[2023-03-14 11:49:37,365] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:37,367] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:37,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg44cd5a44-a072-4c9c-8066-3625cb4d76ba/dqc_reference
[2023-03-14 11:49:38,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:38,963] [INFO] Task started: Prodigal
[2023-03-14 11:49:38,963] [INFO] Running command: cat /var/lib/cwl/stg7bafb29a-234b-40ae-a390-b87be8030161/OceanDNA-b4004.fa | prodigal -d OceanDNA-b4004/cds.fna -a OceanDNA-b4004/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:50:13,920] [INFO] Task succeeded: Prodigal
[2023-03-14 11:50:13,920] [INFO] Task started: HMMsearch
[2023-03-14 11:50:13,920] [INFO] Running command: hmmsearch --tblout OceanDNA-b4004/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44cd5a44-a072-4c9c-8066-3625cb4d76ba/dqc_reference/reference_markers.hmm OceanDNA-b4004/protein.faa > /dev/null
[2023-03-14 11:50:14,167] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:50:14,167] [INFO] Found 6/6 markers.
[2023-03-14 11:50:14,212] [INFO] Query marker FASTA was written to OceanDNA-b4004/markers.fasta
[2023-03-14 11:50:14,214] [INFO] Task started: Blastn
[2023-03-14 11:50:14,214] [INFO] Running command: blastn -query OceanDNA-b4004/markers.fasta -db /var/lib/cwl/stg44cd5a44-a072-4c9c-8066-3625cb4d76ba/dqc_reference/reference_markers.fasta -out OceanDNA-b4004/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:50:14,753] [INFO] Task succeeded: Blastn
[2023-03-14 11:50:14,784] [INFO] Selected 19 target genomes.
[2023-03-14 11:50:14,784] [INFO] Target genome list was writen to OceanDNA-b4004/target_genomes.txt
[2023-03-14 11:50:14,799] [INFO] Task started: fastANI
[2023-03-14 11:50:14,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bafb29a-234b-40ae-a390-b87be8030161/OceanDNA-b4004.fa --refList OceanDNA-b4004/target_genomes.txt --output OceanDNA-b4004/fastani_result.tsv --threads 1
[2023-03-14 11:50:30,339] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:30,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44cd5a44-a072-4c9c-8066-3625cb4d76ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:50:30,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44cd5a44-a072-4c9c-8066-3625cb4d76ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:50:30,347] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:50:30,347] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:50:30,347] [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
Cyclobacterium marinum	strain=DSM 745	GCA_000222485.1	104	104	type	True	86.1917	1371	1553	95	below_threshold
Cyclobacterium amurskyense	strain=KCTC 12363	GCA_001050135.1	320787	320787	type	True	81.0963	922	1553	95	below_threshold
Cyclobacterium qasimii	strain=NBRC 106168	GCA_007991695.1	1350429	1350429	type	True	79.8273	883	1553	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	79.7892	875	1553	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	77.1867	283	1553	95	below_threshold
Cyclobacterium jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	77.1049	219	1553	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	77.0515	204	1553	95	below_threshold
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	76.1603	101	1553	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	75.8999	63	1553	95	below_threshold
Algoriphagus antarcticus	strain=DSM 15986	GCA_002150685.1	238540	238540	type	True	75.5053	51	1553	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:50:30,350] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4004/tc_result.tsv
[2023-03-14 11:50:30,353] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:50:30,353] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:50:30,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44cd5a44-a072-4c9c-8066-3625cb4d76ba/dqc_reference/checkm_data
[2023-03-14 11:50:30,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:50:30,418] [INFO] Task started: CheckM
[2023-03-14 11:50:30,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4004/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4004/checkm_input OceanDNA-b4004/checkm_result
[2023-03-14 11:51:56,028] [INFO] Task succeeded: CheckM
[2023-03-14 11:51:56,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.76%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 11:51:56,178] [INFO] ===== Completeness check finished =====
[2023-03-14 11:51:56,178] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:51:56,178] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4004/markers.fasta)
[2023-03-14 11:51:56,180] [INFO] Task started: Blastn
[2023-03-14 11:51:56,180] [INFO] Running command: blastn -query OceanDNA-b4004/markers.fasta -db /var/lib/cwl/stg44cd5a44-a072-4c9c-8066-3625cb4d76ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4004/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:51:56,921] [INFO] Task succeeded: Blastn
[2023-03-14 11:51:56,925] [INFO] Selected 19 target genomes.
[2023-03-14 11:51:56,925] [INFO] Target genome list was writen to OceanDNA-b4004/target_genomes_gtdb.txt
[2023-03-14 11:51:57,053] [INFO] Task started: fastANI
[2023-03-14 11:51:57,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bafb29a-234b-40ae-a390-b87be8030161/OceanDNA-b4004.fa --refList OceanDNA-b4004/target_genomes_gtdb.txt --output OceanDNA-b4004/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:52:12,987] [INFO] Task succeeded: fastANI
[2023-03-14 11:52:12,996] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:52:12,997] [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_000222485.1	s__Cyclobacterium marinum	86.1917	1371	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	98.85	98.76	0.93	0.93	3	-
GCF_001050135.1	s__Cyclobacterium amurskyense	81.0817	923	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427295.1	s__Cyclobacterium qasimii	79.7856	876	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
GCF_010993705.1	s__Cyclobacterium sp010993705	77.2964	269	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762705.1	s__Cyclobacterium sp014762705	77.2638	296	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	77.1867	283	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994275.1	s__Cyclobacterium jeungdonense	77.1049	219	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119245.1	s__Cyclobacterium sp010119245	77.0515	204	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	76.2447	58	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
GCF_018642165.1	s__Echinicola shivajiensis	76.2052	86	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347495.1	s__Negadavirga sp003347495	76.1603	101	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Negadavirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	75.8999	63	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002735.1	s__Algoriphagus sp002002735	75.8586	51	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	75.8152	70	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	75.7379	61	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166275.1	s__Algoriphagus machipongonensis	75.5608	73	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:52:13,000] [INFO] GTDB search result was written to OceanDNA-b4004/result_gtdb.tsv
[2023-03-14 11:52:13,002] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:52:13,007] [INFO] DFAST_QC result json was written to OceanDNA-b4004/dqc_result.json
[2023-03-14 11:52:13,007] [INFO] DFAST_QC completed!
[2023-03-14 11:52:13,007] [INFO] Total running time: 0h2m36s