[2023-03-15 16:28:44,760] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:28:44,760] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:28:44,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg87588b9d-057e-406d-bf82-4131028e4fd7/dqc_reference
[2023-03-15 16:28:45,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:28:45,895] [INFO] Task started: Prodigal
[2023-03-15 16:28:45,895] [INFO] Running command: cat /var/lib/cwl/stg4d0ca706-0042-4930-a891-9257ad36c31f/OceanDNA-b3980.fa | prodigal -d OceanDNA-b3980/cds.fna -a OceanDNA-b3980/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:29:16,321] [INFO] Task succeeded: Prodigal
[2023-03-15 16:29:16,322] [INFO] Task started: HMMsearch
[2023-03-15 16:29:16,322] [INFO] Running command: hmmsearch --tblout OceanDNA-b3980/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87588b9d-057e-406d-bf82-4131028e4fd7/dqc_reference/reference_markers.hmm OceanDNA-b3980/protein.faa > /dev/null
[2023-03-15 16:29:16,555] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:29:16,556] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4d0ca706-0042-4930-a891-9257ad36c31f/OceanDNA-b3980.fa]
[2023-03-15 16:29:16,592] [INFO] Query marker FASTA was written to OceanDNA-b3980/markers.fasta
[2023-03-15 16:29:16,593] [INFO] Task started: Blastn
[2023-03-15 16:29:16,593] [INFO] Running command: blastn -query OceanDNA-b3980/markers.fasta -db /var/lib/cwl/stg87588b9d-057e-406d-bf82-4131028e4fd7/dqc_reference/reference_markers.fasta -out OceanDNA-b3980/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:29:17,115] [INFO] Task succeeded: Blastn
[2023-03-15 16:29:17,117] [INFO] Selected 12 target genomes.
[2023-03-15 16:29:17,117] [INFO] Target genome list was writen to OceanDNA-b3980/target_genomes.txt
[2023-03-15 16:29:17,124] [INFO] Task started: fastANI
[2023-03-15 16:29:17,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d0ca706-0042-4930-a891-9257ad36c31f/OceanDNA-b3980.fa --refList OceanDNA-b3980/target_genomes.txt --output OceanDNA-b3980/fastani_result.tsv --threads 1
[2023-03-15 16:29:27,700] [INFO] Task succeeded: fastANI
[2023-03-15 16:29:27,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87588b9d-057e-406d-bf82-4131028e4fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:29:27,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87588b9d-057e-406d-bf82-4131028e4fd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:29:27,708] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:29:27,708] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:29:27,708] [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
Algoriphagus locisalis	strain=DSM 23445	GCA_900116615.1	305507	305507	type	True	82.5428	771	1279	95	below_threshold
Algoriphagus yeomjeoni	strain=DSM 23446	GCA_003259505.1	291403	291403	type	True	80.6904	611	1279	95	below_threshold
Algoriphagus aquimarinus	strain=DSM 23399	GCA_900112005.1	237018	237018	type	True	80.4629	617	1279	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	80.2705	603	1279	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_003387655.1	238540	238540	type	True	80.0021	573	1279	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	79.9529	575	1279	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_003254355.1	57028	57028	type	True	79.3699	505	1279	95	below_threshold
Algoriphagus ratkowskyi	strain=DSM 22686	GCA_002150505.1	57028	57028	type	True	79.3494	505	1279	95	below_threshold
Echinicola arenosa	strain=CAU 1574	GCA_014841125.1	2774144	2774144	type	True	75.9073	52	1279	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:29:27,708] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3980/tc_result.tsv
[2023-03-15 16:29:27,708] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:29:27,709] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:29:27,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87588b9d-057e-406d-bf82-4131028e4fd7/dqc_reference/checkm_data
[2023-03-15 16:29:27,709] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:29:27,729] [INFO] Task started: CheckM
[2023-03-15 16:29:27,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3980/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3980/checkm_input OceanDNA-b3980/checkm_result
[2023-03-15 16:30:48,032] [INFO] Task succeeded: CheckM
[2023-03-15 16:30:48,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.00%
Contamintation: 13.89%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 16:30:48,042] [INFO] ===== Completeness check finished =====
[2023-03-15 16:30:48,042] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:30:48,042] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3980/markers.fasta)
[2023-03-15 16:30:48,044] [INFO] Task started: Blastn
[2023-03-15 16:30:48,044] [INFO] Running command: blastn -query OceanDNA-b3980/markers.fasta -db /var/lib/cwl/stg87588b9d-057e-406d-bf82-4131028e4fd7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3980/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:30:48,885] [INFO] Task succeeded: Blastn
[2023-03-15 16:30:48,886] [INFO] Selected 9 target genomes.
[2023-03-15 16:30:48,886] [INFO] Target genome list was writen to OceanDNA-b3980/target_genomes_gtdb.txt
[2023-03-15 16:30:48,924] [INFO] Task started: fastANI
[2023-03-15 16:30:48,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d0ca706-0042-4930-a891-9257ad36c31f/OceanDNA-b3980.fa --refList OceanDNA-b3980/target_genomes_gtdb.txt --output OceanDNA-b3980/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:30:58,595] [INFO] Task succeeded: fastANI
[2023-03-15 16:30:58,601] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:30:58,601] [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_900116615.1	s__Algoriphagus locisalis	82.5248	773	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997215.1	s__Algoriphagus aquimarinus_A	80.716	652	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259505.1	s__Algoriphagus yeomjeoni	80.6904	611	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112005.1	s__Algoriphagus aquimarinus	80.4728	616	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	80.2609	604	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150685.1	s__Algoriphagus antarcticus	79.9627	574	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014838715.1	s__Algoriphagus sp014838715	79.7687	584	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442615.1	s__Algoriphagus resistens	79.7075	598	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150505.1	s__Algoriphagus ratkowskyi	79.34	506	1279	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-15 16:30:58,601] [INFO] GTDB search result was written to OceanDNA-b3980/result_gtdb.tsv
[2023-03-15 16:30:58,601] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:30:58,602] [INFO] DFAST_QC result json was written to OceanDNA-b3980/dqc_result.json
[2023-03-15 16:30:58,602] [INFO] DFAST_QC completed!
[2023-03-15 16:30:58,602] [INFO] Total running time: 0h2m14s