[2023-03-15 15:18:21,953] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:21,954] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:21,954] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbcce487-ff8b-4a00-af7d-02474dbf3e26/dqc_reference
[2023-03-15 15:18:23,069] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,069] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,069] [INFO] Running command: cat /var/lib/cwl/stg15e957ad-1a6d-4238-9d78-8cd7e5aea2ef/OceanDNA-b35111.fa | prodigal -d OceanDNA-b35111/cds.fna -a OceanDNA-b35111/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:32,201] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:32,202] [INFO] Task started: HMMsearch
[2023-03-15 15:18:32,202] [INFO] Running command: hmmsearch --tblout OceanDNA-b35111/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbcce487-ff8b-4a00-af7d-02474dbf3e26/dqc_reference/reference_markers.hmm OceanDNA-b35111/protein.faa > /dev/null
[2023-03-15 15:18:32,410] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:32,410] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg15e957ad-1a6d-4238-9d78-8cd7e5aea2ef/OceanDNA-b35111.fa]
[2023-03-15 15:18:32,435] [INFO] Query marker FASTA was written to OceanDNA-b35111/markers.fasta
[2023-03-15 15:18:32,437] [INFO] Task started: Blastn
[2023-03-15 15:18:32,437] [INFO] Running command: blastn -query OceanDNA-b35111/markers.fasta -db /var/lib/cwl/stgcbcce487-ff8b-4a00-af7d-02474dbf3e26/dqc_reference/reference_markers.fasta -out OceanDNA-b35111/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:32,978] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:32,980] [INFO] Selected 23 target genomes.
[2023-03-15 15:18:32,980] [INFO] Target genome list was writen to OceanDNA-b35111/target_genomes.txt
[2023-03-15 15:18:32,997] [INFO] Task started: fastANI
[2023-03-15 15:18:32,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg15e957ad-1a6d-4238-9d78-8cd7e5aea2ef/OceanDNA-b35111.fa --refList OceanDNA-b35111/target_genomes.txt --output OceanDNA-b35111/fastani_result.tsv --threads 1
[2023-03-15 15:18:47,165] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:47,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbcce487-ff8b-4a00-af7d-02474dbf3e26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:47,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbcce487-ff8b-4a00-af7d-02474dbf3e26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:47,170] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:18:47,170] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:18:47,170] [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 aestuarii	strain=PSC101	GCA_017948405.1	1266052	1266052	type	True	81.9005	324	566	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	79.3547	153	566	95	below_threshold
Psychrosphaera saromensis	strain=SA4-48	GCA_002954545.1	716813	716813	type	True	78.2273	108	566	95	below_threshold
Psychrosphaera saromensis	strain=KCTC 23240	GCA_014652155.1	716813	716813	type	True	78.2009	106	566	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:18:47,173] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35111/tc_result.tsv
[2023-03-15 15:18:47,176] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:47,177] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:47,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbcce487-ff8b-4a00-af7d-02474dbf3e26/dqc_reference/checkm_data
[2023-03-15 15:18:47,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:47,290] [INFO] Task started: CheckM
[2023-03-15 15:18:47,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35111/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35111/checkm_input OceanDNA-b35111/checkm_result
[2023-03-15 15:19:15,068] [INFO] Task succeeded: CheckM
[2023-03-15 15:19:15,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:19:15,082] [INFO] ===== Completeness check finished =====
[2023-03-15 15:19:15,082] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:19:15,082] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35111/markers.fasta)
[2023-03-15 15:19:15,083] [INFO] Task started: Blastn
[2023-03-15 15:19:15,083] [INFO] Running command: blastn -query OceanDNA-b35111/markers.fasta -db /var/lib/cwl/stgcbcce487-ff8b-4a00-af7d-02474dbf3e26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35111/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:19:15,882] [INFO] Task succeeded: Blastn
[2023-03-15 15:19:15,893] [INFO] Selected 13 target genomes.
[2023-03-15 15:19:15,893] [INFO] Target genome list was writen to OceanDNA-b35111/target_genomes_gtdb.txt
[2023-03-15 15:19:15,907] [INFO] Task started: fastANI
[2023-03-15 15:19:15,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg15e957ad-1a6d-4238-9d78-8cd7e5aea2ef/OceanDNA-b35111.fa --refList OceanDNA-b35111/target_genomes_gtdb.txt --output OceanDNA-b35111/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:19:24,454] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:24,459] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:19:24,459] [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_009728465.1	s__Psychrosphaera haliotis	96.6902	529	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017948405.1	s__Psychrosphaera aestuarii	81.9005	324	566	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017638545.1	s__Psychrosphaera sp017638545	79.3489	154	566	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	78.2273	108	566	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	78.1703	107	566	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	78.0542	118	566	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 15:19:24,464] [INFO] GTDB search result was written to OceanDNA-b35111/result_gtdb.tsv
[2023-03-15 15:19:24,472] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:19:24,477] [INFO] DFAST_QC result json was written to OceanDNA-b35111/dqc_result.json
[2023-03-15 15:19:24,477] [INFO] DFAST_QC completed!
[2023-03-15 15:19:24,477] [INFO] Total running time: 0h1m3s