[2023-03-18 05:05:06,081] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:05:06,081] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:05:06,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c6fea62-324e-49c1-a0bc-ec9ef7f75944/dqc_reference
[2023-03-18 05:05:07,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:05:07,237] [INFO] Task started: Prodigal
[2023-03-18 05:05:07,237] [INFO] Running command: cat /var/lib/cwl/stg7b9eeb98-e590-44f6-91c3-42854db2aa24/OceanDNA-b30493.fa | prodigal -d OceanDNA-b30493/cds.fna -a OceanDNA-b30493/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:05:22,883] [INFO] Task succeeded: Prodigal
[2023-03-18 05:05:22,884] [INFO] Task started: HMMsearch
[2023-03-18 05:05:22,884] [INFO] Running command: hmmsearch --tblout OceanDNA-b30493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c6fea62-324e-49c1-a0bc-ec9ef7f75944/dqc_reference/reference_markers.hmm OceanDNA-b30493/protein.faa > /dev/null
[2023-03-18 05:05:23,062] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:05:23,063] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7b9eeb98-e590-44f6-91c3-42854db2aa24/OceanDNA-b30493.fa]
[2023-03-18 05:05:23,099] [INFO] Query marker FASTA was written to OceanDNA-b30493/markers.fasta
[2023-03-18 05:05:23,101] [INFO] Task started: Blastn
[2023-03-18 05:05:23,101] [INFO] Running command: blastn -query OceanDNA-b30493/markers.fasta -db /var/lib/cwl/stg8c6fea62-324e-49c1-a0bc-ec9ef7f75944/dqc_reference/reference_markers.fasta -out OceanDNA-b30493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:05:23,725] [INFO] Task succeeded: Blastn
[2023-03-18 05:05:23,729] [INFO] Selected 22 target genomes.
[2023-03-18 05:05:23,729] [INFO] Target genome list was writen to OceanDNA-b30493/target_genomes.txt
[2023-03-18 05:05:23,748] [INFO] Task started: fastANI
[2023-03-18 05:05:23,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b9eeb98-e590-44f6-91c3-42854db2aa24/OceanDNA-b30493.fa --refList OceanDNA-b30493/target_genomes.txt --output OceanDNA-b30493/fastani_result.tsv --threads 1
[2023-03-18 05:05:38,447] [INFO] Task succeeded: fastANI
[2023-03-18 05:05:38,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c6fea62-324e-49c1-a0bc-ec9ef7f75944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:05:38,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c6fea62-324e-49c1-a0bc-ec9ef7f75944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:05:38,460] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:05:38,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:05:38,460] [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
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	77.1419	252	820	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	76.9099	193	820	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	76.4194	106	820	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	76.4166	109	820	95	below_threshold
Roseobacter denitrificans	strain=DSM 7001	GCA_900113215.1	2434	2434	type	True	76.4064	118	820	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	76.3731	95	820	95	below_threshold
Roseobacter denitrificans	strain=OCh 114	GCA_000014045.1	2434	2434	type	True	76.358	120	820	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.3286	64	820	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.3139	98	820	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	76.2947	112	820	95	below_threshold
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	76.1223	75	820	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.1156	94	820	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.108	75	820	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	76.1071	87	820	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.0985	86	820	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.0853	97	820	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.063	64	820	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	75.9206	97	820	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	75.8944	59	820	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	75.7949	53	820	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	75.6722	74	820	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:05:38,463] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30493/tc_result.tsv
[2023-03-18 05:05:38,463] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:05:38,463] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:05:38,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c6fea62-324e-49c1-a0bc-ec9ef7f75944/dqc_reference/checkm_data
[2023-03-18 05:05:38,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:05:38,485] [INFO] Task started: CheckM
[2023-03-18 05:05:38,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30493/checkm_input OceanDNA-b30493/checkm_result
[2023-03-18 05:06:20,830] [INFO] Task succeeded: CheckM
[2023-03-18 05:06:20,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:06:20,947] [INFO] ===== Completeness check finished =====
[2023-03-18 05:06:20,947] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:06:20,947] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30493/markers.fasta)
[2023-03-18 05:06:20,948] [INFO] Task started: Blastn
[2023-03-18 05:06:20,949] [INFO] Running command: blastn -query OceanDNA-b30493/markers.fasta -db /var/lib/cwl/stg8c6fea62-324e-49c1-a0bc-ec9ef7f75944/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:06:21,983] [INFO] Task succeeded: Blastn
[2023-03-18 05:06:21,986] [INFO] Selected 17 target genomes.
[2023-03-18 05:06:21,987] [INFO] Target genome list was writen to OceanDNA-b30493/target_genomes_gtdb.txt
[2023-03-18 05:06:22,053] [INFO] Task started: fastANI
[2023-03-18 05:06:22,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b9eeb98-e590-44f6-91c3-42854db2aa24/OceanDNA-b30493.fa --refList OceanDNA-b30493/target_genomes_gtdb.txt --output OceanDNA-b30493/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:06:34,616] [INFO] Task succeeded: fastANI
[2023-03-18 05:06:34,626] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:06:34,626] [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_018668195.1	s__Tateyamaria sp018668195	99.4875	649	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001969365.1	s__Tateyamaria omphalii_A	77.2104	221	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000814025.1	s__Tateyamaria sp000814025	76.9845	210	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995245.1	s__Tateyamaria sp007995245	76.8775	223	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143535.1	s__Tateyamaria sp900143535	76.8423	207	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	76.4215	118	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302455.1	s__Ruegeria_E mediterranea	76.4194	106	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	99.84	99.84	0.96	0.96	2	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	76.3476	144	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_004123675.1	s__Leisingera sp004123675	76.3195	86	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	76.3071	97	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109145.1	s__Marinovum algicola	76.1439	88	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_900102535.1	s__Sulfitobacter delicatus	76.1156	94	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923355.1	s__Phaeobacter_A marinintestinus	76.1071	87	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.0985	86	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	75.9251	95	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002405.1	s__Sulfitobacter sp013002405	75.7669	70	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	75.6383	72	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:06:34,630] [INFO] GTDB search result was written to OceanDNA-b30493/result_gtdb.tsv
[2023-03-18 05:06:34,636] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:06:34,641] [INFO] DFAST_QC result json was written to OceanDNA-b30493/dqc_result.json
[2023-03-18 05:06:34,641] [INFO] DFAST_QC completed!
[2023-03-18 05:06:34,641] [INFO] Total running time: 0h1m29s