[2023-03-18 08:55:50,543] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,543] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,543] [INFO] DQC Reference Directory: /var/lib/cwl/stgdea71f5a-4522-49db-b04d-ce5490820d19/dqc_reference
[2023-03-18 08:55:51,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,684] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,684] [INFO] Running command: cat /var/lib/cwl/stgd64ac4cf-c739-4936-8b90-fcdf5633c90a/OceanDNA-b11033.fa | prodigal -d OceanDNA-b11033/cds.fna -a OceanDNA-b11033/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:55:59,363] [INFO] Task succeeded: Prodigal
[2023-03-18 08:55:59,364] [INFO] Task started: HMMsearch
[2023-03-18 08:55:59,364] [INFO] Running command: hmmsearch --tblout OceanDNA-b11033/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdea71f5a-4522-49db-b04d-ce5490820d19/dqc_reference/reference_markers.hmm OceanDNA-b11033/protein.faa > /dev/null
[2023-03-18 08:55:59,582] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:55:59,583] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd64ac4cf-c739-4936-8b90-fcdf5633c90a/OceanDNA-b11033.fa]
[2023-03-18 08:55:59,595] [INFO] Query marker FASTA was written to OceanDNA-b11033/markers.fasta
[2023-03-18 08:55:59,596] [INFO] Task started: Blastn
[2023-03-18 08:55:59,596] [INFO] Running command: blastn -query OceanDNA-b11033/markers.fasta -db /var/lib/cwl/stgdea71f5a-4522-49db-b04d-ce5490820d19/dqc_reference/reference_markers.fasta -out OceanDNA-b11033/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:00,058] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:00,059] [INFO] Selected 15 target genomes.
[2023-03-18 08:56:00,059] [INFO] Target genome list was writen to OceanDNA-b11033/target_genomes.txt
[2023-03-18 08:56:00,075] [INFO] Task started: fastANI
[2023-03-18 08:56:00,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgd64ac4cf-c739-4936-8b90-fcdf5633c90a/OceanDNA-b11033.fa --refList OceanDNA-b11033/target_genomes.txt --output OceanDNA-b11033/fastani_result.tsv --threads 1
[2023-03-18 08:56:08,469] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:08,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdea71f5a-4522-49db-b04d-ce5490820d19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:08,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdea71f5a-4522-49db-b04d-ce5490820d19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:08,479] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:08,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:08,479] [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
Flavicella marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	78.611	162	377	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	78.1001	133	377	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.4716	65	377	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.3073	54	377	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.076	59	377	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.039	69	377	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	75.7918	56	377	95	below_threshold
Tenacibaculum pelagium	strain=S7007	GCA_014062345.1	2759527	2759527	type	True	75.746	55	377	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:08,479] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11033/tc_result.tsv
[2023-03-18 08:56:08,480] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:08,480] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:08,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdea71f5a-4522-49db-b04d-ce5490820d19/dqc_reference/checkm_data
[2023-03-18 08:56:08,481] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:08,486] [INFO] Task started: CheckM
[2023-03-18 08:56:08,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11033/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11033/checkm_input OceanDNA-b11033/checkm_result
[2023-03-18 08:56:33,232] [INFO] Task succeeded: CheckM
[2023-03-18 08:56:33,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:56:33,235] [INFO] ===== Completeness check finished =====
[2023-03-18 08:56:33,236] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:56:33,236] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11033/markers.fasta)
[2023-03-18 08:56:33,237] [INFO] Task started: Blastn
[2023-03-18 08:56:33,237] [INFO] Running command: blastn -query OceanDNA-b11033/markers.fasta -db /var/lib/cwl/stgdea71f5a-4522-49db-b04d-ce5490820d19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11033/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:33,802] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:33,804] [INFO] Selected 16 target genomes.
[2023-03-18 08:56:33,804] [INFO] Target genome list was writen to OceanDNA-b11033/target_genomes_gtdb.txt
[2023-03-18 08:56:33,846] [INFO] Task started: fastANI
[2023-03-18 08:56:33,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgd64ac4cf-c739-4936-8b90-fcdf5633c90a/OceanDNA-b11033.fa --refList OceanDNA-b11033/target_genomes_gtdb.txt --output OceanDNA-b11033/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:56:41,887] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:41,894] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:56:41,894] [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_009193215.1	s__Flavicella marina	78.611	162	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006381105.1	s__Flavicella sediminum	78.0925	134	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	76.4317	55	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_009796785.1	s__Polaribacter sp009796785	76.3835	73	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480405.1	s__Polaribacter sp905480405	76.1045	58	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	76.076	59	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCF_002954605.1	s__Polaribacter butkevichii	76.039	69	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	75.9586	72	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	75.8788	58	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014062345.1	s__Tenacibaculum pelagium	75.746	55	377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:56:41,894] [INFO] GTDB search result was written to OceanDNA-b11033/result_gtdb.tsv
[2023-03-18 08:56:41,895] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:56:41,896] [INFO] DFAST_QC result json was written to OceanDNA-b11033/dqc_result.json
[2023-03-18 08:56:41,896] [INFO] DFAST_QC completed!
[2023-03-18 08:56:41,896] [INFO] Total running time: 0h0m51s