[2023-03-16 00:13:32,257] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:13:32,257] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:13:32,257] [INFO] DQC Reference Directory: /var/lib/cwl/stg63f936a7-89db-4b8c-a914-b578b2999d8b/dqc_reference
[2023-03-16 00:13:33,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:13:33,502] [INFO] Task started: Prodigal
[2023-03-16 00:13:33,502] [INFO] Running command: cat /var/lib/cwl/stg78dd95d5-1aea-406e-a2d3-1a9969e70327/OceanDNA-b23919.fa | prodigal -d OceanDNA-b23919/cds.fna -a OceanDNA-b23919/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:13:49,841] [INFO] Task succeeded: Prodigal
[2023-03-16 00:13:49,842] [INFO] Task started: HMMsearch
[2023-03-16 00:13:49,842] [INFO] Running command: hmmsearch --tblout OceanDNA-b23919/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63f936a7-89db-4b8c-a914-b578b2999d8b/dqc_reference/reference_markers.hmm OceanDNA-b23919/protein.faa > /dev/null
[2023-03-16 00:13:50,045] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:13:50,045] [INFO] Found 6/6 markers.
[2023-03-16 00:13:50,066] [INFO] Query marker FASTA was written to OceanDNA-b23919/markers.fasta
[2023-03-16 00:13:50,067] [INFO] Task started: Blastn
[2023-03-16 00:13:50,068] [INFO] Running command: blastn -query OceanDNA-b23919/markers.fasta -db /var/lib/cwl/stg63f936a7-89db-4b8c-a914-b578b2999d8b/dqc_reference/reference_markers.fasta -out OceanDNA-b23919/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:13:50,819] [INFO] Task succeeded: Blastn
[2023-03-16 00:13:50,823] [INFO] Selected 20 target genomes.
[2023-03-16 00:13:50,823] [INFO] Target genome list was writen to OceanDNA-b23919/target_genomes.txt
[2023-03-16 00:13:50,836] [INFO] Task started: fastANI
[2023-03-16 00:13:50,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg78dd95d5-1aea-406e-a2d3-1a9969e70327/OceanDNA-b23919.fa --refList OceanDNA-b23919/target_genomes.txt --output OceanDNA-b23919/fastani_result.tsv --threads 1
[2023-03-16 00:14:02,554] [INFO] Task succeeded: fastANI
[2023-03-16 00:14:02,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63f936a7-89db-4b8c-a914-b578b2999d8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:14:02,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63f936a7-89db-4b8c-a914-b578b2999d8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:14:02,565] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:14:02,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:14:02,565] [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
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	90.0033	790	873	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	78.8949	421	873	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	78.5483	393	873	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	76.4953	150	873	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	76.4924	150	873	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	76.4401	139	873	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	76.4401	139	873	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.3396	147	873	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	76.2232	120	873	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	76.1956	122	873	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.167	54	873	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	75.7278	74	873	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	75.5143	67	873	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	75.5143	67	873	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.3627	50	873	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:14:02,566] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23919/tc_result.tsv
[2023-03-16 00:14:02,566] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:14:02,566] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:14:02,567] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63f936a7-89db-4b8c-a914-b578b2999d8b/dqc_reference/checkm_data
[2023-03-16 00:14:02,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:14:02,593] [INFO] Task started: CheckM
[2023-03-16 00:14:02,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23919/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23919/checkm_input OceanDNA-b23919/checkm_result
[2023-03-16 00:14:45,779] [INFO] Task succeeded: CheckM
[2023-03-16 00:14:45,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:14:45,784] [INFO] ===== Completeness check finished =====
[2023-03-16 00:14:45,784] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:14:45,784] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23919/markers.fasta)
[2023-03-16 00:14:45,786] [INFO] Task started: Blastn
[2023-03-16 00:14:45,786] [INFO] Running command: blastn -query OceanDNA-b23919/markers.fasta -db /var/lib/cwl/stg63f936a7-89db-4b8c-a914-b578b2999d8b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23919/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:14:47,298] [INFO] Task succeeded: Blastn
[2023-03-16 00:14:47,302] [INFO] Selected 12 target genomes.
[2023-03-16 00:14:47,302] [INFO] Target genome list was writen to OceanDNA-b23919/target_genomes_gtdb.txt
[2023-03-16 00:14:47,313] [INFO] Task started: fastANI
[2023-03-16 00:14:47,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg78dd95d5-1aea-406e-a2d3-1a9969e70327/OceanDNA-b23919.fa --refList OceanDNA-b23919/target_genomes_gtdb.txt --output OceanDNA-b23919/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:14:55,255] [INFO] Task succeeded: fastANI
[2023-03-16 00:14:55,263] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:14:55,263] [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_900103475.1	s__Maricaulis salignorans	90.0033	790	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	78.8949	421	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_000014745.1	s__Maricaulis maris_A	78.8127	401	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_015665295.1	s__Maricaulis sp015665295	78.5979	403	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871165.1	s__Maricaulis sp005871165	78.5483	393	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016817355.1	s__Maricaulis parjimensis	78.4303	378	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480005.1	s__Maricaulis sp905480005	78.3943	367	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	78.3562	442	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643475.1	s__Maricaulis sp017643475	77.7017	281	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122085.1	s__WD6-1 sp003122085	76.3396	147	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050155.1	s__Nitratireductor soli	75.697	76	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	75.4992	68	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 00:14:55,266] [INFO] GTDB search result was written to OceanDNA-b23919/result_gtdb.tsv
[2023-03-16 00:14:55,267] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:14:55,270] [INFO] DFAST_QC result json was written to OceanDNA-b23919/dqc_result.json
[2023-03-16 00:14:55,270] [INFO] DFAST_QC completed!
[2023-03-16 00:14:55,270] [INFO] Total running time: 0h1m23s