[2023-03-18 03:09:35,421] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:35,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:35,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb863222-1780-44cf-a389-c0bfa4600d50/dqc_reference
[2023-03-18 03:09:36,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:36,637] [INFO] Task started: Prodigal
[2023-03-18 03:09:36,637] [INFO] Running command: cat /var/lib/cwl/stg72ea7e83-e667-431f-8b33-f126034cc371/OceanDNA-b41451.fa | prodigal -d OceanDNA-b41451/cds.fna -a OceanDNA-b41451/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:56,284] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:56,285] [INFO] Task started: HMMsearch
[2023-03-18 03:09:56,285] [INFO] Running command: hmmsearch --tblout OceanDNA-b41451/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb863222-1780-44cf-a389-c0bfa4600d50/dqc_reference/reference_markers.hmm OceanDNA-b41451/protein.faa > /dev/null
[2023-03-18 03:09:56,594] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:56,595] [INFO] Found 6/6 markers.
[2023-03-18 03:09:56,617] [INFO] Query marker FASTA was written to OceanDNA-b41451/markers.fasta
[2023-03-18 03:09:56,617] [INFO] Task started: Blastn
[2023-03-18 03:09:56,617] [INFO] Running command: blastn -query OceanDNA-b41451/markers.fasta -db /var/lib/cwl/stgfb863222-1780-44cf-a389-c0bfa4600d50/dqc_reference/reference_markers.fasta -out OceanDNA-b41451/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:57,342] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:57,343] [INFO] Selected 31 target genomes.
[2023-03-18 03:09:57,344] [INFO] Target genome list was writen to OceanDNA-b41451/target_genomes.txt
[2023-03-18 03:09:57,365] [INFO] Task started: fastANI
[2023-03-18 03:09:57,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ea7e83-e667-431f-8b33-f126034cc371/OceanDNA-b41451.fa --refList OceanDNA-b41451/target_genomes.txt --output OceanDNA-b41451/fastani_result.tsv --threads 1
[2023-03-18 03:10:20,130] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:20,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb863222-1780-44cf-a389-c0bfa4600d50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:20,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb863222-1780-44cf-a389-c0bfa4600d50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:20,139] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:10:20,139] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:10:20,139] [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 pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	76.9284	96	1081	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	76.8613	86	1081	95	below_threshold
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	76.8279	114	1081	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	76.7098	100	1081	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	76.7009	110	1081	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	76.4731	90	1081	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.4162	64	1081	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	76.0938	57	1081	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	76.0887	57	1081	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.0379	68	1081	95	below_threshold
Pseudomaricurvus alkylphenolicus	strain=KCTC 32386	GCA_011683955.1	1306991	1306991	type	True	75.9874	55	1081	95	below_threshold
Atopomonas hussainii	strain=JCM 19513	GCA_900109735.1	1429083	1429083	type	True	75.9254	58	1081	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	75.6041	54	1081	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:20,140] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41451/tc_result.tsv
[2023-03-18 03:10:20,140] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:20,140] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:20,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb863222-1780-44cf-a389-c0bfa4600d50/dqc_reference/checkm_data
[2023-03-18 03:10:20,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:20,146] [INFO] Task started: CheckM
[2023-03-18 03:10:20,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41451/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41451/checkm_input OceanDNA-b41451/checkm_result
[2023-03-18 03:11:10,308] [INFO] Task succeeded: CheckM
[2023-03-18 03:11:10,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:11:10,311] [INFO] ===== Completeness check finished =====
[2023-03-18 03:11:10,311] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:11:10,312] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41451/markers.fasta)
[2023-03-18 03:11:10,312] [INFO] Task started: Blastn
[2023-03-18 03:11:10,312] [INFO] Running command: blastn -query OceanDNA-b41451/markers.fasta -db /var/lib/cwl/stgfb863222-1780-44cf-a389-c0bfa4600d50/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41451/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:11:11,508] [INFO] Task succeeded: Blastn
[2023-03-18 03:11:11,509] [INFO] Selected 32 target genomes.
[2023-03-18 03:11:11,509] [INFO] Target genome list was writen to OceanDNA-b41451/target_genomes_gtdb.txt
[2023-03-18 03:11:11,650] [INFO] Task started: fastANI
[2023-03-18 03:11:11,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg72ea7e83-e667-431f-8b33-f126034cc371/OceanDNA-b41451.fa --refList OceanDNA-b41451/target_genomes_gtdb.txt --output OceanDNA-b41451/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:11:32,984] [INFO] Task succeeded: fastANI
[2023-03-18 03:11:32,992] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:11:32,993] [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_000422345.1	s__Spongiibacter marinus_A	77.0512	83	1081	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	76.9491	81	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	-
GCF_014705705.1	s__KMU-158 sp014705705	76.9284	96	1081	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	76.8445	113	1081	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	76.7098	100	1081	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_000420325.1	s__Spongiibacter tropicus	76.7009	110	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCF_012272835.1	s__Spongiibacter sp012272835	76.4731	90	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	76.4162	64	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	76.1665	62	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202945.1	s__Zhongshania antarctica	76.0938	57	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008064635.1	s__Parahaliea aestuarii	76.0379	68	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011683955.1	s__Pseudomaricurvus alkylphenolicus	75.9874	55	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109735.1	s__Pseudomonas_L hussainii	75.9254	58	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_L	95.0	95.93	95.93	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:11:32,993] [INFO] GTDB search result was written to OceanDNA-b41451/result_gtdb.tsv
[2023-03-18 03:11:32,993] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:11:32,994] [INFO] DFAST_QC result json was written to OceanDNA-b41451/dqc_result.json
[2023-03-18 03:11:32,994] [INFO] DFAST_QC completed!
[2023-03-18 03:11:32,995] [INFO] Total running time: 0h1m58s