[2023-03-18 20:59:43,923] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,924] [INFO] DQC Reference Directory: /var/lib/cwl/stgd52dfaf6-0a28-42ff-9c2a-6a58bda30a1d/dqc_reference
[2023-03-18 20:59:45,686] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,686] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,687] [INFO] Running command: cat /var/lib/cwl/stgdd0bbc08-183f-49b8-8c36-f66d072d0787/OceanDNA-b36663.fa | prodigal -d OceanDNA-b36663/cds.fna -a OceanDNA-b36663/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:00:10,791] [INFO] Task succeeded: Prodigal
[2023-03-18 21:00:10,791] [INFO] Task started: HMMsearch
[2023-03-18 21:00:10,791] [INFO] Running command: hmmsearch --tblout OceanDNA-b36663/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd52dfaf6-0a28-42ff-9c2a-6a58bda30a1d/dqc_reference/reference_markers.hmm OceanDNA-b36663/protein.faa > /dev/null
[2023-03-18 21:00:11,061] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:00:11,062] [INFO] Found 6/6 markers.
[2023-03-18 21:00:11,091] [INFO] Query marker FASTA was written to OceanDNA-b36663/markers.fasta
[2023-03-18 21:00:11,092] [INFO] Task started: Blastn
[2023-03-18 21:00:11,092] [INFO] Running command: blastn -query OceanDNA-b36663/markers.fasta -db /var/lib/cwl/stgd52dfaf6-0a28-42ff-9c2a-6a58bda30a1d/dqc_reference/reference_markers.fasta -out OceanDNA-b36663/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:11,744] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:11,745] [INFO] Selected 31 target genomes.
[2023-03-18 21:00:11,745] [INFO] Target genome list was writen to OceanDNA-b36663/target_genomes.txt
[2023-03-18 21:00:11,761] [INFO] Task started: fastANI
[2023-03-18 21:00:11,761] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd0bbc08-183f-49b8-8c36-f66d072d0787/OceanDNA-b36663.fa --refList OceanDNA-b36663/target_genomes.txt --output OceanDNA-b36663/fastani_result.tsv --threads 1
[2023-03-18 21:00:34,399] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:34,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd52dfaf6-0a28-42ff-9c2a-6a58bda30a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:34,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd52dfaf6-0a28-42ff-9c2a-6a58bda30a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:34,406] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:34,406] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:34,406] [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
Cellvibrio zantedeschiae	strain=KCTC 32239	GCA_014652535.1	1237077	1237077	type	True	78.0698	251	1390	95	below_threshold
Cellvibrio japonicus	strain=Ueda107	GCA_000019225.1	155077	155077	type	True	77.8395	305	1390	95	below_threshold
Cellvibrio polysaccharolyticus	strain=Ka43	GCA_015182315.1	2082724	2082724	type	True	77.1296	180	1390	95	below_threshold
Gilvimarinus chinensis	strain=DSM 19667	GCA_000377745.1	396005	396005	type	True	76.718	95	1390	95	below_threshold
Marinimicrobium koreense	strain=DSM 16974	GCA_003762925.1	306545	306545	type	True	76.4771	52	1390	95	below_threshold
Gilvimarinus polysaccharolyticus	strain=YN3	GCA_001187555.1	863921	863921	type	True	76.2967	75	1390	95	below_threshold
Marinimicrobium agarilyticum	strain=DSM 16975	GCA_000423345.1	306546	306546	type	True	75.8841	66	1390	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:34,407] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36663/tc_result.tsv
[2023-03-18 21:00:34,407] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:34,407] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:34,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd52dfaf6-0a28-42ff-9c2a-6a58bda30a1d/dqc_reference/checkm_data
[2023-03-18 21:00:34,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:34,415] [INFO] Task started: CheckM
[2023-03-18 21:00:34,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36663/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36663/checkm_input OceanDNA-b36663/checkm_result
[2023-03-18 21:01:36,522] [INFO] Task succeeded: CheckM
[2023-03-18 21:01:36,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:01:36,526] [INFO] ===== Completeness check finished =====
[2023-03-18 21:01:36,526] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:01:36,526] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36663/markers.fasta)
[2023-03-18 21:01:36,527] [INFO] Task started: Blastn
[2023-03-18 21:01:36,527] [INFO] Running command: blastn -query OceanDNA-b36663/markers.fasta -db /var/lib/cwl/stgd52dfaf6-0a28-42ff-9c2a-6a58bda30a1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36663/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:01:37,607] [INFO] Task succeeded: Blastn
[2023-03-18 21:01:37,608] [INFO] Selected 10 target genomes.
[2023-03-18 21:01:37,609] [INFO] Target genome list was writen to OceanDNA-b36663/target_genomes_gtdb.txt
[2023-03-18 21:01:37,653] [INFO] Task started: fastANI
[2023-03-18 21:01:37,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd0bbc08-183f-49b8-8c36-f66d072d0787/OceanDNA-b36663.fa --refList OceanDNA-b36663/target_genomes_gtdb.txt --output OceanDNA-b36663/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:46,377] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:46,384] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:01:46,384] [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_000953825.1	s__Cellvibrio sp000953825	85.288	1032	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003524365.1	s__Cellvibrio sp003524365	82.7148	790	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483145.1	s__Cellvibrio sp002483145	82.6606	930	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858205.1	s__Cellvibrio sp903858205	82.0276	649	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363885.1	s__Cellvibrio sp004363885	80.8687	724	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806955.1	s__Cellvibrio sp000263355	80.3142	642	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	98.02	97.81	0.88	0.84	3	-
GCF_001183545.1	s__Cellvibrio sp001183545	79.8658	681	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002007605.1	s__Cellvibrio sp002007605	79.8069	612	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	97.66	97.66	0.90	0.90	2	-
GCF_014652535.1	s__Cellvibrio zantedeschiae	78.0316	253	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712405.1	s__Cellvibrio sp016712405	77.6617	189	1390	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Cellvibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:46,385] [INFO] GTDB search result was written to OceanDNA-b36663/result_gtdb.tsv
[2023-03-18 21:01:46,386] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:46,388] [INFO] DFAST_QC result json was written to OceanDNA-b36663/dqc_result.json
[2023-03-18 21:01:46,388] [INFO] DFAST_QC completed!
[2023-03-18 21:01:46,388] [INFO] Total running time: 0h2m2s