[2023-03-19 02:51:48,227] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:51:48,227] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:51:48,227] [INFO] DQC Reference Directory: /var/lib/cwl/stga318590e-fbe5-4588-a51f-17eb03a65ae3/dqc_reference
[2023-03-19 02:51:49,327] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:51:49,327] [INFO] Task started: Prodigal
[2023-03-19 02:51:49,327] [INFO] Running command: cat /var/lib/cwl/stg1f8bfa26-acbb-40e6-9bd2-cfcac87256ef/OceanDNA-b31474.fa | prodigal -d OceanDNA-b31474/cds.fna -a OceanDNA-b31474/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:52:12,093] [INFO] Task succeeded: Prodigal
[2023-03-19 02:52:12,093] [INFO] Task started: HMMsearch
[2023-03-19 02:52:12,093] [INFO] Running command: hmmsearch --tblout OceanDNA-b31474/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga318590e-fbe5-4588-a51f-17eb03a65ae3/dqc_reference/reference_markers.hmm OceanDNA-b31474/protein.faa > /dev/null
[2023-03-19 02:52:12,301] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:52:12,301] [INFO] Found 6/6 markers.
[2023-03-19 02:52:12,337] [INFO] Query marker FASTA was written to OceanDNA-b31474/markers.fasta
[2023-03-19 02:52:12,338] [INFO] Task started: Blastn
[2023-03-19 02:52:12,338] [INFO] Running command: blastn -query OceanDNA-b31474/markers.fasta -db /var/lib/cwl/stga318590e-fbe5-4588-a51f-17eb03a65ae3/dqc_reference/reference_markers.fasta -out OceanDNA-b31474/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:52:12,964] [INFO] Task succeeded: Blastn
[2023-03-19 02:52:12,965] [INFO] Selected 21 target genomes.
[2023-03-19 02:52:12,965] [INFO] Target genome list was writen to OceanDNA-b31474/target_genomes.txt
[2023-03-19 02:52:12,976] [INFO] Task started: fastANI
[2023-03-19 02:52:12,976] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f8bfa26-acbb-40e6-9bd2-cfcac87256ef/OceanDNA-b31474.fa --refList OceanDNA-b31474/target_genomes.txt --output OceanDNA-b31474/fastani_result.tsv --threads 1
[2023-03-19 02:52:27,260] [INFO] Task succeeded: fastANI
[2023-03-19 02:52:27,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga318590e-fbe5-4588-a51f-17eb03a65ae3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:52:27,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga318590e-fbe5-4588-a51f-17eb03a65ae3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:52:27,266] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2023-03-19 02:52:27,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 02:52:27,267] [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
Paremcibacter congregatus	strain=ZYL	GCA_002740695.1	2043170	2043170	type	True	97.5166	1058	1251	95	conclusive
Paremcibacter congregatus	strain=ZYLT	GCA_006385135.1	2043170	2043170	type	True	97.5	1056	1251	95	conclusive
Emcibacter nanhaiensis	strain=MCCC 1A06723	GCA_006385175.1	1505037	1505037	type	True	76.9283	200	1251	95	below_threshold
Luteithermobacter gelatinilyticus	strain=MEBiC09520	GCA_005849285.1	2582913	2582913	type	True	76.226	143	1251	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	75.3814	50	1251	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:52:27,267] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31474/tc_result.tsv
[2023-03-19 02:52:27,267] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:52:27,267] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:52:27,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga318590e-fbe5-4588-a51f-17eb03a65ae3/dqc_reference/checkm_data
[2023-03-19 02:52:27,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:52:27,275] [INFO] Task started: CheckM
[2023-03-19 02:52:27,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31474/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31474/checkm_input OceanDNA-b31474/checkm_result
[2023-03-19 02:53:25,019] [INFO] Task succeeded: CheckM
[2023-03-19 02:53:25,019] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:53:25,029] [INFO] ===== Completeness check finished =====
[2023-03-19 02:53:25,029] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:53:25,029] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31474/markers.fasta)
[2023-03-19 02:53:25,031] [INFO] Task started: Blastn
[2023-03-19 02:53:25,031] [INFO] Running command: blastn -query OceanDNA-b31474/markers.fasta -db /var/lib/cwl/stga318590e-fbe5-4588-a51f-17eb03a65ae3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31474/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:53:26,133] [INFO] Task succeeded: Blastn
[2023-03-19 02:53:26,134] [INFO] Selected 18 target genomes.
[2023-03-19 02:53:26,134] [INFO] Target genome list was writen to OceanDNA-b31474/target_genomes_gtdb.txt
[2023-03-19 02:53:26,146] [INFO] Task started: fastANI
[2023-03-19 02:53:26,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f8bfa26-acbb-40e6-9bd2-cfcac87256ef/OceanDNA-b31474.fa --refList OceanDNA-b31474/target_genomes_gtdb.txt --output OceanDNA-b31474/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:53:37,641] [INFO] Task succeeded: fastANI
[2023-03-19 02:53:37,647] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:53:37,647] [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_006385135.1	s__Paremcibacter congregatus	97.5217	1055	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_002401455.1	s__Paremcibacter sp002401455	77.725	246	1251	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	77.6047	271	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051815.1	s__Paremcibacter sp011051815	77.4802	156	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401545.1	s__Paremcibacter sp002401545	77.3226	223	1251	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	77.2287	260	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152615.1	s__Paremcibacter sp013152615	77.1007	156	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385175.1	s__Emcibacter nanhaiensis	76.9283	200	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Emcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005849285.1	s__Luteithermobacter gelatinilyticus	76.226	143	1251	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Luteithermobacter	95.0	99.04	99.04	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:53:37,647] [INFO] GTDB search result was written to OceanDNA-b31474/result_gtdb.tsv
[2023-03-19 02:53:37,647] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:53:37,648] [INFO] DFAST_QC result json was written to OceanDNA-b31474/dqc_result.json
[2023-03-19 02:53:37,648] [INFO] DFAST_QC completed!
[2023-03-19 02:53:37,648] [INFO] Total running time: 0h1m49s