[2023-03-14 10:56:00,375] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:56:00,375] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:56:00,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b67ef62-64fa-440d-8bfb-17e73acb4384/dqc_reference
[2023-03-14 10:56:01,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:01,549] [INFO] Task started: Prodigal
[2023-03-14 10:56:01,549] [INFO] Running command: cat /var/lib/cwl/stg1f9dc3ad-8b36-40c0-ab51-471a4c3869d5/OceanDNA-b4114.fa | prodigal -d OceanDNA-b4114/cds.fna -a OceanDNA-b4114/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:25,467] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:25,467] [INFO] Task started: HMMsearch
[2023-03-14 10:56:25,467] [INFO] Running command: hmmsearch --tblout OceanDNA-b4114/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b67ef62-64fa-440d-8bfb-17e73acb4384/dqc_reference/reference_markers.hmm OceanDNA-b4114/protein.faa > /dev/null
[2023-03-14 10:56:25,770] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:25,771] [INFO] Found 6/6 markers.
[2023-03-14 10:56:25,790] [INFO] Query marker FASTA was written to OceanDNA-b4114/markers.fasta
[2023-03-14 10:56:25,791] [INFO] Task started: Blastn
[2023-03-14 10:56:25,791] [INFO] Running command: blastn -query OceanDNA-b4114/markers.fasta -db /var/lib/cwl/stg9b67ef62-64fa-440d-8bfb-17e73acb4384/dqc_reference/reference_markers.fasta -out OceanDNA-b4114/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:26,349] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:26,350] [INFO] Selected 24 target genomes.
[2023-03-14 10:56:26,350] [INFO] Target genome list was writen to OceanDNA-b4114/target_genomes.txt
[2023-03-14 10:56:26,366] [INFO] Task started: fastANI
[2023-03-14 10:56:26,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f9dc3ad-8b36-40c0-ab51-471a4c3869d5/OceanDNA-b4114.fa --refList OceanDNA-b4114/target_genomes.txt --output OceanDNA-b4114/fastani_result.tsv --threads 1
[2023-03-14 10:56:44,642] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:44,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b67ef62-64fa-440d-8bfb-17e73acb4384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:44,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b67ef62-64fa-440d-8bfb-17e73acb4384/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:44,647] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:44,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:44,647] [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	85.4445	954	1210	95	below_threshold
Marivirga sericea	strain=DSM 4125	GCA_900177665.1	1028	1028	type	True	80.6009	671	1210	95	below_threshold
Marivirga lumbricoides	strain=CGMCC 1.10832	GCA_014636295.1	1046115	1046115	type	True	76.8392	201	1210	95	below_threshold
Marivirga atlantica	strain=SM1354	GCA_016734805.1	1548457	1548457	type	True	76.5693	162	1210	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:44,647] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4114/tc_result.tsv
[2023-03-14 10:56:44,647] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:44,648] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:44,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b67ef62-64fa-440d-8bfb-17e73acb4384/dqc_reference/checkm_data
[2023-03-14 10:56:44,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:44,654] [INFO] Task started: CheckM
[2023-03-14 10:56:44,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4114/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4114/checkm_input OceanDNA-b4114/checkm_result
[2023-03-14 10:57:44,002] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:44,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:44,005] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:44,005] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:44,005] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4114/markers.fasta)
[2023-03-14 10:57:44,005] [INFO] Task started: Blastn
[2023-03-14 10:57:44,005] [INFO] Running command: blastn -query OceanDNA-b4114/markers.fasta -db /var/lib/cwl/stg9b67ef62-64fa-440d-8bfb-17e73acb4384/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4114/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:44,753] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:44,754] [INFO] Selected 15 target genomes.
[2023-03-14 10:57:44,754] [INFO] Target genome list was writen to OceanDNA-b4114/target_genomes_gtdb.txt
[2023-03-14 10:57:44,771] [INFO] Task started: fastANI
[2023-03-14 10:57:44,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f9dc3ad-8b36-40c0-ab51-471a4c3869d5/OceanDNA-b4114.fa --refList OceanDNA-b4114/target_genomes_gtdb.txt --output OceanDNA-b4114/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:56,245] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:56,250] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 10:57:56,250] [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	97.412	787	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000183425.1	s__Marivirga tractuosa	85.4445	954	1210	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	80.6192	669	1210	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	77.1338	226	1210	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	76.8615	199	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	97.82	97.82	0.87	0.87	2	-
GCF_016734805.1	s__Marivirga atlantica	76.5693	162	1210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:56,250] [INFO] GTDB search result was written to OceanDNA-b4114/result_gtdb.tsv
[2023-03-14 10:57:56,250] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:56,251] [INFO] DFAST_QC result json was written to OceanDNA-b4114/dqc_result.json
[2023-03-14 10:57:56,251] [INFO] DFAST_QC completed!
[2023-03-14 10:57:56,251] [INFO] Total running time: 0h1m56s