[2023-03-16 23:05:03,913] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,913] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,913] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fd7bbae-3527-49b5-9236-1437c5f2457f/dqc_reference
[2023-03-16 23:05:05,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stge5187ad4-4b44-4358-ae3b-8a78712e6630/OceanDNA-b40104.fa | prodigal -d OceanDNA-b40104/cds.fna -a OceanDNA-b40104/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:21,763] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:21,764] [INFO] Task started: HMMsearch
[2023-03-16 23:05:21,764] [INFO] Running command: hmmsearch --tblout OceanDNA-b40104/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fd7bbae-3527-49b5-9236-1437c5f2457f/dqc_reference/reference_markers.hmm OceanDNA-b40104/protein.faa > /dev/null
[2023-03-16 23:05:22,007] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:22,007] [INFO] Found 6/6 markers.
[2023-03-16 23:05:22,025] [INFO] Query marker FASTA was written to OceanDNA-b40104/markers.fasta
[2023-03-16 23:05:22,025] [INFO] Task started: Blastn
[2023-03-16 23:05:22,025] [INFO] Running command: blastn -query OceanDNA-b40104/markers.fasta -db /var/lib/cwl/stg9fd7bbae-3527-49b5-9236-1437c5f2457f/dqc_reference/reference_markers.fasta -out OceanDNA-b40104/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:22,648] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:22,649] [INFO] Selected 26 target genomes.
[2023-03-16 23:05:22,649] [INFO] Target genome list was writen to OceanDNA-b40104/target_genomes.txt
[2023-03-16 23:05:22,661] [INFO] Task started: fastANI
[2023-03-16 23:05:22,662] [INFO] Running command: fastANI --query /var/lib/cwl/stge5187ad4-4b44-4358-ae3b-8a78712e6630/OceanDNA-b40104.fa --refList OceanDNA-b40104/target_genomes.txt --output OceanDNA-b40104/fastani_result.tsv --threads 1
[2023-03-16 23:05:40,427] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:40,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fd7bbae-3527-49b5-9236-1437c5f2457f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:40,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fd7bbae-3527-49b5-9236-1437c5f2457f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:40,431] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:40,431] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:40,431] [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
Porticoccus hydrocarbonoclasticus	strain=MCTG13d	GCA_000744735.1	1073414	1073414	type	True	94.6026	766	882	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	75.721	56	882	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:40,431] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40104/tc_result.tsv
[2023-03-16 23:05:40,432] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:40,432] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:40,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fd7bbae-3527-49b5-9236-1437c5f2457f/dqc_reference/checkm_data
[2023-03-16 23:05:40,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:40,437] [INFO] Task started: CheckM
[2023-03-16 23:05:40,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40104/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40104/checkm_input OceanDNA-b40104/checkm_result
[2023-03-16 23:06:23,943] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:23,944] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:23,946] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:23,946] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:23,947] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40104/markers.fasta)
[2023-03-16 23:06:23,947] [INFO] Task started: Blastn
[2023-03-16 23:06:23,947] [INFO] Running command: blastn -query OceanDNA-b40104/markers.fasta -db /var/lib/cwl/stg9fd7bbae-3527-49b5-9236-1437c5f2457f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40104/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:25,077] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:25,078] [INFO] Selected 11 target genomes.
[2023-03-16 23:06:25,078] [INFO] Target genome list was writen to OceanDNA-b40104/target_genomes_gtdb.txt
[2023-03-16 23:06:25,359] [INFO] Task started: fastANI
[2023-03-16 23:06:25,359] [INFO] Running command: fastANI --query /var/lib/cwl/stge5187ad4-4b44-4358-ae3b-8a78712e6630/OceanDNA-b40104.fa --refList OceanDNA-b40104/target_genomes_gtdb.txt --output OceanDNA-b40104/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:06:31,593] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:31,599] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:06:31,599] [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_002341315.1	s__Porticoccus sp002341315	97.6968	762	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000744735.1	s__Porticoccus hydrocarbonoclasticus	94.6026	766	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.20	98.73	0.89	0.78	4	-
GCA_002707685.1	s__Porticoccus sp002707685	94.5208	762	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	99.58	99.58	0.96	0.96	2	-
GCA_002733125.1	s__Porticoccus sp002733125	93.1501	629	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226995.1	s__Porticoccus sp006226995	77.5353	94	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961645.1	s__BRH-c0 sp000961645	76.9752	68	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__BRH-c0	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227015.1	s__Porticoccus sp006227015	76.8064	89	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746985.1	s__Porticoccus sp002746985	76.3173	75	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	97.07	97.07	0.91	0.91	2	-
GCF_011440395.1	s__Pseudomaricurvus alcaniphilus	75.7384	57	882	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	98.35	98.35	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-16 23:06:31,599] [INFO] GTDB search result was written to OceanDNA-b40104/result_gtdb.tsv
[2023-03-16 23:06:31,599] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:06:31,600] [INFO] DFAST_QC result json was written to OceanDNA-b40104/dqc_result.json
[2023-03-16 23:06:31,600] [INFO] DFAST_QC completed!
[2023-03-16 23:06:31,601] [INFO] Total running time: 0h1m28s