[2023-03-18 09:42:02,226] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:42:02,226] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:42:02,226] [INFO] DQC Reference Directory: /var/lib/cwl/stgd54a5cfd-28eb-4022-96ac-65e2655e1ab8/dqc_reference
[2023-03-18 09:42:03,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:42:03,333] [INFO] Task started: Prodigal
[2023-03-18 09:42:03,333] [INFO] Running command: cat /var/lib/cwl/stg6c528345-d17e-47c1-922b-ffeee4702723/OceanDNA-b2811.fa | prodigal -d OceanDNA-b2811/cds.fna -a OceanDNA-b2811/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:42:10,821] [INFO] Task succeeded: Prodigal
[2023-03-18 09:42:10,822] [INFO] Task started: HMMsearch
[2023-03-18 09:42:10,822] [INFO] Running command: hmmsearch --tblout OceanDNA-b2811/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd54a5cfd-28eb-4022-96ac-65e2655e1ab8/dqc_reference/reference_markers.hmm OceanDNA-b2811/protein.faa > /dev/null
[2023-03-18 09:42:10,940] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:42:10,941] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6c528345-d17e-47c1-922b-ffeee4702723/OceanDNA-b2811.fa]
[2023-03-18 09:42:10,953] [INFO] Query marker FASTA was written to OceanDNA-b2811/markers.fasta
[2023-03-18 09:42:10,954] [INFO] Task started: Blastn
[2023-03-18 09:42:10,954] [INFO] Running command: blastn -query OceanDNA-b2811/markers.fasta -db /var/lib/cwl/stgd54a5cfd-28eb-4022-96ac-65e2655e1ab8/dqc_reference/reference_markers.fasta -out OceanDNA-b2811/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:11,677] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:11,677] [INFO] Selected 11 target genomes.
[2023-03-18 09:42:11,677] [INFO] Target genome list was writen to OceanDNA-b2811/target_genomes.txt
[2023-03-18 09:42:11,685] [INFO] Task started: fastANI
[2023-03-18 09:42:11,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c528345-d17e-47c1-922b-ffeee4702723/OceanDNA-b2811.fa --refList OceanDNA-b2811/target_genomes.txt --output OceanDNA-b2811/fastani_result.tsv --threads 1
[2023-03-18 09:42:17,218] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:17,218] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd54a5cfd-28eb-4022-96ac-65e2655e1ab8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:42:17,218] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd54a5cfd-28eb-4022-96ac-65e2655e1ab8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:42:17,227] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:42:17,227] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 09:42:17,228] [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
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	81.7608	293	406	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	81.7419	298	406	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	80.0881	257	406	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	80.0234	262	406	95	below_threshold
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	79.9075	263	406	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	78.8088	237	406	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.2286	231	406	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	78.209	206	406	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	77.9252	187	406	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	77.7701	170	406	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	77.743	165	406	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:42:17,228] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2811/tc_result.tsv
[2023-03-18 09:42:17,228] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:42:17,228] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:42:17,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd54a5cfd-28eb-4022-96ac-65e2655e1ab8/dqc_reference/checkm_data
[2023-03-18 09:42:17,229] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:42:17,232] [INFO] Task started: CheckM
[2023-03-18 09:42:17,232] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2811/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2811/checkm_input OceanDNA-b2811/checkm_result
[2023-03-18 09:42:40,259] [INFO] Task succeeded: CheckM
[2023-03-18 09:42:40,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:42:40,262] [INFO] ===== Completeness check finished =====
[2023-03-18 09:42:40,262] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:42:40,262] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2811/markers.fasta)
[2023-03-18 09:42:40,263] [INFO] Task started: Blastn
[2023-03-18 09:42:40,263] [INFO] Running command: blastn -query OceanDNA-b2811/markers.fasta -db /var/lib/cwl/stgd54a5cfd-28eb-4022-96ac-65e2655e1ab8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2811/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:42:41,103] [INFO] Task succeeded: Blastn
[2023-03-18 09:42:41,104] [INFO] Selected 7 target genomes.
[2023-03-18 09:42:41,104] [INFO] Target genome list was writen to OceanDNA-b2811/target_genomes_gtdb.txt
[2023-03-18 09:42:41,109] [INFO] Task started: fastANI
[2023-03-18 09:42:41,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c528345-d17e-47c1-922b-ffeee4702723/OceanDNA-b2811.fa --refList OceanDNA-b2811/target_genomes_gtdb.txt --output OceanDNA-b2811/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:42:44,134] [INFO] Task succeeded: fastANI
[2023-03-18 09:42:44,139] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:42:44,140] [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_009371975.2	s__Marinisubtilis pacificus	93.7922	382	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	97.81	97.81	0.83	0.83	2	-
GCF_013414345.1	s__Marinisubtilis indicus	93.1248	373	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCF_002813345.1	s__Marinisubtilis sp002813345	85.0013	322	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464255.1	s__Chryseoglobus sp001464255	82.658	246	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	82.5253	200	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012530535.1	s__Yonghaparkia sp012530535	82.1588	299	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	81.8812	303	406	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 09:42:44,140] [INFO] GTDB search result was written to OceanDNA-b2811/result_gtdb.tsv
[2023-03-18 09:42:44,140] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:42:44,141] [INFO] DFAST_QC result json was written to OceanDNA-b2811/dqc_result.json
[2023-03-18 09:42:44,141] [INFO] DFAST_QC completed!
[2023-03-18 09:42:44,141] [INFO] Total running time: 0h0m42s