[2023-03-17 05:16:58,085] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:16:58,085] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:16:58,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e4eb6c3-d32c-4eeb-8b0b-cf86677e1c25/dqc_reference
[2023-03-17 05:16:59,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:16:59,895] [INFO] Task started: Prodigal
[2023-03-17 05:16:59,896] [INFO] Running command: cat /var/lib/cwl/stgf273868b-6ebc-47bb-8755-9ec912019306/OceanDNA-b31476.fa | prodigal -d OceanDNA-b31476/cds.fna -a OceanDNA-b31476/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:17:17,071] [INFO] Task succeeded: Prodigal
[2023-03-17 05:17:17,071] [INFO] Task started: HMMsearch
[2023-03-17 05:17:17,071] [INFO] Running command: hmmsearch --tblout OceanDNA-b31476/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e4eb6c3-d32c-4eeb-8b0b-cf86677e1c25/dqc_reference/reference_markers.hmm OceanDNA-b31476/protein.faa > /dev/null
[2023-03-17 05:17:17,245] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:17:17,245] [INFO] Found 6/6 markers.
[2023-03-17 05:17:17,262] [INFO] Query marker FASTA was written to OceanDNA-b31476/markers.fasta
[2023-03-17 05:17:17,263] [INFO] Task started: Blastn
[2023-03-17 05:17:17,263] [INFO] Running command: blastn -query OceanDNA-b31476/markers.fasta -db /var/lib/cwl/stg9e4eb6c3-d32c-4eeb-8b0b-cf86677e1c25/dqc_reference/reference_markers.fasta -out OceanDNA-b31476/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:17:17,868] [INFO] Task succeeded: Blastn
[2023-03-17 05:17:17,869] [INFO] Selected 24 target genomes.
[2023-03-17 05:17:17,870] [INFO] Target genome list was writen to OceanDNA-b31476/target_genomes.txt
[2023-03-17 05:17:17,985] [INFO] Task started: fastANI
[2023-03-17 05:17:17,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgf273868b-6ebc-47bb-8755-9ec912019306/OceanDNA-b31476.fa --refList OceanDNA-b31476/target_genomes.txt --output OceanDNA-b31476/fastani_result.tsv --threads 1
[2023-03-17 05:17:34,993] [INFO] Task succeeded: fastANI
[2023-03-17 05:17:34,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e4eb6c3-d32c-4eeb-8b0b-cf86677e1c25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:17:34,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e4eb6c3-d32c-4eeb-8b0b-cf86677e1c25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:17:34,998] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 05:17:34,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:17:34,998] [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
Luteithermobacter gelatinilyticus	strain=MEBiC09520	GCA_005849285.1	2582913	2582913	type	True	99.0323	896	931	95	conclusive
Emcibacter nanhaiensis	strain=MCCC 1A06723	GCA_006385175.1	1505037	1505037	type	True	77.7924	321	931	95	below_threshold
Paremcibacter congregatus	strain=ZYL	GCA_002740695.1	2043170	2043170	type	True	76.5134	124	931	95	below_threshold
Paremcibacter congregatus	strain=ZYLT	GCA_006385135.1	2043170	2043170	type	True	76.482	126	931	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:17:34,998] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31476/tc_result.tsv
[2023-03-17 05:17:34,999] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:17:34,999] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:17:34,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e4eb6c3-d32c-4eeb-8b0b-cf86677e1c25/dqc_reference/checkm_data
[2023-03-17 05:17:34,999] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:17:35,004] [INFO] Task started: CheckM
[2023-03-17 05:17:35,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31476/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31476/checkm_input OceanDNA-b31476/checkm_result
[2023-03-17 05:18:19,613] [INFO] Task succeeded: CheckM
[2023-03-17 05:18:19,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:18:19,616] [INFO] ===== Completeness check finished =====
[2023-03-17 05:18:19,616] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:18:19,616] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31476/markers.fasta)
[2023-03-17 05:18:19,617] [INFO] Task started: Blastn
[2023-03-17 05:18:19,617] [INFO] Running command: blastn -query OceanDNA-b31476/markers.fasta -db /var/lib/cwl/stg9e4eb6c3-d32c-4eeb-8b0b-cf86677e1c25/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31476/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:18:20,533] [INFO] Task succeeded: Blastn
[2023-03-17 05:18:20,535] [INFO] Selected 21 target genomes.
[2023-03-17 05:18:20,536] [INFO] Target genome list was writen to OceanDNA-b31476/target_genomes_gtdb.txt
[2023-03-17 05:18:20,776] [INFO] Task started: fastANI
[2023-03-17 05:18:20,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgf273868b-6ebc-47bb-8755-9ec912019306/OceanDNA-b31476.fa --refList OceanDNA-b31476/target_genomes_gtdb.txt --output OceanDNA-b31476/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:18:32,454] [INFO] Task succeeded: fastANI
[2023-03-17 05:18:32,459] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:18:32,459] [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_005849285.1	s__Luteithermobacter gelatinilyticus	99.0323	896	931	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Luteithermobacter	95.0	99.04	99.04	0.96	0.96	2	conclusive
GCF_006385175.1	s__Emcibacter nanhaiensis	77.7924	321	931	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Emcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051815.1	s__Paremcibacter sp011051815	76.4334	60	931	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152755.1	s__Paremcibacter sp013152755	76.3184	106	931	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401455.1	s__Paremcibacter sp002401455	76.3073	74	931	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002749135.1	s__Paremcibacter sp002749135	76.2605	107	931	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226495.1	s__Kordiimonas sp006226495	76.0415	53	931	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:18:32,460] [INFO] GTDB search result was written to OceanDNA-b31476/result_gtdb.tsv
[2023-03-17 05:18:32,460] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:18:32,461] [INFO] DFAST_QC result json was written to OceanDNA-b31476/dqc_result.json
[2023-03-17 05:18:32,461] [INFO] DFAST_QC completed!
[2023-03-17 05:18:32,461] [INFO] Total running time: 0h1m34s