[2023-03-17 02:31:12,851] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,851] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg968bcd6b-8900-4d34-bd22-e33c885d0052/dqc_reference
[2023-03-17 02:31:14,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,378] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,378] [INFO] Running command: cat /var/lib/cwl/stg5231316b-55bf-4cc9-9cf6-2b03fcba3d38/OceanDNA-b35290.fa | prodigal -d OceanDNA-b35290/cds.fna -a OceanDNA-b35290/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:20,644] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:20,644] [INFO] Task started: HMMsearch
[2023-03-17 02:31:20,644] [INFO] Running command: hmmsearch --tblout OceanDNA-b35290/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg968bcd6b-8900-4d34-bd22-e33c885d0052/dqc_reference/reference_markers.hmm OceanDNA-b35290/protein.faa > /dev/null
[2023-03-17 02:31:20,809] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:20,809] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5231316b-55bf-4cc9-9cf6-2b03fcba3d38/OceanDNA-b35290.fa]
[2023-03-17 02:31:20,817] [INFO] Query marker FASTA was written to OceanDNA-b35290/markers.fasta
[2023-03-17 02:31:20,817] [INFO] Task started: Blastn
[2023-03-17 02:31:20,817] [INFO] Running command: blastn -query OceanDNA-b35290/markers.fasta -db /var/lib/cwl/stg968bcd6b-8900-4d34-bd22-e33c885d0052/dqc_reference/reference_markers.fasta -out OceanDNA-b35290/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:21,281] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:21,281] [INFO] Selected 14 target genomes.
[2023-03-17 02:31:21,282] [INFO] Target genome list was writen to OceanDNA-b35290/target_genomes.txt
[2023-03-17 02:31:21,290] [INFO] Task started: fastANI
[2023-03-17 02:31:21,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg5231316b-55bf-4cc9-9cf6-2b03fcba3d38/OceanDNA-b35290.fa --refList OceanDNA-b35290/target_genomes.txt --output OceanDNA-b35290/fastani_result.tsv --threads 1
[2023-03-17 02:31:31,170] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:31,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg968bcd6b-8900-4d34-bd22-e33c885d0052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:31,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg968bcd6b-8900-4d34-bd22-e33c885d0052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:31,179] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 02:31:31,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 02:31:31,180] [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
Vibrio aquimaris	strain=THAF100	GCA_009363415.1	2587862	2587862	type	True	95.3291	330	377	95	conclusive
Vibrio pectenicida	strain=CAIM 594	GCA_003937805.1	62763	62763	type	True	82.3598	259	377	95	below_threshold
Vibrio pectenicida	strain=LMG 19642	GCA_024347015.1	62763	62763	type	True	82.2813	274	377	95	below_threshold
Vibrio bivalvicida	strain=605	GCA_001399455.2	1276888	1276888	type	True	79.9334	135	377	95	below_threshold
Vibrio europaeus	strain=PP-638	GCA_001695575.1	300876	300876	type	True	79.8473	144	377	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000772105.1	29498	29498	suspected-type	True	79.7634	150	377	95	below_threshold
Vibrio tubiashii	strain=ATCC 19109	GCA_000222665.2	29498	29498	suspected-type	True	79.6544	149	377	95	below_threshold
Vibrio ichthyoenteri	strain=ATCC 700023	GCA_000222605.2	142461	142461	type	True	79.246	110	377	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	78.8867	103	377	95	below_threshold
Vibrio marinisediminis	strain=404	GCA_014050145.1	2758441	2758441	type	True	78.8629	121	377	95	below_threshold
Vibrio marisflavi	strain=CECT 7928	GCA_921294215.1	1216040	1216040	type	True	78.816	80	377	95	below_threshold
Vibrio sonorensis	strain=CAIM 1076	GCA_001854765.1	1004316	1004316	type	True	78.7399	115	377	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	78.5502	88	377	95	below_threshold
Vibrio echinoideorum	strain=DSM 107264	GCA_024347455.1	2100116	2100116	type	True	78.4123	95	377	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:31:31,180] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35290/tc_result.tsv
[2023-03-17 02:31:31,180] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:31,180] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:31,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg968bcd6b-8900-4d34-bd22-e33c885d0052/dqc_reference/checkm_data
[2023-03-17 02:31:31,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:31,184] [INFO] Task started: CheckM
[2023-03-17 02:31:31,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35290/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35290/checkm_input OceanDNA-b35290/checkm_result
[2023-03-17 02:31:52,397] [INFO] Task succeeded: CheckM
[2023-03-17 02:31:52,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:31:52,399] [INFO] ===== Completeness check finished =====
[2023-03-17 02:31:52,399] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:31:52,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35290/markers.fasta)
[2023-03-17 02:31:52,399] [INFO] Task started: Blastn
[2023-03-17 02:31:52,399] [INFO] Running command: blastn -query OceanDNA-b35290/markers.fasta -db /var/lib/cwl/stg968bcd6b-8900-4d34-bd22-e33c885d0052/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35290/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:52,878] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:52,879] [INFO] Selected 9 target genomes.
[2023-03-17 02:31:52,879] [INFO] Target genome list was writen to OceanDNA-b35290/target_genomes_gtdb.txt
[2023-03-17 02:31:53,057] [INFO] Task started: fastANI
[2023-03-17 02:31:53,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg5231316b-55bf-4cc9-9cf6-2b03fcba3d38/OceanDNA-b35290.fa --refList OceanDNA-b35290/target_genomes_gtdb.txt --output OceanDNA-b35290/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:31:59,699] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:59,705] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 02:31:59,706] [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_003350295.1	s__Vibrio tetraodonis	95.7882	327	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	95.28	95.28	0.88	0.88	2	inconclusive
GCF_009363415.1	s__Vibrio aquimaris	95.3291	330	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_018860525.1	s__Vibrio hepatarius_B	82.3844	256	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937805.1	s__Vibrio pectenicida	82.3598	259	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.20	98.20	0.85	0.85	2	-
GCF_001399455.2	s__Vibrio bivalvicida	79.9334	135	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.39	98.39	0.93	0.93	2	-
GCF_000772105.1	s__Vibrio tubiashii	79.7634	150	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.61	95.85	0.96	0.87	4	-
GCF_009938165.1	s__Vibrio taketomensis	79.4088	104	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	98.31	98.31	0.99	0.99	2	-
GCF_014050145.1	s__Vibrio marinisediminis	78.8629	121	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854765.1	s__Vibrio sonorensis	78.7399	115	377	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:31:59,706] [INFO] GTDB search result was written to OceanDNA-b35290/result_gtdb.tsv
[2023-03-17 02:31:59,706] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:31:59,708] [INFO] DFAST_QC result json was written to OceanDNA-b35290/dqc_result.json
[2023-03-17 02:31:59,708] [INFO] DFAST_QC completed!
[2023-03-17 02:31:59,708] [INFO] Total running time: 0h0m47s