[2023-03-14 11:36:02,659] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:36:02,661] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:36:02,661] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdb5115b-b79d-4a3e-912c-5c603dfbd651/dqc_reference
[2023-03-14 11:36:04,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:36:04,406] [INFO] Task started: Prodigal
[2023-03-14 11:36:04,407] [INFO] Running command: cat /var/lib/cwl/stgb23ae57f-231d-4d04-bb27-a8c582ed8410/OceanDNA-b4005.fa | prodigal -d OceanDNA-b4005/cds.fna -a OceanDNA-b4005/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:36:48,240] [INFO] Task succeeded: Prodigal
[2023-03-14 11:36:48,240] [INFO] Task started: HMMsearch
[2023-03-14 11:36:48,240] [INFO] Running command: hmmsearch --tblout OceanDNA-b4005/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdb5115b-b79d-4a3e-912c-5c603dfbd651/dqc_reference/reference_markers.hmm OceanDNA-b4005/protein.faa > /dev/null
[2023-03-14 11:36:48,501] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:36:48,502] [INFO] Found 6/6 markers.
[2023-03-14 11:36:48,538] [INFO] Query marker FASTA was written to OceanDNA-b4005/markers.fasta
[2023-03-14 11:36:48,539] [INFO] Task started: Blastn
[2023-03-14 11:36:48,540] [INFO] Running command: blastn -query OceanDNA-b4005/markers.fasta -db /var/lib/cwl/stgbdb5115b-b79d-4a3e-912c-5c603dfbd651/dqc_reference/reference_markers.fasta -out OceanDNA-b4005/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:49,109] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:49,110] [INFO] Selected 16 target genomes.
[2023-03-14 11:36:49,110] [INFO] Target genome list was writen to OceanDNA-b4005/target_genomes.txt
[2023-03-14 11:36:49,122] [INFO] Task started: fastANI
[2023-03-14 11:36:49,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgb23ae57f-231d-4d04-bb27-a8c582ed8410/OceanDNA-b4005.fa --refList OceanDNA-b4005/target_genomes.txt --output OceanDNA-b4005/fastani_result.tsv --threads 1
[2023-03-14 11:37:03,689] [INFO] Task succeeded: fastANI
[2023-03-14 11:37:03,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdb5115b-b79d-4a3e-912c-5c603dfbd651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:37:03,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdb5115b-b79d-4a3e-912c-5c603dfbd651/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:37:03,697] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:37:03,697] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:37:03,697] [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	84.0664	1495	2039	95	below_threshold
Cyclobacterium amurskyense	strain=KCTC 12363	GCA_001050135.1	320787	320787	type	True	80.7254	1088	2039	95	below_threshold
Cyclobacterium qasimii	strain=NBRC 106168	GCA_007991695.1	1350429	1350429	type	True	80.3992	1048	2039	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	80.3692	1068	2039	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	77.5296	325	2039	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	77.3767	180	2039	95	below_threshold
Pleomorphovibrio marinus	strain=SW125	GCA_003347495.1	2164132	2164132	type	True	76.1502	124	2039	95	below_threshold
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	76.0776	63	2039	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	76.0005	100	2039	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	75.5766	60	2039	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:37:03,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4005/tc_result.tsv
[2023-03-14 11:37:03,698] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:37:03,698] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:37:03,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdb5115b-b79d-4a3e-912c-5c603dfbd651/dqc_reference/checkm_data
[2023-03-14 11:37:03,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:37:03,706] [INFO] Task started: CheckM
[2023-03-14 11:37:03,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4005/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4005/checkm_input OceanDNA-b4005/checkm_result
[2023-03-14 11:38:47,441] [INFO] Task succeeded: CheckM
[2023-03-14 11:38:47,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:38:47,451] [INFO] ===== Completeness check finished =====
[2023-03-14 11:38:47,451] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:38:47,451] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4005/markers.fasta)
[2023-03-14 11:38:47,453] [INFO] Task started: Blastn
[2023-03-14 11:38:47,453] [INFO] Running command: blastn -query OceanDNA-b4005/markers.fasta -db /var/lib/cwl/stgbdb5115b-b79d-4a3e-912c-5c603dfbd651/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4005/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:38:48,350] [INFO] Task succeeded: Blastn
[2023-03-14 11:38:48,353] [INFO] Selected 17 target genomes.
[2023-03-14 11:38:48,353] [INFO] Target genome list was writen to OceanDNA-b4005/target_genomes_gtdb.txt
[2023-03-14 11:38:48,518] [INFO] Task started: fastANI
[2023-03-14 11:38:48,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgb23ae57f-231d-4d04-bb27-a8c582ed8410/OceanDNA-b4005.fa --refList OceanDNA-b4005/target_genomes_gtdb.txt --output OceanDNA-b4005/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:39:03,013] [INFO] Task succeeded: fastANI
[2023-03-14 11:39:03,021] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:39:03,021] [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	84.0727	1494	2039	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	80.7331	1086	2039	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	80.3844	1067	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
GCF_011290685.1	s__Cyclobacterium plantarum	77.5338	326	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009467825.1	s__Cyclobacterium xiamenense	77.367	177	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	97.69	97.69	0.89	0.89	2	-
GCF_900143075.1	s__Cyclobacterium lianum	77.3548	246	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	77.1556	299	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124425.1	s__Lunatimonas sp016124425	76.2247	69	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	76.0776	63	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	76.0156	70	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	76.0064	101	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006575665.1	s__Echinicola sp006575665	75.7922	71	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101705.1	s__Algoriphagus faecimaris	75.5116	56	2039	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-14 11:39:03,022] [INFO] GTDB search result was written to OceanDNA-b4005/result_gtdb.tsv
[2023-03-14 11:39:03,022] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:39:03,024] [INFO] DFAST_QC result json was written to OceanDNA-b4005/dqc_result.json
[2023-03-14 11:39:03,024] [INFO] DFAST_QC completed!
[2023-03-14 11:39:03,024] [INFO] Total running time: 0h3m0s