[2023-03-17 04:48:53,967] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:53,967] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:53,967] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf5315eb-be08-4fa1-a97e-46dae6c30f47/dqc_reference
[2023-03-17 04:48:55,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,155] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,155] [INFO] Running command: cat /var/lib/cwl/stg9e39d92f-9b54-40b8-a495-8fc283fb7f69/OceanDNA-b38504.fa | prodigal -d OceanDNA-b38504/cds.fna -a OceanDNA-b38504/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:14,860] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:14,860] [INFO] Task started: HMMsearch
[2023-03-17 04:49:14,860] [INFO] Running command: hmmsearch --tblout OceanDNA-b38504/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf5315eb-be08-4fa1-a97e-46dae6c30f47/dqc_reference/reference_markers.hmm OceanDNA-b38504/protein.faa > /dev/null
[2023-03-17 04:49:15,078] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:15,078] [INFO] Found 6/6 markers.
[2023-03-17 04:49:15,100] [INFO] Query marker FASTA was written to OceanDNA-b38504/markers.fasta
[2023-03-17 04:49:15,100] [INFO] Task started: Blastn
[2023-03-17 04:49:15,100] [INFO] Running command: blastn -query OceanDNA-b38504/markers.fasta -db /var/lib/cwl/stgaf5315eb-be08-4fa1-a97e-46dae6c30f47/dqc_reference/reference_markers.fasta -out OceanDNA-b38504/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:15,729] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:15,730] [INFO] Selected 18 target genomes.
[2023-03-17 04:49:15,730] [INFO] Target genome list was writen to OceanDNA-b38504/target_genomes.txt
[2023-03-17 04:49:15,740] [INFO] Task started: fastANI
[2023-03-17 04:49:15,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e39d92f-9b54-40b8-a495-8fc283fb7f69/OceanDNA-b38504.fa --refList OceanDNA-b38504/target_genomes.txt --output OceanDNA-b38504/fastani_result.tsv --threads 1
[2023-03-17 04:49:30,349] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:30,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf5315eb-be08-4fa1-a97e-46dae6c30f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:30,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf5315eb-be08-4fa1-a97e-46dae6c30f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:30,358] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 04:49:30,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 04:49:30,358] [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
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	98.2308	1071	1150	95	conclusive
Marinomonas profundimaris	strain=D104	GCA_000508165.1	1208321	1208321	type	True	82.8931	823	1150	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	81.1308	759	1150	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	80.8156	738	1150	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	80.3422	615	1150	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	80.233	676	1150	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	80.1682	670	1150	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	80.1472	597	1150	95	below_threshold
Marinomonas ushuaiensis	strain=DSM 15871	GCA_000521805.1	263818	263818	type	True	80.1063	507	1150	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	80.0242	635	1150	95	below_threshold
Marinomonas arctica	strain=CGMCC 1.6498	GCA_014645175.1	383750	383750	type	True	79.9893	648	1150	95	below_threshold
Marinomonas colpomeniae	strain=SM2066	GCA_014803385.1	2774408	2774408	type	True	79.7561	520	1150	95	below_threshold
Marinomonas hwangdonensis	strain=HDW-15	GCA_003721245.1	1053647	1053647	type	True	79.5381	448	1150	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:49:30,358] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38504/tc_result.tsv
[2023-03-17 04:49:30,359] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:30,359] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:30,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf5315eb-be08-4fa1-a97e-46dae6c30f47/dqc_reference/checkm_data
[2023-03-17 04:49:30,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:30,364] [INFO] Task started: CheckM
[2023-03-17 04:49:30,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38504/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38504/checkm_input OceanDNA-b38504/checkm_result
[2023-03-17 04:50:22,718] [INFO] Task succeeded: CheckM
[2023-03-17 04:50:22,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:50:22,721] [INFO] ===== Completeness check finished =====
[2023-03-17 04:50:22,721] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:50:22,721] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38504/markers.fasta)
[2023-03-17 04:50:22,722] [INFO] Task started: Blastn
[2023-03-17 04:50:22,722] [INFO] Running command: blastn -query OceanDNA-b38504/markers.fasta -db /var/lib/cwl/stgaf5315eb-be08-4fa1-a97e-46dae6c30f47/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38504/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:50:23,713] [INFO] Task succeeded: Blastn
[2023-03-17 04:50:23,714] [INFO] Selected 13 target genomes.
[2023-03-17 04:50:23,714] [INFO] Target genome list was writen to OceanDNA-b38504/target_genomes_gtdb.txt
[2023-03-17 04:50:23,779] [INFO] Task started: fastANI
[2023-03-17 04:50:23,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e39d92f-9b54-40b8-a495-8fc283fb7f69/OceanDNA-b38504.fa --refList OceanDNA-b38504/target_genomes_gtdb.txt --output OceanDNA-b38504/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:50:35,313] [INFO] Task succeeded: fastANI
[2023-03-17 04:50:35,320] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:50:35,321] [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_013372285.1	s__Marinomonas primoryensis	98.2308	1071	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	96.98	96.98	0.86	0.86	2	conclusive
GCF_000508165.1	s__Marinomonas profundimaris	82.8829	824	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129155.1	s__Marinomonas polaris	81.1337	759	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_018336955.1	s__Marinomonas sp018336955	80.799	731	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017285.1	s__Marinomonas sp000017285	80.6146	712	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_003315485.1	s__Marinomonas rhizomae	80.2416	674	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003208215.1	s__Marinomonas alcarazii	80.137	597	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_000521805.1	s__Marinomonas ushuaiensis	80.1174	506	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259225.1	s__Marinomonas arctica	80.0071	637	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_018336975.1	s__Marinomonas sp013373235	79.7532	619	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.11	98.11	0.83	0.83	2	-
GCF_014803385.1	s__Marinomonas colpomeniae	79.7518	520	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016463975.1	s__Marinomonas sp016463975	79.282	441	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153025.1	s__Marinomonas sp000153025	77.651	138	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:50:35,321] [INFO] GTDB search result was written to OceanDNA-b38504/result_gtdb.tsv
[2023-03-17 04:50:35,321] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:50:35,322] [INFO] DFAST_QC result json was written to OceanDNA-b38504/dqc_result.json
[2023-03-17 04:50:35,323] [INFO] DFAST_QC completed!
[2023-03-17 04:50:35,323] [INFO] Total running time: 0h1m41s