[2023-03-16 08:37:21,708] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:37:21,708] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:37:21,709] [INFO] DQC Reference Directory: /var/lib/cwl/stgd91b89f9-49e3-4893-9af1-71563f463ffe/dqc_reference
[2023-03-16 08:37:22,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:37:22,948] [INFO] Task started: Prodigal
[2023-03-16 08:37:22,948] [INFO] Running command: cat /var/lib/cwl/stg7b8ef5ff-ac47-45d5-8f52-eb1a0f146586/OceanDNA-b41456.fa | prodigal -d OceanDNA-b41456/cds.fna -a OceanDNA-b41456/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:37:38,330] [INFO] Task succeeded: Prodigal
[2023-03-16 08:37:38,330] [INFO] Task started: HMMsearch
[2023-03-16 08:37:38,330] [INFO] Running command: hmmsearch --tblout OceanDNA-b41456/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd91b89f9-49e3-4893-9af1-71563f463ffe/dqc_reference/reference_markers.hmm OceanDNA-b41456/protein.faa > /dev/null
[2023-03-16 08:37:38,506] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:37:38,507] [INFO] Found 6/6 markers.
[2023-03-16 08:37:38,523] [INFO] Query marker FASTA was written to OceanDNA-b41456/markers.fasta
[2023-03-16 08:37:38,524] [INFO] Task started: Blastn
[2023-03-16 08:37:38,524] [INFO] Running command: blastn -query OceanDNA-b41456/markers.fasta -db /var/lib/cwl/stgd91b89f9-49e3-4893-9af1-71563f463ffe/dqc_reference/reference_markers.fasta -out OceanDNA-b41456/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:37:39,168] [INFO] Task succeeded: Blastn
[2023-03-16 08:37:39,171] [INFO] Selected 28 target genomes.
[2023-03-16 08:37:39,172] [INFO] Target genome list was writen to OceanDNA-b41456/target_genomes.txt
[2023-03-16 08:37:39,205] [INFO] Task started: fastANI
[2023-03-16 08:37:39,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b8ef5ff-ac47-45d5-8f52-eb1a0f146586/OceanDNA-b41456.fa --refList OceanDNA-b41456/target_genomes.txt --output OceanDNA-b41456/fastani_result.tsv --threads 1
[2023-03-16 08:37:56,619] [INFO] Task succeeded: fastANI
[2023-03-16 08:37:56,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd91b89f9-49e3-4893-9af1-71563f463ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:37:56,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd91b89f9-49e3-4893-9af1-71563f463ffe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:37:56,626] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:37:56,626] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:37:56,626] [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
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	76.7439	70	826	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	76.627	57	826	95	below_threshold
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	76.5924	83	826	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	76.5137	62	826	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	76.4602	70	826	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	76.4074	59	826	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	75.9641	56	826	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	75.9641	56	826	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:37:56,629] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41456/tc_result.tsv
[2023-03-16 08:37:56,630] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:37:56,630] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:37:56,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd91b89f9-49e3-4893-9af1-71563f463ffe/dqc_reference/checkm_data
[2023-03-16 08:37:56,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:37:56,636] [INFO] Task started: CheckM
[2023-03-16 08:37:56,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41456/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41456/checkm_input OceanDNA-b41456/checkm_result
[2023-03-16 08:38:37,541] [INFO] Task succeeded: CheckM
[2023-03-16 08:38:37,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:38:37,544] [INFO] ===== Completeness check finished =====
[2023-03-16 08:38:37,544] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:38:37,544] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41456/markers.fasta)
[2023-03-16 08:38:37,545] [INFO] Task started: Blastn
[2023-03-16 08:38:37,545] [INFO] Running command: blastn -query OceanDNA-b41456/markers.fasta -db /var/lib/cwl/stgd91b89f9-49e3-4893-9af1-71563f463ffe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41456/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:38:38,590] [INFO] Task succeeded: Blastn
[2023-03-16 08:38:38,594] [INFO] Selected 28 target genomes.
[2023-03-16 08:38:38,594] [INFO] Target genome list was writen to OceanDNA-b41456/target_genomes_gtdb.txt
[2023-03-16 08:38:38,644] [INFO] Task started: fastANI
[2023-03-16 08:38:38,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b8ef5ff-ac47-45d5-8f52-eb1a0f146586/OceanDNA-b41456.fa --refList OceanDNA-b41456/target_genomes_gtdb.txt --output OceanDNA-b41456/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:38:56,589] [INFO] Task succeeded: fastANI
[2023-03-16 08:38:56,595] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:38:56,595] [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
GCA_002415025.1	s__Litorivivens sp002415025	77.2838	65	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	99.88	99.82	0.96	0.94	3	-
GCF_000422345.1	s__Spongiibacter marinus_A	76.9032	70	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906995.1	s__Spongiibacter marinus	76.8061	66	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	-
GCF_000420325.1	s__Spongiibacter tropicus	76.7766	69	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_014705705.1	s__KMU-158 sp014705705	76.6652	56	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191715.1	s__Litorivivens lipolytica	76.6104	81	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016132545.1	s__CSC3-9 sp016132545	76.5469	61	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272835.1	s__Spongiibacter sp012272835	76.4602	70	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202945.1	s__Zhongshania antarctica	75.9409	55	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-16 08:38:56,596] [INFO] GTDB search result was written to OceanDNA-b41456/result_gtdb.tsv
[2023-03-16 08:38:56,596] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:38:56,597] [INFO] DFAST_QC result json was written to OceanDNA-b41456/dqc_result.json
[2023-03-16 08:38:56,597] [INFO] DFAST_QC completed!
[2023-03-16 08:38:56,597] [INFO] Total running time: 0h1m35s