[2023-03-15 17:20:51,341] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:20:51,343] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:20:51,343] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd033c5c-38eb-4fee-8ec9-54da22e8d469/dqc_reference
[2023-03-15 17:20:52,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:20:52,477] [INFO] Task started: Prodigal
[2023-03-15 17:20:52,477] [INFO] Running command: cat /var/lib/cwl/stg5e3b7797-08b5-4d84-87ad-b00632783178/OceanDNA-b38499.fa | prodigal -d OceanDNA-b38499/cds.fna -a OceanDNA-b38499/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:21:18,673] [INFO] Task succeeded: Prodigal
[2023-03-15 17:21:18,673] [INFO] Task started: HMMsearch
[2023-03-15 17:21:18,673] [INFO] Running command: hmmsearch --tblout OceanDNA-b38499/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd033c5c-38eb-4fee-8ec9-54da22e8d469/dqc_reference/reference_markers.hmm OceanDNA-b38499/protein.faa > /dev/null
[2023-03-15 17:21:18,912] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:21:18,912] [INFO] Found 6/6 markers.
[2023-03-15 17:21:18,956] [INFO] Query marker FASTA was written to OceanDNA-b38499/markers.fasta
[2023-03-15 17:21:18,957] [INFO] Task started: Blastn
[2023-03-15 17:21:18,958] [INFO] Running command: blastn -query OceanDNA-b38499/markers.fasta -db /var/lib/cwl/stgdd033c5c-38eb-4fee-8ec9-54da22e8d469/dqc_reference/reference_markers.fasta -out OceanDNA-b38499/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:21:19,594] [INFO] Task succeeded: Blastn
[2023-03-15 17:21:19,602] [INFO] Selected 12 target genomes.
[2023-03-15 17:21:19,602] [INFO] Target genome list was writen to OceanDNA-b38499/target_genomes.txt
[2023-03-15 17:21:19,608] [INFO] Task started: fastANI
[2023-03-15 17:21:19,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3b7797-08b5-4d84-87ad-b00632783178/OceanDNA-b38499.fa --refList OceanDNA-b38499/target_genomes.txt --output OceanDNA-b38499/fastani_result.tsv --threads 1
[2023-03-15 17:21:30,307] [INFO] Task succeeded: fastANI
[2023-03-15 17:21:30,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd033c5c-38eb-4fee-8ec9-54da22e8d469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:21:30,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd033c5c-38eb-4fee-8ec9-54da22e8d469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:21:30,314] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 17:21:30,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 17:21:30,315] [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 polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	97.7939	1385	1549	95	conclusive
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	88.6302	1133	1549	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	84.7564	1012	1549	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	84.7353	1025	1549	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	83.7087	888	1549	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	82.9562	931	1549	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	82.3437	860	1549	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	82.3175	925	1549	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	80.9939	808	1549	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:21:30,319] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38499/tc_result.tsv
[2023-03-15 17:21:30,323] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:21:30,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:21:30,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd033c5c-38eb-4fee-8ec9-54da22e8d469/dqc_reference/checkm_data
[2023-03-15 17:21:30,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:21:30,345] [INFO] Task started: CheckM
[2023-03-15 17:21:30,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38499/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38499/checkm_input OceanDNA-b38499/checkm_result
[2023-03-15 17:22:34,826] [INFO] Task succeeded: CheckM
[2023-03-15 17:22:34,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:22:34,929] [INFO] ===== Completeness check finished =====
[2023-03-15 17:22:34,930] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:22:34,930] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38499/markers.fasta)
[2023-03-15 17:22:34,931] [INFO] Task started: Blastn
[2023-03-15 17:22:34,931] [INFO] Running command: blastn -query OceanDNA-b38499/markers.fasta -db /var/lib/cwl/stgdd033c5c-38eb-4fee-8ec9-54da22e8d469/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38499/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:22:35,931] [INFO] Task succeeded: Blastn
[2023-03-15 17:22:35,935] [INFO] Selected 7 target genomes.
[2023-03-15 17:22:35,935] [INFO] Target genome list was writen to OceanDNA-b38499/target_genomes_gtdb.txt
[2023-03-15 17:22:35,953] [INFO] Task started: fastANI
[2023-03-15 17:22:35,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e3b7797-08b5-4d84-87ad-b00632783178/OceanDNA-b38499.fa --refList OceanDNA-b38499/target_genomes_gtdb.txt --output OceanDNA-b38499/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:22:43,424] [INFO] Task succeeded: fastANI
[2023-03-15 17:22:43,430] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:22:43,430] [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_900129155.1	s__Marinomonas polaris	97.7939	1385	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	conclusive
GCF_000017285.1	s__Marinomonas sp000017285	92.0798	1252	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_018336955.1	s__Marinomonas sp018336955	88.6218	1129	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315485.1	s__Marinomonas rhizomae	84.7514	1024	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337275.1	s__Marinomonas foliarum	83.6927	890	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_003208215.1	s__Marinomonas alcarazii	82.3232	862	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_003259175.1	s__Marinomonas shanghaiensis	82.3117	926	1549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:22:43,432] [INFO] GTDB search result was written to OceanDNA-b38499/result_gtdb.tsv
[2023-03-15 17:22:43,435] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:22:43,440] [INFO] DFAST_QC result json was written to OceanDNA-b38499/dqc_result.json
[2023-03-15 17:22:43,440] [INFO] DFAST_QC completed!
[2023-03-15 17:22:43,440] [INFO] Total running time: 0h1m52s