[2023-03-16 06:31:19,222] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:31:19,222] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:31:19,222] [INFO] DQC Reference Directory: /var/lib/cwl/stg93b2cd5b-52d2-4582-ad12-5e0c220e4ea9/dqc_reference
[2023-03-16 06:31:20,355] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:31:20,356] [INFO] Task started: Prodigal
[2023-03-16 06:31:20,356] [INFO] Running command: cat /var/lib/cwl/stg08064fc7-a51e-4093-9197-4772cdc7a147/OceanDNA-b4002.fa | prodigal -d OceanDNA-b4002/cds.fna -a OceanDNA-b4002/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:31:49,090] [INFO] Task succeeded: Prodigal
[2023-03-16 06:31:49,091] [INFO] Task started: HMMsearch
[2023-03-16 06:31:49,091] [INFO] Running command: hmmsearch --tblout OceanDNA-b4002/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93b2cd5b-52d2-4582-ad12-5e0c220e4ea9/dqc_reference/reference_markers.hmm OceanDNA-b4002/protein.faa > /dev/null
[2023-03-16 06:31:49,321] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:31:49,322] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg08064fc7-a51e-4093-9197-4772cdc7a147/OceanDNA-b4002.fa]
[2023-03-16 06:31:49,357] [INFO] Query marker FASTA was written to OceanDNA-b4002/markers.fasta
[2023-03-16 06:31:49,358] [INFO] Task started: Blastn
[2023-03-16 06:31:49,358] [INFO] Running command: blastn -query OceanDNA-b4002/markers.fasta -db /var/lib/cwl/stg93b2cd5b-52d2-4582-ad12-5e0c220e4ea9/dqc_reference/reference_markers.fasta -out OceanDNA-b4002/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:49,922] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:49,926] [INFO] Selected 20 target genomes.
[2023-03-16 06:31:49,926] [INFO] Target genome list was writen to OceanDNA-b4002/target_genomes.txt
[2023-03-16 06:31:49,942] [INFO] Task started: fastANI
[2023-03-16 06:31:49,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg08064fc7-a51e-4093-9197-4772cdc7a147/OceanDNA-b4002.fa --refList OceanDNA-b4002/target_genomes.txt --output OceanDNA-b4002/fastani_result.tsv --threads 1
[2023-03-16 06:32:04,650] [INFO] Task succeeded: fastANI
[2023-03-16 06:32:04,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93b2cd5b-52d2-4582-ad12-5e0c220e4ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:32:04,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93b2cd5b-52d2-4582-ad12-5e0c220e4ea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:32:04,660] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:32:04,660] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:32:04,660] [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
Aquiflexum lacus	strain=CUG 91378	GCA_015476655.1	2483805	2483805	type	True	81.1057	703	1106	95	below_threshold
Aquiflexum balticum	strain=DSM 16537	GCA_900176595.1	280473	280473	type	True	80.0464	610	1106	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	77.1396	162	1106	95	below_threshold
Mongoliitalea daihaiensis	strain=X100-76	GCA_021596945.1	2782006	2782006	type	True	77.0768	114	1106	95	below_threshold
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	76.8624	119	1106	95	below_threshold
Belliella aquatica	strain=JCM 19468	GCA_022549755.1	1323734	1323734	type	True	76.8527	127	1106	95	below_threshold
Belliella baltica	strain=DSM 15883	GCA_000265405.1	232259	232259	type	True	76.7775	120	1106	95	below_threshold
Belliella aquatica	strain=CGMCC 1.12479	GCA_014637795.1	1323734	1323734	type	True	76.7708	127	1106	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	76.6336	58	1106	95	below_threshold
Litoribacter populi	strain=XAAS-A1	GCA_007483685.1	2598460	2598460	type	True	76.6317	52	1106	95	below_threshold
Algoriphagus pacificus	strain=YJ13C	GCA_017254845.1	2811234	2811234	type	True	76.3682	58	1106	95	below_threshold
Algoriphagus chordae	strain=DSM 19830	GCA_003254055.1	237019	237019	type	True	76.2114	52	1106	95	below_threshold
Algoriphagus halophilus	strain=DSM 15292	GCA_900129785.1	226505	226505	type	True	76.1823	72	1106	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	76.0772	52	1106	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:32:04,663] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4002/tc_result.tsv
[2023-03-16 06:32:04,665] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:32:04,665] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:32:04,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93b2cd5b-52d2-4582-ad12-5e0c220e4ea9/dqc_reference/checkm_data
[2023-03-16 06:32:04,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:32:04,674] [INFO] Task started: CheckM
[2023-03-16 06:32:04,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4002/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4002/checkm_input OceanDNA-b4002/checkm_result
[2023-03-16 06:33:18,358] [INFO] Task succeeded: CheckM
[2023-03-16 06:33:18,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.86%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:33:18,502] [INFO] ===== Completeness check finished =====
[2023-03-16 06:33:18,502] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:33:18,502] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4002/markers.fasta)
[2023-03-16 06:33:18,504] [INFO] Task started: Blastn
[2023-03-16 06:33:18,504] [INFO] Running command: blastn -query OceanDNA-b4002/markers.fasta -db /var/lib/cwl/stg93b2cd5b-52d2-4582-ad12-5e0c220e4ea9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4002/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:33:19,346] [INFO] Task succeeded: Blastn
[2023-03-16 06:33:19,382] [INFO] Selected 17 target genomes.
[2023-03-16 06:33:19,382] [INFO] Target genome list was writen to OceanDNA-b4002/target_genomes_gtdb.txt
[2023-03-16 06:33:19,397] [INFO] Task started: fastANI
[2023-03-16 06:33:19,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg08064fc7-a51e-4093-9197-4772cdc7a147/OceanDNA-b4002.fa --refList OceanDNA-b4002/target_genomes_gtdb.txt --output OceanDNA-b4002/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:33:33,029] [INFO] Task succeeded: fastANI
[2023-03-16 06:33:33,038] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:33:33,039] [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_015476655.1	s__Aquiflexum lacus	81.0781	706	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176595.1	s__Aquiflexum balticum	80.0338	611	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003797895.1	s__Cecembia sp003797895	78.1718	272	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003005.1	s__Mongoliibacter ruber	77.4426	164	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Mongoliibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000295935.2	s__Indibacter alkaliphilus	77.4283	177	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838715.1	s__Algoriphagus sp014838715	77.1545	56	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000298295.1	s__Cecembia lonarensis	77.1396	162	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216715.1	s__Cecembia calidifontis	77.0819	176	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692705.1	s__Mongoliibacter sp007692705	76.9651	175	1106	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	76.8624	119	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265405.1	s__Belliella baltica	76.7775	120	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637795.1	s__Belliella aquatica	76.7708	127	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254055.1	s__Algoriphagus chordae	76.2114	52	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129785.1	s__Algoriphagus halophilus	76.1823	72	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429465.1	s__Algoriphagus vanfongensis	76.0772	52	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:33:33,042] [INFO] GTDB search result was written to OceanDNA-b4002/result_gtdb.tsv
[2023-03-16 06:33:33,046] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:33:33,052] [INFO] DFAST_QC result json was written to OceanDNA-b4002/dqc_result.json
[2023-03-16 06:33:33,052] [INFO] DFAST_QC completed!
[2023-03-16 06:33:33,052] [INFO] Total running time: 0h2m14s