[2023-03-16 09:50:49,820] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:50:49,825] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:50:49,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bb03e29-486c-485e-a365-875721c4930f/dqc_reference
[2023-03-16 09:50:50,951] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:50:50,951] [INFO] Task started: Prodigal
[2023-03-16 09:50:50,952] [INFO] Running command: cat /var/lib/cwl/stg7abe57f3-5f6c-44ff-a6c9-940f09f7afad/OceanDNA-b9718.fa | prodigal -d OceanDNA-b9718/cds.fna -a OceanDNA-b9718/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:50:59,717] [INFO] Task succeeded: Prodigal
[2023-03-16 09:50:59,717] [INFO] Task started: HMMsearch
[2023-03-16 09:50:59,717] [INFO] Running command: hmmsearch --tblout OceanDNA-b9718/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bb03e29-486c-485e-a365-875721c4930f/dqc_reference/reference_markers.hmm OceanDNA-b9718/protein.faa > /dev/null
[2023-03-16 09:50:59,908] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:50:59,908] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7abe57f3-5f6c-44ff-a6c9-940f09f7afad/OceanDNA-b9718.fa]
[2023-03-16 09:50:59,989] [INFO] Query marker FASTA was written to OceanDNA-b9718/markers.fasta
[2023-03-16 09:50:59,990] [INFO] Task started: Blastn
[2023-03-16 09:50:59,990] [INFO] Running command: blastn -query OceanDNA-b9718/markers.fasta -db /var/lib/cwl/stg2bb03e29-486c-485e-a365-875721c4930f/dqc_reference/reference_markers.fasta -out OceanDNA-b9718/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:51:00,521] [INFO] Task succeeded: Blastn
[2023-03-16 09:51:00,526] [INFO] Selected 7 target genomes.
[2023-03-16 09:51:00,526] [INFO] Target genome list was writen to OceanDNA-b9718/target_genomes.txt
[2023-03-16 09:51:00,533] [INFO] Task started: fastANI
[2023-03-16 09:51:00,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg7abe57f3-5f6c-44ff-a6c9-940f09f7afad/OceanDNA-b9718.fa --refList OceanDNA-b9718/target_genomes.txt --output OceanDNA-b9718/fastani_result.tsv --threads 1
[2023-03-16 09:51:04,149] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:04,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bb03e29-486c-485e-a365-875721c4930f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:51:04,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bb03e29-486c-485e-a365-875721c4930f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:51:04,155] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:51:04,155] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:51:04,156] [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
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	91.0858	335	366	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	91.0721	333	366	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	90.6255	340	366	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	85.6705	322	366	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	79.2791	216	366	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	79.1532	232	366	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	78.8833	209	366	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:51:04,164] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9718/tc_result.tsv
[2023-03-16 09:51:04,181] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:51:04,181] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:51:04,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bb03e29-486c-485e-a365-875721c4930f/dqc_reference/checkm_data
[2023-03-16 09:51:04,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:51:04,191] [INFO] Task started: CheckM
[2023-03-16 09:51:04,191] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9718/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9718/checkm_input OceanDNA-b9718/checkm_result
[2023-03-16 09:51:31,582] [INFO] Task succeeded: CheckM
[2023-03-16 09:51:31,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.97%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:51:31,633] [INFO] ===== Completeness check finished =====
[2023-03-16 09:51:31,633] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:51:31,634] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9718/markers.fasta)
[2023-03-16 09:51:31,634] [INFO] Task started: Blastn
[2023-03-16 09:51:31,634] [INFO] Running command: blastn -query OceanDNA-b9718/markers.fasta -db /var/lib/cwl/stg2bb03e29-486c-485e-a365-875721c4930f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9718/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:51:32,362] [INFO] Task succeeded: Blastn
[2023-03-16 09:51:32,368] [INFO] Selected 13 target genomes.
[2023-03-16 09:51:32,368] [INFO] Target genome list was writen to OceanDNA-b9718/target_genomes_gtdb.txt
[2023-03-16 09:51:32,464] [INFO] Task started: fastANI
[2023-03-16 09:51:32,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg7abe57f3-5f6c-44ff-a6c9-940f09f7afad/OceanDNA-b9718.fa --refList OceanDNA-b9718/target_genomes_gtdb.txt --output OceanDNA-b9718/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:51:40,044] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:40,052] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:51:40,053] [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_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	90.6255	340	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_014764305.1	s__Mesoflavibacter profundi	85.6362	323	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_000518485.1	s__Olleya marilimosa	79.2791	216	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_003259525.1	s__Olleya aquimaris	79.1228	234	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114005.1	s__Olleya namhaensis	78.8833	209	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_000211855.2	s__Lacinutrix sp000211855	78.483	183	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004843725.1	s__Olleya sp004843725	78.3923	190	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831645.1	s__Olleya sp002831645	78.3821	185	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	78.0685	194	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067265.1	s__Oceanihabitans sp018067265	77.9231	122	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.7407	150	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.3276	126	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	76.991	116	366	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:51:40,056] [INFO] GTDB search result was written to OceanDNA-b9718/result_gtdb.tsv
[2023-03-16 09:51:40,058] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:51:40,062] [INFO] DFAST_QC result json was written to OceanDNA-b9718/dqc_result.json
[2023-03-16 09:51:40,063] [INFO] DFAST_QC completed!
[2023-03-16 09:51:40,063] [INFO] Total running time: 0h0m50s