[2023-03-17 09:05:02,629] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,630] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,630] [INFO] DQC Reference Directory: /var/lib/cwl/stga1e8198e-a831-4818-be0f-b8fa6ced6bd2/dqc_reference
[2023-03-17 09:05:03,784] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,785] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,785] [INFO] Running command: cat /var/lib/cwl/stge395ff46-d99e-4f1b-a1a3-f684cbfdff6d/OceanDNA-b4099.fa | prodigal -d OceanDNA-b4099/cds.fna -a OceanDNA-b4099/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:15,818] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:15,818] [INFO] Task started: HMMsearch
[2023-03-17 09:05:15,818] [INFO] Running command: hmmsearch --tblout OceanDNA-b4099/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1e8198e-a831-4818-be0f-b8fa6ced6bd2/dqc_reference/reference_markers.hmm OceanDNA-b4099/protein.faa > /dev/null
[2023-03-17 09:05:16,001] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:16,002] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge395ff46-d99e-4f1b-a1a3-f684cbfdff6d/OceanDNA-b4099.fa]
[2023-03-17 09:05:16,023] [INFO] Query marker FASTA was written to OceanDNA-b4099/markers.fasta
[2023-03-17 09:05:16,024] [INFO] Task started: Blastn
[2023-03-17 09:05:16,024] [INFO] Running command: blastn -query OceanDNA-b4099/markers.fasta -db /var/lib/cwl/stga1e8198e-a831-4818-be0f-b8fa6ced6bd2/dqc_reference/reference_markers.fasta -out OceanDNA-b4099/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:16,531] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:16,532] [INFO] Selected 12 target genomes.
[2023-03-17 09:05:16,532] [INFO] Target genome list was writen to OceanDNA-b4099/target_genomes.txt
[2023-03-17 09:05:16,570] [INFO] Task started: fastANI
[2023-03-17 09:05:16,570] [INFO] Running command: fastANI --query /var/lib/cwl/stge395ff46-d99e-4f1b-a1a3-f684cbfdff6d/OceanDNA-b4099.fa --refList OceanDNA-b4099/target_genomes.txt --output OceanDNA-b4099/fastani_result.tsv --threads 1
[2023-03-17 09:05:24,514] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:24,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1e8198e-a831-4818-be0f-b8fa6ced6bd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:24,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1e8198e-a831-4818-be0f-b8fa6ced6bd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:24,519] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 09:05:24,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 09:05:24,520] [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
Roseivirga spongicola	strain=UST030701-084	GCA_001592965.1	333140	333140	type	True	98.691	296	297	95	conclusive
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	79.0399	67	297	95	below_threshold
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	78.7683	66	297	95	below_threshold
Roseivirga thermotolerans	strain=CGMCC 1.15111	GCA_014653175.1	1758176	1758176	type	True	78.122	85	297	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:05:24,520] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4099/tc_result.tsv
[2023-03-17 09:05:24,520] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:24,520] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:24,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1e8198e-a831-4818-be0f-b8fa6ced6bd2/dqc_reference/checkm_data
[2023-03-17 09:05:24,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:24,561] [INFO] Task started: CheckM
[2023-03-17 09:05:24,561] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4099/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4099/checkm_input OceanDNA-b4099/checkm_result
[2023-03-17 09:06:00,197] [INFO] Task succeeded: CheckM
[2023-03-17 09:06:00,198] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.00%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:06:00,200] [INFO] ===== Completeness check finished =====
[2023-03-17 09:06:00,201] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:06:00,201] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4099/markers.fasta)
[2023-03-17 09:06:00,202] [INFO] Task started: Blastn
[2023-03-17 09:06:00,202] [INFO] Running command: blastn -query OceanDNA-b4099/markers.fasta -db /var/lib/cwl/stga1e8198e-a831-4818-be0f-b8fa6ced6bd2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4099/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:06:00,863] [INFO] Task succeeded: Blastn
[2023-03-17 09:06:00,864] [INFO] Selected 17 target genomes.
[2023-03-17 09:06:00,864] [INFO] Target genome list was writen to OceanDNA-b4099/target_genomes_gtdb.txt
[2023-03-17 09:06:00,898] [INFO] Task started: fastANI
[2023-03-17 09:06:00,898] [INFO] Running command: fastANI --query /var/lib/cwl/stge395ff46-d99e-4f1b-a1a3-f684cbfdff6d/OceanDNA-b4099.fa --refList OceanDNA-b4099/target_genomes_gtdb.txt --output OceanDNA-b4099/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:06:11,560] [INFO] Task succeeded: fastANI
[2023-03-17 09:06:11,564] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:06:11,564] [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_001592965.1	s__Fabibacter spongicola	98.691	296	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	conclusive
GCF_900111145.1	s__Fabibacter pacificus	79.0399	67	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013373005.1	s__Fabibacter sp013373005	78.7689	141	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653175.1	s__Fabibacter thermotolerans	78.1656	84	297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	98.67	98.61	0.92	0.91	4	-
--------------------------------------------------------------------------------
[2023-03-17 09:06:11,564] [INFO] GTDB search result was written to OceanDNA-b4099/result_gtdb.tsv
[2023-03-17 09:06:11,564] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:06:11,565] [INFO] DFAST_QC result json was written to OceanDNA-b4099/dqc_result.json
[2023-03-17 09:06:11,565] [INFO] DFAST_QC completed!
[2023-03-17 09:06:11,565] [INFO] Total running time: 0h1m9s