[2023-03-17 00:17:04,440] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,440] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg754b3240-2b13-487d-b1e6-dbeabc4f485d/dqc_reference
[2023-03-17 00:17:05,541] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,541] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,541] [INFO] Running command: cat /var/lib/cwl/stg747c09e3-650f-43a2-a4c0-a705d482c96e/OceanDNA-b13079.fa | prodigal -d OceanDNA-b13079/cds.fna -a OceanDNA-b13079/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:21,851] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:21,851] [INFO] Task started: HMMsearch
[2023-03-17 00:17:21,851] [INFO] Running command: hmmsearch --tblout OceanDNA-b13079/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg754b3240-2b13-487d-b1e6-dbeabc4f485d/dqc_reference/reference_markers.hmm OceanDNA-b13079/protein.faa > /dev/null
[2023-03-17 00:17:21,981] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:21,982] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg747c09e3-650f-43a2-a4c0-a705d482c96e/OceanDNA-b13079.fa]
[2023-03-17 00:17:21,996] [INFO] Query marker FASTA was written to OceanDNA-b13079/markers.fasta
[2023-03-17 00:17:21,996] [INFO] Task started: Blastn
[2023-03-17 00:17:21,996] [INFO] Running command: blastn -query OceanDNA-b13079/markers.fasta -db /var/lib/cwl/stg754b3240-2b13-487d-b1e6-dbeabc4f485d/dqc_reference/reference_markers.fasta -out OceanDNA-b13079/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:22,430] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:22,431] [INFO] Selected 9 target genomes.
[2023-03-17 00:17:22,431] [INFO] Target genome list was writen to OceanDNA-b13079/target_genomes.txt
[2023-03-17 00:17:22,436] [INFO] Task started: fastANI
[2023-03-17 00:17:22,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg747c09e3-650f-43a2-a4c0-a705d482c96e/OceanDNA-b13079.fa --refList OceanDNA-b13079/target_genomes.txt --output OceanDNA-b13079/fastani_result.tsv --threads 1
[2023-03-17 00:17:29,000] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:29,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg754b3240-2b13-487d-b1e6-dbeabc4f485d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:29,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg754b3240-2b13-487d-b1e6-dbeabc4f485d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:29,005] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:29,005] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:17:29,005] [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
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	79.1719	444	716	95	below_threshold
Rubricoccus marinus	strain=SG-29	GCA_002257665.1	716817	716817	type	True	76.8259	264	716	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	74.7291	58	716	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	74.6579	142	716	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:17:29,005] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13079/tc_result.tsv
[2023-03-17 00:17:29,005] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:29,006] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:29,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg754b3240-2b13-487d-b1e6-dbeabc4f485d/dqc_reference/checkm_data
[2023-03-17 00:17:29,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:29,021] [INFO] Task started: CheckM
[2023-03-17 00:17:29,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13079/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13079/checkm_input OceanDNA-b13079/checkm_result
[2023-03-17 00:18:10,291] [INFO] Task succeeded: CheckM
[2023-03-17 00:18:10,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 00:18:10,297] [INFO] ===== Completeness check finished =====
[2023-03-17 00:18:10,297] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:18:10,297] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13079/markers.fasta)
[2023-03-17 00:18:10,298] [INFO] Task started: Blastn
[2023-03-17 00:18:10,298] [INFO] Running command: blastn -query OceanDNA-b13079/markers.fasta -db /var/lib/cwl/stg754b3240-2b13-487d-b1e6-dbeabc4f485d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13079/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:18:10,733] [INFO] Task succeeded: Blastn
[2023-03-17 00:18:10,733] [INFO] Selected 10 target genomes.
[2023-03-17 00:18:10,734] [INFO] Target genome list was writen to OceanDNA-b13079/target_genomes_gtdb.txt
[2023-03-17 00:18:10,747] [INFO] Task started: fastANI
[2023-03-17 00:18:10,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg747c09e3-650f-43a2-a4c0-a705d482c96e/OceanDNA-b13079.fa --refList OceanDNA-b13079/target_genomes_gtdb.txt --output OceanDNA-b13079/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:18:17,679] [INFO] Task succeeded: fastANI
[2023-03-17 00:18:17,683] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:18:17,683] [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_002283365.1	s__Rubrivirga marina	79.2038	441	716	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269805.1	s__Rubrivirga sp012269805	78.8971	321	716	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002283555.1	s__Rubrivirga sp002283555	78.2415	372	716	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubrivirga	95.0	98.32	98.29	0.93	0.92	3	-
GCA_012960515.1	s__Rubricoccus sp012960515	77.1794	230	716	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257665.1	s__Rubricoccus marinus	76.8342	262	716	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Rhodothermales;f__Rubricoccaceae;g__Rubricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003220595.1	s__AR19 sp003220595	74.6361	75	716	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR19	95.0	98.36	98.36	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:18:17,683] [INFO] GTDB search result was written to OceanDNA-b13079/result_gtdb.tsv
[2023-03-17 00:18:17,683] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:18:17,684] [INFO] DFAST_QC result json was written to OceanDNA-b13079/dqc_result.json
[2023-03-17 00:18:17,684] [INFO] DFAST_QC completed!
[2023-03-17 00:18:17,684] [INFO] Total running time: 0h1m13s