[2023-03-17 05:16:57,860] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:57,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:57,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg82b5b7c5-1768-47e1-9be0-4167b9b7cbd6/dqc_reference
[2023-03-17 05:16:59,366] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,367] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,367] [INFO] Running command: cat /var/lib/cwl/stg78718c74-bf92-4ed8-9fed-594d5dc3af14/OceanDNA-b4111.fa | prodigal -d OceanDNA-b4111/cds.fna -a OceanDNA-b4111/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:23,690] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:23,691] [INFO] Task started: HMMsearch
[2023-03-17 05:17:23,691] [INFO] Running command: hmmsearch --tblout OceanDNA-b4111/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82b5b7c5-1768-47e1-9be0-4167b9b7cbd6/dqc_reference/reference_markers.hmm OceanDNA-b4111/protein.faa > /dev/null
[2023-03-17 05:17:23,884] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:23,885] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg78718c74-bf92-4ed8-9fed-594d5dc3af14/OceanDNA-b4111.fa]
[2023-03-17 05:17:23,908] [INFO] Query marker FASTA was written to OceanDNA-b4111/markers.fasta
[2023-03-17 05:17:23,909] [INFO] Task started: Blastn
[2023-03-17 05:17:23,909] [INFO] Running command: blastn -query OceanDNA-b4111/markers.fasta -db /var/lib/cwl/stg82b5b7c5-1768-47e1-9be0-4167b9b7cbd6/dqc_reference/reference_markers.fasta -out OceanDNA-b4111/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:24,433] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:24,434] [INFO] Selected 21 target genomes.
[2023-03-17 05:17:24,434] [INFO] Target genome list was writen to OceanDNA-b4111/target_genomes.txt
[2023-03-17 05:17:24,635] [INFO] Task started: fastANI
[2023-03-17 05:17:24,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg78718c74-bf92-4ed8-9fed-594d5dc3af14/OceanDNA-b4111.fa --refList OceanDNA-b4111/target_genomes.txt --output OceanDNA-b4111/fastani_result.tsv --threads 1
[2023-03-17 05:17:40,063] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:40,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82b5b7c5-1768-47e1-9be0-4167b9b7cbd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:40,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82b5b7c5-1768-47e1-9be0-4167b9b7cbd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:40,068] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:17:40,068] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:17:40,068] [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
Marivirga tractuosa	strain=DSM 4126	GCA_000183425.1	1006	1006	type	True	83.6016	896	1237	95	below_threshold
Marivirga sericea	strain=DSM 4125	GCA_900177665.1	1028	1028	type	True	80.1579	664	1237	95	below_threshold
Marivirga atlantica	strain=SM1354	GCA_016734805.1	1548457	1548457	type	True	76.812	140	1237	95	below_threshold
Marivirga lumbricoides	strain=CGMCC 1.10832	GCA_014636295.1	1046115	1046115	type	True	76.4736	189	1237	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:17:40,068] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4111/tc_result.tsv
[2023-03-17 05:17:40,068] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:40,068] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:40,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82b5b7c5-1768-47e1-9be0-4167b9b7cbd6/dqc_reference/checkm_data
[2023-03-17 05:17:40,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:40,135] [INFO] Task started: CheckM
[2023-03-17 05:17:40,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4111/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4111/checkm_input OceanDNA-b4111/checkm_result
[2023-03-17 05:18:41,151] [INFO] Task succeeded: CheckM
[2023-03-17 05:18:41,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:18:41,156] [INFO] ===== Completeness check finished =====
[2023-03-17 05:18:41,156] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:18:41,156] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4111/markers.fasta)
[2023-03-17 05:18:41,156] [INFO] Task started: Blastn
[2023-03-17 05:18:41,156] [INFO] Running command: blastn -query OceanDNA-b4111/markers.fasta -db /var/lib/cwl/stg82b5b7c5-1768-47e1-9be0-4167b9b7cbd6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4111/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:18:41,886] [INFO] Task succeeded: Blastn
[2023-03-17 05:18:41,888] [INFO] Selected 13 target genomes.
[2023-03-17 05:18:41,888] [INFO] Target genome list was writen to OceanDNA-b4111/target_genomes_gtdb.txt
[2023-03-17 05:18:42,165] [INFO] Task started: fastANI
[2023-03-17 05:18:42,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg78718c74-bf92-4ed8-9fed-594d5dc3af14/OceanDNA-b4111.fa --refList OceanDNA-b4111/target_genomes_gtdb.txt --output OceanDNA-b4111/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:18:51,241] [INFO] Task succeeded: fastANI
[2023-03-17 05:18:51,246] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:18:51,246] [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_003973485.1	s__Marivirga sp003973485	83.8704	678	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183425.1	s__Marivirga tractuosa	83.5872	897	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177665.1	s__Marivirga sericea	80.1579	664	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734805.1	s__Marivirga atlantica	76.812	140	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016679925.1	s__Marivirga sp016679925	76.8083	213	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636295.1	s__Marivirga lumbricoides	76.4745	190	1237	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	97.82	97.82	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:18:51,247] [INFO] GTDB search result was written to OceanDNA-b4111/result_gtdb.tsv
[2023-03-17 05:18:51,249] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:18:51,251] [INFO] DFAST_QC result json was written to OceanDNA-b4111/dqc_result.json
[2023-03-17 05:18:51,251] [INFO] DFAST_QC completed!
[2023-03-17 05:18:51,251] [INFO] Total running time: 0h1m53s