[2023-03-14 13:55:26,896] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:55:26,896] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:55:26,897] [INFO] DQC Reference Directory: /var/lib/cwl/stge7dc09ba-e1b2-431b-b6c6-1459e7a2aa27/dqc_reference
[2023-03-14 13:55:28,599] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:55:28,601] [INFO] Task started: Prodigal
[2023-03-14 13:55:28,601] [INFO] Running command: cat /var/lib/cwl/stged25d3a8-8ba8-4b12-9e7a-235ea67f3712/OceanDNA-b10354.fa | prodigal -d OceanDNA-b10354/cds.fna -a OceanDNA-b10354/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:55:57,735] [INFO] Task succeeded: Prodigal
[2023-03-14 13:55:57,735] [INFO] Task started: HMMsearch
[2023-03-14 13:55:57,735] [INFO] Running command: hmmsearch --tblout OceanDNA-b10354/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7dc09ba-e1b2-431b-b6c6-1459e7a2aa27/dqc_reference/reference_markers.hmm OceanDNA-b10354/protein.faa > /dev/null
[2023-03-14 13:55:58,274] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:55:58,275] [WARNING] Found 5/6 markers. [/var/lib/cwl/stged25d3a8-8ba8-4b12-9e7a-235ea67f3712/OceanDNA-b10354.fa]
[2023-03-14 13:55:58,311] [INFO] Query marker FASTA was written to OceanDNA-b10354/markers.fasta
[2023-03-14 13:55:58,314] [INFO] Task started: Blastn
[2023-03-14 13:55:58,314] [INFO] Running command: blastn -query OceanDNA-b10354/markers.fasta -db /var/lib/cwl/stge7dc09ba-e1b2-431b-b6c6-1459e7a2aa27/dqc_reference/reference_markers.fasta -out OceanDNA-b10354/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:56:00,048] [INFO] Task succeeded: Blastn
[2023-03-14 13:56:00,049] [INFO] Selected 14 target genomes.
[2023-03-14 13:56:00,049] [INFO] Target genome list was writen to OceanDNA-b10354/target_genomes.txt
[2023-03-14 13:56:00,058] [INFO] Task started: fastANI
[2023-03-14 13:56:00,058] [INFO] Running command: fastANI --query /var/lib/cwl/stged25d3a8-8ba8-4b12-9e7a-235ea67f3712/OceanDNA-b10354.fa --refList OceanDNA-b10354/target_genomes.txt --output OceanDNA-b10354/fastani_result.tsv --threads 1
[2023-03-14 13:56:17,254] [INFO] Task succeeded: fastANI
[2023-03-14 13:56:17,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7dc09ba-e1b2-431b-b6c6-1459e7a2aa27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:56:17,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7dc09ba-e1b2-431b-b6c6-1459e7a2aa27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:56:17,263] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 13:56:17,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 13:56:17,264] [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
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	95.7581	1045	1187	95	conclusive
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	88.247	966	1187	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	88.1503	989	1187	95	below_threshold
Salegentibacter salinarum	strain=KCTC 12975	GCA_002833365.1	447422	447422	type	True	87.9702	980	1187	95	below_threshold
Salegentibacter salinarum	strain=DSM 23400	GCA_900168115.1	447422	447422	type	True	87.9489	982	1187	95	below_threshold
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	86.0352	816	1187	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	85.9257	836	1187	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	85.9226	919	1187	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_001752425.1	435906	435906	type	True	85.9182	836	1187	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	85.7758	869	1187	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	84.1271	838	1187	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.8052	68	1187	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.4488	99	1187	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	75.7761	60	1187	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:56:17,264] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10354/tc_result.tsv
[2023-03-14 13:56:17,264] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:56:17,264] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:56:17,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7dc09ba-e1b2-431b-b6c6-1459e7a2aa27/dqc_reference/checkm_data
[2023-03-14 13:56:17,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:56:17,272] [INFO] Task started: CheckM
[2023-03-14 13:56:17,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10354/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10354/checkm_input OceanDNA-b10354/checkm_result
[2023-03-14 13:57:15,915] [INFO] Task succeeded: CheckM
[2023-03-14 13:57:15,916] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:57:15,918] [INFO] ===== Completeness check finished =====
[2023-03-14 13:57:15,918] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:57:15,918] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10354/markers.fasta)
[2023-03-14 13:57:15,920] [INFO] Task started: Blastn
[2023-03-14 13:57:15,920] [INFO] Running command: blastn -query OceanDNA-b10354/markers.fasta -db /var/lib/cwl/stge7dc09ba-e1b2-431b-b6c6-1459e7a2aa27/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10354/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:57:16,757] [INFO] Task succeeded: Blastn
[2023-03-14 13:57:16,758] [INFO] Selected 8 target genomes.
[2023-03-14 13:57:16,758] [INFO] Target genome list was writen to OceanDNA-b10354/target_genomes_gtdb.txt
[2023-03-14 13:57:16,763] [INFO] Task started: fastANI
[2023-03-14 13:57:16,763] [INFO] Running command: fastANI --query /var/lib/cwl/stged25d3a8-8ba8-4b12-9e7a-235ea67f3712/OceanDNA-b10354.fa --refList OceanDNA-b10354/target_genomes_gtdb.txt --output OceanDNA-b10354/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:57:23,357] [INFO] Task succeeded: fastANI
[2023-03-14 13:57:23,362] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:57:23,363] [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_900113135.1	s__Salegentibacter agarivorans	95.7581	1045	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	conclusive
GCF_900142975.1	s__Salegentibacter salegens	88.1503	989	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900168115.1	s__Salegentibacter salinarum	87.9489	982	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900168265.1	s__Salegentibacter salarius	86.0352	816	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_002900095.1	s__Salegentibacter mishustinae	85.7802	869	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_000745315.1	s__Salegentibacter sp000745315	85.3008	874	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	84.1834	834	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	76.1763	68	1187	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:57:23,363] [INFO] GTDB search result was written to OceanDNA-b10354/result_gtdb.tsv
[2023-03-14 13:57:23,363] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:57:23,364] [INFO] DFAST_QC result json was written to OceanDNA-b10354/dqc_result.json
[2023-03-14 13:57:23,364] [INFO] DFAST_QC completed!
[2023-03-14 13:57:23,364] [INFO] Total running time: 0h1m56s