[2023-03-15 15:55:16,219] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:16,219] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:16,220] [INFO] DQC Reference Directory: /var/lib/cwl/stgf13c10e0-dcbb-4461-8d3f-e3620e897781/dqc_reference
[2023-03-15 15:55:17,912] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:17,913] [INFO] Task started: Prodigal
[2023-03-15 15:55:17,913] [INFO] Running command: cat /var/lib/cwl/stgeba7d7f7-f798-4e34-9ff9-2196d6baecaa/OceanDNA-b35218.fa | prodigal -d OceanDNA-b35218/cds.fna -a OceanDNA-b35218/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:43,037] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:43,038] [INFO] Task started: HMMsearch
[2023-03-15 15:55:43,038] [INFO] Running command: hmmsearch --tblout OceanDNA-b35218/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf13c10e0-dcbb-4461-8d3f-e3620e897781/dqc_reference/reference_markers.hmm OceanDNA-b35218/protein.faa > /dev/null
[2023-03-15 15:55:43,336] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:43,337] [INFO] Found 6/6 markers.
[2023-03-15 15:55:43,378] [INFO] Query marker FASTA was written to OceanDNA-b35218/markers.fasta
[2023-03-15 15:55:43,379] [INFO] Task started: Blastn
[2023-03-15 15:55:43,380] [INFO] Running command: blastn -query OceanDNA-b35218/markers.fasta -db /var/lib/cwl/stgf13c10e0-dcbb-4461-8d3f-e3620e897781/dqc_reference/reference_markers.fasta -out OceanDNA-b35218/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:44,072] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:44,073] [INFO] Selected 10 target genomes.
[2023-03-15 15:55:44,073] [INFO] Target genome list was writen to OceanDNA-b35218/target_genomes.txt
[2023-03-15 15:55:44,081] [INFO] Task started: fastANI
[2023-03-15 15:55:44,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgeba7d7f7-f798-4e34-9ff9-2196d6baecaa/OceanDNA-b35218.fa --refList OceanDNA-b35218/target_genomes.txt --output OceanDNA-b35218/fastani_result.tsv --threads 1
[2023-03-15 15:55:53,304] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:53,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf13c10e0-dcbb-4461-8d3f-e3620e897781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:53,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf13c10e0-dcbb-4461-8d3f-e3620e897781/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:53,312] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:53,312] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:55:53,312] [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
Moritella yayanosii	strain=DB21MT 5	GCA_900465055.1	69539	69539	type	True	93.216	1192	1529	95	below_threshold
Moritella dasanensis	strain=ArB 0140	GCA_000276805.1	428031	428031	type	True	85.3214	1160	1529	95	below_threshold
Moritella marina	strain=ATCC 15381	GCA_000291685.1	90736	90736	type	True	84.1448	1049	1529	95	below_threshold
Moritella marina	strain=MP-1	GCA_000381865.1	90736	90736	type	True	84.1305	1074	1529	95	below_threshold
Moritella marina	strain=MP-1	GCA_008931805.1	90736	90736	type	True	84.122	1061	1529	95	below_threshold
Motilimonas eburnea	strain=YH6	GCA_021295345.1	1737488	1737488	type	True	76.7077	59	1529	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.5478	64	1529	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.2899	63	1529	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	76.2132	61	1529	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:55:53,312] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35218/tc_result.tsv
[2023-03-15 15:55:53,312] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:53,312] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:53,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf13c10e0-dcbb-4461-8d3f-e3620e897781/dqc_reference/checkm_data
[2023-03-15 15:55:53,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:53,319] [INFO] Task started: CheckM
[2023-03-15 15:55:53,320] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35218/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35218/checkm_input OceanDNA-b35218/checkm_result
[2023-03-15 15:56:55,265] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:55,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:55,268] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:55,269] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:55,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35218/markers.fasta)
[2023-03-15 15:56:55,270] [INFO] Task started: Blastn
[2023-03-15 15:56:55,270] [INFO] Running command: blastn -query OceanDNA-b35218/markers.fasta -db /var/lib/cwl/stgf13c10e0-dcbb-4461-8d3f-e3620e897781/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35218/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:56,343] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:56,344] [INFO] Selected 6 target genomes.
[2023-03-15 15:56:56,344] [INFO] Target genome list was writen to OceanDNA-b35218/target_genomes_gtdb.txt
[2023-03-15 15:56:56,350] [INFO] Task started: fastANI
[2023-03-15 15:56:56,350] [INFO] Running command: fastANI --query /var/lib/cwl/stgeba7d7f7-f798-4e34-9ff9-2196d6baecaa/OceanDNA-b35218.fa --refList OceanDNA-b35218/target_genomes_gtdb.txt --output OceanDNA-b35218/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:57:03,608] [INFO] Task succeeded: fastANI
[2023-03-15 15:57:03,613] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:57:03,613] [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_000170855.1	s__Moritella sp000170855	95.3572	1275	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	97.45	95.37	0.88	0.83	4	conclusive
GCA_013215705.1	s__Moritella sp013215705	93.7324	1254	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	95.77	95.77	0.82	0.82	2	-
GCF_900465055.1	s__Moritella yayanosii	93.216	1192	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001574435.1	s__Moritella sp001574435	87.3376	1095	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219455.1	s__Moritella sp018219455	86.4377	1102	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	96.81	96.78	0.88	0.87	3	-
GCA_000953735.1	s__Moritella viscosa	86.1014	1090	1529	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	99.48	99.13	0.93	0.91	13	-
--------------------------------------------------------------------------------
[2023-03-15 15:57:03,613] [INFO] GTDB search result was written to OceanDNA-b35218/result_gtdb.tsv
[2023-03-15 15:57:03,614] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:57:03,615] [INFO] DFAST_QC result json was written to OceanDNA-b35218/dqc_result.json
[2023-03-15 15:57:03,615] [INFO] DFAST_QC completed!
[2023-03-15 15:57:03,615] [INFO] Total running time: 0h1m47s