNA-b6190/markers.fasta -db /var/lib/cwl/stg122ceb0b-2afb-468e-92f2-2a35e40928cd/dqc_reference/reference_markers.fasta -out OceanDNA-b6190/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:04,170] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:04,175] [INFO] Selected 24 target genomes.
[2023-03-15 16:15:04,176] [INFO] Target genome list was writen to OceanDNA-b6190/target_genomes.txt
[2023-03-15 16:15:04,192] [INFO] Task started: fastANI
[2023-03-15 16:15:04,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd775a2f-df09-4200-9817-2c9969966044/OceanDNA-b6190.fa --refList OceanDNA-b6190/target_genomes.txt --output OceanDNA-b6190/fastani_result.tsv --threads 1
[2023-03-15 16:15:19,986] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:19,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg122ceb0b-2afb-468e-92f2-2a35e40928cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:15:19,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg122ceb0b-2afb-468e-92f2-2a35e40928cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:15:19,997] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:15:19,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:15:19,997] [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
Cellulophaga lytica	strain=DSM 7489	GCA_000190595.1	979	979	type	True	77.3724	143	656	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	77.0206	148	656	95	below_threshold
Cellulophaga fucicola	strain=DSM 24786	GCA_900119145.1	76595	76595	type	True	76.9708	141	656	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.9211	142	656	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.8381	124	656	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	76.7795	125	656	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.441	93	656	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.4246	94	656	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.063	55	656	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	75.9683	73	656	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	75.9483	74	656	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	75.8677	53	656	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	75.824	55	656	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	75.7135	50	656	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	75.7135	50	656	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.6205	62	656	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.482	53	656	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:15:20,000] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6190/tc_result.tsv
[2023-03-15 16:15:20,003] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:15:20,004] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:15:20,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg122ceb0b-2afb-468e-92f2-2a35e40928cd/dqc_reference/checkm_data
[2023-03-15 16:15:20,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:15:20,016] [INFO] Task started: CheckM
[2023-03-15 16:15:20,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6190/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6190/checkm_input OceanDNA-b6190/checkm_result
[2023-03-15 16:15:58,163] [INFO] Task succeeded: CheckM
[2023-03-15 16:15:58,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 16:15:58,166] [INFO] ===== Completeness check finished =====
[2023-03-15 16:15:58,166] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:15:58,166] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6190/markers.fasta)
[2023-03-15 16:15:58,166] [INFO] Task started: Blastn
[2023-03-15 16:15:58,166] [INFO] Running command: blastn -query OceanDNA-b6190/markers.fasta -db /var/lib/cwl/stg122ceb0b-2afb-468e-92f2-2a35e40928cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6190/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:58,946] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:58,947] [INFO] Selected 24 target genomes.
[2023-03-15 16:15:58,947] [INFO] Target genome list was writen to OceanDNA-b6190/target_genomes_gtdb.txt
[2023-03-15 16:15:58,990] [INFO] Task started: fastANI
[2023-03-15 16:15:58,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd775a2f-df09-4200-9817-2c9969966044/OceanDNA-b6190.fa --refList OceanDNA-b6190/target_genomes_gtdb.txt --output OceanDNA-b6190/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:16:15,504] [INFO] Task succeeded: fastANI
[2023-03-15 16:16:15,515] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:16:15,515] [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_000190595.1	s__Cellulophaga lytica	77.3724	143	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_002813425.1	s__Cellulophaga sp002813425	77.3582	135	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	77.0206	148	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	76.9211	142	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	76.8381	124	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.8288	145	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.799	122	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	76.7795	125	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_000153165.2	s__Maribacter_A sp000153165	76.6228	62	656	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_018860825.1	s__Oceanihabitans sp018860825	76.5599	69	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009797025.1	s__Cellulophaga sp009797025	76.5527	132	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603515.1	s__Zobellia sp018603515	76.441	93	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	76.4246	94	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144745.1	s__Croceivirga sp005144745	76.247	95	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.80	97.80	0.93	0.93	2	-
GCF_018100785.1	s__Maribacter sp018100785	75.9792	66	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337215.1	s__Oceanihabitans sediminis	75.9483	74	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016864015.1	s__Oceanihabitans sp016864015	75.9395	65	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	75.9185	58	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003148645.1	s__Xanthomarina spongicola	75.8616	54	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	75.7135	50	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 16:16:15,516] [INFO] GTDB search result was written to OceanDNA-b6190/result_gtdb.tsv
[2023-03-15 16:16:15,516] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:16:15,519] [INFO] DFAST_QC result json was written to OceanDNA-b6190/dqc_result.json
[2023-03-15 16:16:15,519] [INFO] DFAST_QC completed!
[2023-03-15 16:16:15,519] [INFO] Total running time: 0h1m28s