[2023-03-18 22:39:28,799] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:39:28,800] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:39:28,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg18101e3f-50be-4b27-8fea-feaa0d0eb0b2/dqc_reference
[2023-03-18 22:39:29,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:39:29,948] [INFO] Task started: Prodigal
[2023-03-18 22:39:29,948] [INFO] Running command: cat /var/lib/cwl/stg15bab4c6-c407-4e13-b0c5-427e5b22ec8f/OceanDNA-b34861.fa | prodigal -d OceanDNA-b34861/cds.fna -a OceanDNA-b34861/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:39:36,110] [INFO] Task succeeded: Prodigal
[2023-03-18 22:39:36,110] [INFO] Task started: HMMsearch
[2023-03-18 22:39:36,110] [INFO] Running command: hmmsearch --tblout OceanDNA-b34861/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18101e3f-50be-4b27-8fea-feaa0d0eb0b2/dqc_reference/reference_markers.hmm OceanDNA-b34861/protein.faa > /dev/null
[2023-03-18 22:39:36,270] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:39:36,271] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg15bab4c6-c407-4e13-b0c5-427e5b22ec8f/OceanDNA-b34861.fa]
[2023-03-18 22:39:36,285] [INFO] Query marker FASTA was written to OceanDNA-b34861/markers.fasta
[2023-03-18 22:39:36,286] [INFO] Task started: Blastn
[2023-03-18 22:39:36,286] [INFO] Running command: blastn -query OceanDNA-b34861/markers.fasta -db /var/lib/cwl/stg18101e3f-50be-4b27-8fea-feaa0d0eb0b2/dqc_reference/reference_markers.fasta -out OceanDNA-b34861/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:39:36,737] [INFO] Task succeeded: Blastn
[2023-03-18 22:39:36,738] [INFO] Selected 18 target genomes.
[2023-03-18 22:39:36,738] [INFO] Target genome list was writen to OceanDNA-b34861/target_genomes.txt
[2023-03-18 22:39:36,750] [INFO] Task started: fastANI
[2023-03-18 22:39:36,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg15bab4c6-c407-4e13-b0c5-427e5b22ec8f/OceanDNA-b34861.fa --refList OceanDNA-b34861/target_genomes.txt --output OceanDNA-b34861/fastani_result.tsv --threads 1
[2023-03-18 22:39:47,182] [INFO] Task succeeded: fastANI
[2023-03-18 22:39:47,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18101e3f-50be-4b27-8fea-feaa0d0eb0b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:39:47,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18101e3f-50be-4b27-8fea-feaa0d0eb0b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:39:47,194] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 22:39:47,194] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 22:39:47,194] [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
Idiomarina aquatica	strain=SN-14	GCA_003987185.1	1327752	1327752	type	True	98.1033	198	217	95	conclusive
Idiomarina seosinensis	strain=CL-SP19	GCA_003987275.1	281739	281739	type	True	78.7998	63	217	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:39:47,194] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34861/tc_result.tsv
[2023-03-18 22:39:47,194] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:39:47,194] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:39:47,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18101e3f-50be-4b27-8fea-feaa0d0eb0b2/dqc_reference/checkm_data
[2023-03-18 22:39:47,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:39:47,198] [INFO] Task started: CheckM
[2023-03-18 22:39:47,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34861/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34861/checkm_input OceanDNA-b34861/checkm_result
[2023-03-18 22:40:08,927] [INFO] Task succeeded: CheckM
[2023-03-18 22:40:08,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.41%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:40:08,929] [INFO] ===== Completeness check finished =====
[2023-03-18 22:40:08,930] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:40:08,930] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34861/markers.fasta)
[2023-03-18 22:40:08,931] [INFO] Task started: Blastn
[2023-03-18 22:40:08,931] [INFO] Running command: blastn -query OceanDNA-b34861/markers.fasta -db /var/lib/cwl/stg18101e3f-50be-4b27-8fea-feaa0d0eb0b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34861/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:40:09,518] [INFO] Task succeeded: Blastn
[2023-03-18 22:40:09,519] [INFO] Selected 16 target genomes.
[2023-03-18 22:40:09,519] [INFO] Target genome list was writen to OceanDNA-b34861/target_genomes_gtdb.txt
[2023-03-18 22:40:09,530] [INFO] Task started: fastANI
[2023-03-18 22:40:09,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg15bab4c6-c407-4e13-b0c5-427e5b22ec8f/OceanDNA-b34861.fa --refList OceanDNA-b34861/target_genomes_gtdb.txt --output OceanDNA-b34861/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:40:16,541] [INFO] Task succeeded: fastANI
[2023-03-18 22:40:16,544] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:40:16,544] [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_003987185.1	s__Idiomarina aquatica	98.1033	198	217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	conclusive
GCF_004362895.1	s__Idiomarina sp002729675	79.87	98	217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.61	97.37	0.88	0.80	5	-
GCF_003987275.1	s__Idiomarina seosinensis	78.7998	63	217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:40:16,545] [INFO] GTDB search result was written to OceanDNA-b34861/result_gtdb.tsv
[2023-03-18 22:40:16,545] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:40:16,545] [INFO] DFAST_QC result json was written to OceanDNA-b34861/dqc_result.json
[2023-03-18 22:40:16,545] [INFO] DFAST_QC completed!
[2023-03-18 22:40:16,545] [INFO] Total running time: 0h0m48s