[2023-03-14 12:44:46,933] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:44:46,933] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:44:46,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg56b96d91-437e-404a-ba11-c3058854407b/dqc_reference
[2023-03-14 12:44:48,098] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:44:48,098] [INFO] Task started: Prodigal
[2023-03-14 12:44:48,098] [INFO] Running command: cat /var/lib/cwl/stg6d1b6678-53a8-460c-84ed-56f321870e93/OceanDNA-b9721.fa | prodigal -d OceanDNA-b9721/cds.fna -a OceanDNA-b9721/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:45:02,367] [INFO] Task succeeded: Prodigal
[2023-03-14 12:45:02,367] [INFO] Task started: HMMsearch
[2023-03-14 12:45:02,367] [INFO] Running command: hmmsearch --tblout OceanDNA-b9721/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56b96d91-437e-404a-ba11-c3058854407b/dqc_reference/reference_markers.hmm OceanDNA-b9721/protein.faa > /dev/null
[2023-03-14 12:45:02,549] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:45:02,550] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6d1b6678-53a8-460c-84ed-56f321870e93/OceanDNA-b9721.fa]
[2023-03-14 12:45:02,570] [INFO] Query marker FASTA was written to OceanDNA-b9721/markers.fasta
[2023-03-14 12:45:02,570] [INFO] Task started: Blastn
[2023-03-14 12:45:02,570] [INFO] Running command: blastn -query OceanDNA-b9721/markers.fasta -db /var/lib/cwl/stg56b96d91-437e-404a-ba11-c3058854407b/dqc_reference/reference_markers.fasta -out OceanDNA-b9721/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:45:03,108] [INFO] Task succeeded: Blastn
[2023-03-14 12:45:03,109] [INFO] Selected 11 target genomes.
[2023-03-14 12:45:03,110] [INFO] Target genome list was writen to OceanDNA-b9721/target_genomes.txt
[2023-03-14 12:45:03,118] [INFO] Task started: fastANI
[2023-03-14 12:45:03,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d1b6678-53a8-460c-84ed-56f321870e93/OceanDNA-b9721.fa --refList OceanDNA-b9721/target_genomes.txt --output OceanDNA-b9721/fastani_result.tsv --threads 1
[2023-03-14 12:45:10,749] [INFO] Task succeeded: fastANI
[2023-03-14 12:45:10,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56b96d91-437e-404a-ba11-c3058854407b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:45:10,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56b96d91-437e-404a-ba11-c3058854407b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:45:10,761] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2023-03-14 12:45:10,761] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 12:45:10,761] [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	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	97.6135	716	753	95	conclusive
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	97.3721	712	753	95	conclusive
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	97.3569	712	753	95	conclusive
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	86.5321	609	753	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	79.1778	428	753	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	78.6716	384	753	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3437	201	753	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.0452	184	753	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.009	192	753	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.9803	173	753	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.9445	164	753	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:45:10,762] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9721/tc_result.tsv
[2023-03-14 12:45:10,762] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:45:10,762] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:45:10,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56b96d91-437e-404a-ba11-c3058854407b/dqc_reference/checkm_data
[2023-03-14 12:45:10,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:45:10,770] [INFO] Task started: CheckM
[2023-03-14 12:45:10,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9721/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9721/checkm_input OceanDNA-b9721/checkm_result
[2023-03-14 12:46:00,011] [INFO] Task succeeded: CheckM
[2023-03-14 12:46:00,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:46:00,020] [INFO] ===== Completeness check finished =====
[2023-03-14 12:46:00,020] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:46:00,020] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9721/markers.fasta)
[2023-03-14 12:46:00,022] [INFO] Task started: Blastn
[2023-03-14 12:46:00,022] [INFO] Running command: blastn -query OceanDNA-b9721/markers.fasta -db /var/lib/cwl/stg56b96d91-437e-404a-ba11-c3058854407b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9721/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:46:01,569] [INFO] Task succeeded: Blastn
[2023-03-14 12:46:01,570] [INFO] Selected 12 target genomes.
[2023-03-14 12:46:01,570] [INFO] Target genome list was writen to OceanDNA-b9721/target_genomes_gtdb.txt
[2023-03-14 12:46:01,589] [INFO] Task started: fastANI
[2023-03-14 12:46:01,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d1b6678-53a8-460c-84ed-56f321870e93/OceanDNA-b9721.fa --refList OceanDNA-b9721/target_genomes_gtdb.txt --output OceanDNA-b9721/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:46:10,006] [INFO] Task succeeded: fastANI
[2023-03-14 12:46:10,013] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:46:10,013] [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	97.6135	716	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	conclusive
GCF_014764305.1	s__Mesoflavibacter profundi	86.5319	609	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_003259525.1	s__Olleya aquimaris	79.1778	428	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785945.1	s__Olleya sediminilitoris	79.093	426	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_000518485.1	s__Olleya marilimosa	79.048	424	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_007827365.1	s__Olleya sp002323495	78.7673	439	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_900114005.1	s__Olleya namhaensis	78.6716	384	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCA_001874145.1	s__Lacinutrix sp001874145	78.5278	365	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	78.4868	348	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_000211855.2	s__Lacinutrix sp000211855	78.4712	365	753	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	78.4169	372	753	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	78.3061	371	753	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:46:10,014] [INFO] GTDB search result was written to OceanDNA-b9721/result_gtdb.tsv
[2023-03-14 12:46:10,015] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:46:10,016] [INFO] DFAST_QC result json was written to OceanDNA-b9721/dqc_result.json
[2023-03-14 12:46:10,016] [INFO] DFAST_QC completed!
[2023-03-14 12:46:10,016] [INFO] Total running time: 0h1m23s