[2023-03-15 11:24:11,468] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:24:11,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:24:11,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bb3946f-7aa8-495b-9c53-c1997337b948/dqc_reference
[2023-03-15 11:24:12,580] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:24:12,580] [INFO] Task started: Prodigal
[2023-03-15 11:24:12,580] [INFO] Running command: cat /var/lib/cwl/stgf6300548-1714-4d77-b718-383e1edb0373/OceanDNA-b3674.fa | prodigal -d OceanDNA-b3674/cds.fna -a OceanDNA-b3674/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:24:31,722] [INFO] Task succeeded: Prodigal
[2023-03-15 11:24:31,723] [INFO] Task started: HMMsearch
[2023-03-15 11:24:31,723] [INFO] Running command: hmmsearch --tblout OceanDNA-b3674/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bb3946f-7aa8-495b-9c53-c1997337b948/dqc_reference/reference_markers.hmm OceanDNA-b3674/protein.faa > /dev/null
[2023-03-15 11:24:31,939] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:24:31,939] [INFO] Found 6/6 markers.
[2023-03-15 11:24:31,958] [INFO] Query marker FASTA was written to OceanDNA-b3674/markers.fasta
[2023-03-15 11:24:31,958] [INFO] Task started: Blastn
[2023-03-15 11:24:31,958] [INFO] Running command: blastn -query OceanDNA-b3674/markers.fasta -db /var/lib/cwl/stg7bb3946f-7aa8-495b-9c53-c1997337b948/dqc_reference/reference_markers.fasta -out OceanDNA-b3674/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:32,499] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:32,500] [INFO] Selected 30 target genomes.
[2023-03-15 11:24:32,500] [INFO] Target genome list was writen to OceanDNA-b3674/target_genomes.txt
[2023-03-15 11:24:32,514] [INFO] Task started: fastANI
[2023-03-15 11:24:32,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6300548-1714-4d77-b718-383e1edb0373/OceanDNA-b3674.fa --refList OceanDNA-b3674/target_genomes.txt --output OceanDNA-b3674/fastani_result.tsv --threads 1
[2023-03-15 11:24:53,310] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:53,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bb3946f-7aa8-495b-9c53-c1997337b948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:24:53,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bb3946f-7aa8-495b-9c53-c1997337b948/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:24:53,316] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:24:53,316] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:24:53,316] [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
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	76.2063	64	682	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	76.1592	66	682	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	75.6692	50	682	95	below_threshold
Hymenobacter caeli	strain=9A	GCA_013294115.1	2735894	2735894	type	True	75.6585	52	682	95	below_threshold
Hymenobacter ruricola	strain=BT662	GCA_015694525.1	2791023	2791023	type	True	75.4172	54	682	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	74.7733	70	682	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	74.7409	107	682	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:24:53,317] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3674/tc_result.tsv
[2023-03-15 11:24:53,317] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:24:53,317] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:24:53,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bb3946f-7aa8-495b-9c53-c1997337b948/dqc_reference/checkm_data
[2023-03-15 11:24:53,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:24:53,389] [INFO] Task started: CheckM
[2023-03-15 11:24:53,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3674/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3674/checkm_input OceanDNA-b3674/checkm_result
[2023-03-15 11:25:41,706] [INFO] Task succeeded: CheckM
[2023-03-15 11:25:41,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:25:41,710] [INFO] ===== Completeness check finished =====
[2023-03-15 11:25:41,710] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:25:41,710] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3674/markers.fasta)
[2023-03-15 11:25:41,711] [INFO] Task started: Blastn
[2023-03-15 11:25:41,712] [INFO] Running command: blastn -query OceanDNA-b3674/markers.fasta -db /var/lib/cwl/stg7bb3946f-7aa8-495b-9c53-c1997337b948/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3674/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:25:42,532] [INFO] Task succeeded: Blastn
[2023-03-15 11:25:42,534] [INFO] Selected 34 target genomes.
[2023-03-15 11:25:42,534] [INFO] Target genome list was writen to OceanDNA-b3674/target_genomes_gtdb.txt
[2023-03-15 11:25:42,572] [INFO] Task started: fastANI
[2023-03-15 11:25:42,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6300548-1714-4d77-b718-383e1edb0373/OceanDNA-b3674.fa --refList OceanDNA-b3674/target_genomes_gtdb.txt --output OceanDNA-b3674/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:26:01,255] [INFO] Task succeeded: fastANI
[2023-03-15 11:26:01,259] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:26:01,259] [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_002631205.1	s__Lewinella_A marina	76.1592	66	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004803465.1	s__Lewinella_A litorea	75.6692	50	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294115.1	s__Hymenobacter caeli	75.6595	52	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390915.1	s__Lewinella_A sp003390915	75.5483	57	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686995.1	s__GCA-2686995 sp002686995	74.8352	51	682	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__GCA-2686995	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:26:01,260] [INFO] GTDB search result was written to OceanDNA-b3674/result_gtdb.tsv
[2023-03-15 11:26:01,263] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:26:01,265] [INFO] DFAST_QC result json was written to OceanDNA-b3674/dqc_result.json
[2023-03-15 11:26:01,265] [INFO] DFAST_QC completed!
[2023-03-15 11:26:01,265] [INFO] Total running time: 0h1m50s