[2023-03-16 11:50:51,365] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:50:51,365] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:50:51,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c3c1270-040f-4c12-9bfe-b053ce51bd98/dqc_reference
[2023-03-16 11:50:53,566] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:50:53,566] [INFO] Task started: Prodigal
[2023-03-16 11:50:53,569] [INFO] Running command: cat /var/lib/cwl/stg3a8d7031-4391-4522-97e0-39b09815044a/OceanDNA-b27533.fa | prodigal -d OceanDNA-b27533/cds.fna -a OceanDNA-b27533/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:51:10,879] [INFO] Task succeeded: Prodigal
[2023-03-16 11:51:10,880] [INFO] Task started: HMMsearch
[2023-03-16 11:51:10,880] [INFO] Running command: hmmsearch --tblout OceanDNA-b27533/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c3c1270-040f-4c12-9bfe-b053ce51bd98/dqc_reference/reference_markers.hmm OceanDNA-b27533/protein.faa > /dev/null
[2023-03-16 11:51:11,073] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:51:11,074] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3a8d7031-4391-4522-97e0-39b09815044a/OceanDNA-b27533.fa]
[2023-03-16 11:51:11,097] [INFO] Query marker FASTA was written to OceanDNA-b27533/markers.fasta
[2023-03-16 11:51:11,097] [INFO] Task started: Blastn
[2023-03-16 11:51:11,097] [INFO] Running command: blastn -query OceanDNA-b27533/markers.fasta -db /var/lib/cwl/stg6c3c1270-040f-4c12-9bfe-b053ce51bd98/dqc_reference/reference_markers.fasta -out OceanDNA-b27533/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:51:11,629] [INFO] Task succeeded: Blastn
[2023-03-16 11:51:11,629] [INFO] Selected 24 target genomes.
[2023-03-16 11:51:11,630] [INFO] Target genome list was writen to OceanDNA-b27533/target_genomes.txt
[2023-03-16 11:51:11,640] [INFO] Task started: fastANI
[2023-03-16 11:51:11,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a8d7031-4391-4522-97e0-39b09815044a/OceanDNA-b27533.fa --refList OceanDNA-b27533/target_genomes.txt --output OceanDNA-b27533/fastani_result.tsv --threads 1
[2023-03-16 11:51:25,393] [INFO] Task succeeded: fastANI
[2023-03-16 11:51:25,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c3c1270-040f-4c12-9bfe-b053ce51bd98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:51:25,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c3c1270-040f-4c12-9bfe-b053ce51bd98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:51:25,403] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:51:25,404] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:51:25,404] [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
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.2325	67	837	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.1236	57	837	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.0941	58	837	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	75.9599	84	837	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	75.9584	50	837	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.9228	94	837	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	75.7179	75	837	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	75.6952	94	837	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	75.6698	58	837	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	75.6613	75	837	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	75.6597	78	837	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	75.6333	70	837	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	75.4762	60	837	95	below_threshold
Rubricella aquisinus	strain=DSM 103377	GCA_014199445.1	2028108	2028108	type	True	75.4609	73	837	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	75.2634	52	837	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:51:25,404] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27533/tc_result.tsv
[2023-03-16 11:51:25,404] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:51:25,404] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:51:25,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c3c1270-040f-4c12-9bfe-b053ce51bd98/dqc_reference/checkm_data
[2023-03-16 11:51:25,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:51:25,471] [INFO] Task started: CheckM
[2023-03-16 11:51:25,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27533/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27533/checkm_input OceanDNA-b27533/checkm_result
[2023-03-16 11:52:11,129] [INFO] Task succeeded: CheckM
[2023-03-16 11:52:11,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:52:11,132] [INFO] ===== Completeness check finished =====
[2023-03-16 11:52:11,132] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:52:11,132] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27533/markers.fasta)
[2023-03-16 11:52:11,134] [INFO] Task started: Blastn
[2023-03-16 11:52:11,134] [INFO] Running command: blastn -query OceanDNA-b27533/markers.fasta -db /var/lib/cwl/stg6c3c1270-040f-4c12-9bfe-b053ce51bd98/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27533/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:52:11,890] [INFO] Task succeeded: Blastn
[2023-03-16 11:52:11,891] [INFO] Selected 25 target genomes.
[2023-03-16 11:52:11,891] [INFO] Target genome list was writen to OceanDNA-b27533/target_genomes_gtdb.txt
[2023-03-16 11:52:12,007] [INFO] Task started: fastANI
[2023-03-16 11:52:12,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a8d7031-4391-4522-97e0-39b09815044a/OceanDNA-b27533.fa --refList OceanDNA-b27533/target_genomes_gtdb.txt --output OceanDNA-b27533/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:52:34,842] [INFO] Task succeeded: fastANI
[2023-03-16 11:52:34,855] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:52:34,855] [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_004365965.1	s__Rhodovulum visakhapatnamense	76.2325	67	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	76.2244	85	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	76.1236	57	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_014901205.1	s__Fluviibacterium sp014901205	76.1179	82	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487165.1	s__UBA5972 sp015487165	76.0732	59	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA5972	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	75.9671	88	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	75.9599	84	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	75.9584	50	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900100085.1	s__Salipiger marinus	75.9228	94	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_010500245.1	s__Ruegeria_B sp010500245	75.8988	99	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000255.1	s__Nioella ostreopsis	75.879	83	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	75.7179	75	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003116585.1	s__Albibacillus kandeliae	75.6986	72	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	75.6816	71	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_002847305.1	s__Paracoccus sp002847305	75.6698	58	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	75.6161	73	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_005887635.2	s__Paroceanicella profunda	75.4943	59	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	75.4743	72	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_014199445.1	s__Rubricella aquisinus	75.4609	73	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubricella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	75.4345	78	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609055.1	s__Pseudogemmobacter humi	75.3802	73	837	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:52:34,856] [INFO] GTDB search result was written to OceanDNA-b27533/result_gtdb.tsv
[2023-03-16 11:52:34,856] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:52:34,858] [INFO] DFAST_QC result json was written to OceanDNA-b27533/dqc_result.json
[2023-03-16 11:52:34,858] [INFO] DFAST_QC completed!
[2023-03-16 11:52:34,858] [INFO] Total running time: 0h1m43s