[2023-03-15 13:45:07,861] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:45:07,861] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:45:07,861] [INFO] DQC Reference Directory: /var/lib/cwl/stgc36bc550-32f9-41ce-b85b-cd8d3ec231ea/dqc_reference
[2023-03-15 13:45:09,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:45:09,270] [INFO] Task started: Prodigal
[2023-03-15 13:45:09,270] [INFO] Running command: cat /var/lib/cwl/stg73c5a4ee-d4c1-437e-98e0-6b85386f2d49/OceanDNA-b35107.fa | prodigal -d OceanDNA-b35107/cds.fna -a OceanDNA-b35107/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:45:16,172] [INFO] Task succeeded: Prodigal
[2023-03-15 13:45:16,173] [INFO] Task started: HMMsearch
[2023-03-15 13:45:16,173] [INFO] Running command: hmmsearch --tblout OceanDNA-b35107/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc36bc550-32f9-41ce-b85b-cd8d3ec231ea/dqc_reference/reference_markers.hmm OceanDNA-b35107/protein.faa > /dev/null
[2023-03-15 13:45:16,351] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:45:16,352] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg73c5a4ee-d4c1-437e-98e0-6b85386f2d49/OceanDNA-b35107.fa]
[2023-03-15 13:45:16,367] [INFO] Query marker FASTA was written to OceanDNA-b35107/markers.fasta
[2023-03-15 13:45:16,369] [INFO] Task started: Blastn
[2023-03-15 13:45:16,369] [INFO] Running command: blastn -query OceanDNA-b35107/markers.fasta -db /var/lib/cwl/stgc36bc550-32f9-41ce-b85b-cd8d3ec231ea/dqc_reference/reference_markers.fasta -out OceanDNA-b35107/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:16,976] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:16,977] [INFO] Selected 30 target genomes.
[2023-03-15 13:45:16,977] [INFO] Target genome list was writen to OceanDNA-b35107/target_genomes.txt
[2023-03-15 13:45:16,996] [INFO] Task started: fastANI
[2023-03-15 13:45:16,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg73c5a4ee-d4c1-437e-98e0-6b85386f2d49/OceanDNA-b35107.fa --refList OceanDNA-b35107/target_genomes.txt --output OceanDNA-b35107/fastani_result.tsv --threads 1
[2023-03-15 13:45:34,323] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:34,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc36bc550-32f9-41ce-b85b-cd8d3ec231ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:45:34,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc36bc550-32f9-41ce-b85b-cd8d3ec231ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:45:34,329] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:45:34,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:45:34,329] [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
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	80.0323	177	373	95	below_threshold
Psychrosphaera aestuarii	strain=PSC101	GCA_017948405.1	1266052	1266052	type	True	78.6418	111	373	95	below_threshold
Psychrosphaera saromensis	strain=SA4-48	GCA_002954545.1	716813	716813	type	True	77.8081	53	373	95	below_threshold
Psychrosphaera saromensis	strain=KCTC 23240	GCA_014652155.1	716813	716813	type	True	77.7678	52	373	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:45:34,329] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35107/tc_result.tsv
[2023-03-15 13:45:34,330] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:45:34,330] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:45:34,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc36bc550-32f9-41ce-b85b-cd8d3ec231ea/dqc_reference/checkm_data
[2023-03-15 13:45:34,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:45:34,334] [INFO] Task started: CheckM
[2023-03-15 13:45:34,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35107/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35107/checkm_input OceanDNA-b35107/checkm_result
[2023-03-15 13:45:57,240] [INFO] Task succeeded: CheckM
[2023-03-15 13:45:57,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:45:57,242] [INFO] ===== Completeness check finished =====
[2023-03-15 13:45:57,243] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:45:57,243] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35107/markers.fasta)
[2023-03-15 13:45:57,244] [INFO] Task started: Blastn
[2023-03-15 13:45:57,244] [INFO] Running command: blastn -query OceanDNA-b35107/markers.fasta -db /var/lib/cwl/stgc36bc550-32f9-41ce-b85b-cd8d3ec231ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35107/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:58,188] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:58,190] [INFO] Selected 25 target genomes.
[2023-03-15 13:45:58,190] [INFO] Target genome list was writen to OceanDNA-b35107/target_genomes_gtdb.txt
[2023-03-15 13:45:58,217] [INFO] Task started: fastANI
[2023-03-15 13:45:58,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg73c5a4ee-d4c1-437e-98e0-6b85386f2d49/OceanDNA-b35107.fa --refList OceanDNA-b35107/target_genomes_gtdb.txt --output OceanDNA-b35107/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:46:13,905] [INFO] Task succeeded: fastANI
[2023-03-15 13:46:13,910] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:46:13,910] [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_017638545.1	s__Psychrosphaera sp017638545	80.0323	177	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728465.1	s__Psychrosphaera haliotis	78.811	112	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948405.1	s__Psychrosphaera aestuarii	78.6418	111	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954545.1	s__Psychrosphaera saromensis	77.8081	53	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018861025.1	s__Psychrosphaera sp018861025	77.7752	54	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018860345.1	s__Psychrosphaera sp018860345	77.5999	62	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373245.1	s__Psychrosphaera sp013373245	76.8833	54	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:46:13,911] [INFO] GTDB search result was written to OceanDNA-b35107/result_gtdb.tsv
[2023-03-15 13:46:13,911] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:46:13,912] [INFO] DFAST_QC result json was written to OceanDNA-b35107/dqc_result.json
[2023-03-15 13:46:13,912] [INFO] DFAST_QC completed!
[2023-03-15 13:46:13,912] [INFO] Total running time: 0h1m6s