[2023-03-15 10:21:46,236] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,236] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f622bbb-7848-4ad2-a828-70643b1f0b28/dqc_reference
[2023-03-15 10:21:47,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,933] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,933] [INFO] Running command: cat /var/lib/cwl/stg65fd28de-5857-4e40-bbb5-3ed935f4be45/OceanDNA-b3969.fa | prodigal -d OceanDNA-b3969/cds.fna -a OceanDNA-b3969/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:22:03,114] [INFO] Task succeeded: Prodigal
[2023-03-15 10:22:03,114] [INFO] Task started: HMMsearch
[2023-03-15 10:22:03,114] [INFO] Running command: hmmsearch --tblout OceanDNA-b3969/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f622bbb-7848-4ad2-a828-70643b1f0b28/dqc_reference/reference_markers.hmm OceanDNA-b3969/protein.faa > /dev/null
[2023-03-15 10:22:03,361] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:22:03,362] [INFO] Found 6/6 markers.
[2023-03-15 10:22:03,379] [INFO] Query marker FASTA was written to OceanDNA-b3969/markers.fasta
[2023-03-15 10:22:03,381] [INFO] Task started: Blastn
[2023-03-15 10:22:03,381] [INFO] Running command: blastn -query OceanDNA-b3969/markers.fasta -db /var/lib/cwl/stg9f622bbb-7848-4ad2-a828-70643b1f0b28/dqc_reference/reference_markers.fasta -out OceanDNA-b3969/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:03,964] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:03,965] [INFO] Selected 19 target genomes.
[2023-03-15 10:22:03,965] [INFO] Target genome list was writen to OceanDNA-b3969/target_genomes.txt
[2023-03-15 10:22:03,999] [INFO] Task started: fastANI
[2023-03-15 10:22:03,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg65fd28de-5857-4e40-bbb5-3ed935f4be45/OceanDNA-b3969.fa --refList OceanDNA-b3969/target_genomes.txt --output OceanDNA-b3969/fastani_result.tsv --threads 1
[2023-03-15 10:22:18,379] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:18,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f622bbb-7848-4ad2-a828-70643b1f0b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:18,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f622bbb-7848-4ad2-a828-70643b1f0b28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:18,389] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:18,389] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:22:18,389] [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 mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	77.9093	97	510	95	below_threshold
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	77.6823	90	510	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	77.6483	85	510	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	77.6391	141	510	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	77.4916	90	510	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	77.4718	114	510	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	77.4337	97	510	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	77.3661	97	510	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	77.1289	110	510	95	below_threshold
Algoriphagus marincola	strain=DSM 16067	GCA_000429405.1	264027	264027	type	True	76.9837	63	510	95	below_threshold
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	76.9753	63	510	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	76.9395	94	510	95	below_threshold
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	76.9195	69	510	95	below_threshold
Algoriphagus kandeliae	strain=XY-J91	GCA_004571135.1	2562278	2562278	type	True	76.7774	60	510	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	76.7162	69	510	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:22:18,389] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3969/tc_result.tsv
[2023-03-15 10:22:18,389] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:18,389] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:18,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f622bbb-7848-4ad2-a828-70643b1f0b28/dqc_reference/checkm_data
[2023-03-15 10:22:18,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:18,394] [INFO] Task started: CheckM
[2023-03-15 10:22:18,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3969/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3969/checkm_input OceanDNA-b3969/checkm_result
[2023-03-15 10:23:00,194] [INFO] Task succeeded: CheckM
[2023-03-15 10:23:00,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:23:00,197] [INFO] ===== Completeness check finished =====
[2023-03-15 10:23:00,197] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:23:00,198] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3969/markers.fasta)
[2023-03-15 10:23:00,198] [INFO] Task started: Blastn
[2023-03-15 10:23:00,198] [INFO] Running command: blastn -query OceanDNA-b3969/markers.fasta -db /var/lib/cwl/stg9f622bbb-7848-4ad2-a828-70643b1f0b28/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3969/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:23:01,027] [INFO] Task succeeded: Blastn
[2023-03-15 10:23:01,028] [INFO] Selected 22 target genomes.
[2023-03-15 10:23:01,028] [INFO] Target genome list was writen to OceanDNA-b3969/target_genomes_gtdb.txt
[2023-03-15 10:23:02,098] [INFO] Task started: fastANI
[2023-03-15 10:23:02,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg65fd28de-5857-4e40-bbb5-3ed935f4be45/OceanDNA-b3969.fa --refList OceanDNA-b3969/target_genomes_gtdb.txt --output OceanDNA-b3969/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:23:17,275] [INFO] Task succeeded: fastANI
[2023-03-15 10:23:17,284] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:23:17,284] [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_005788235.1	s__Algoriphagus sp005788235	88.4296	377	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903952135.1	s__Algoriphagus sp903952135	84.3323	406	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.47	99.47	0.91	0.91	2	-
GCA_016866385.1	s__Algoriphagus sp016866385	80.2935	203	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	77.6419	138	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253485.1	s__Algoriphagus aquaeductus	77.6391	141	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	77.5077	141	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583985.1	s__Algoriphagus lacus	77.4718	114	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103735.1	s__Algoriphagus alkaliphilus	77.4337	97	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCF_004362805.1	s__Algoriphagus boseongensis	77.3661	97	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259255.1	s__Algoriphagus litoralis	77.129	110	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429405.1	s__Algoriphagus marincola	76.9837	63	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.35	97.35	0.90	0.90	2	-
GCA_013373065.1	s__Algoriphagus sp013373065	76.9675	51	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807035.1	s__Algoriphagus formosus	76.9195	69	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCF_004571135.1	s__Algoriphagus kandeliae	76.7774	60	510	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:23:17,284] [INFO] GTDB search result was written to OceanDNA-b3969/result_gtdb.tsv
[2023-03-15 10:23:17,285] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:23:17,286] [INFO] DFAST_QC result json was written to OceanDNA-b3969/dqc_result.json
[2023-03-15 10:23:17,286] [INFO] DFAST_QC completed!
[2023-03-15 10:23:17,286] [INFO] Total running time: 0h1m31s