[2023-03-18 20:40:39,438] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,454] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a6c6c75-9a60-4c6f-99e4-63ab1944cf04/dqc_reference
[2023-03-18 20:40:41,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,208] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,208] [INFO] Running command: cat /var/lib/cwl/stg7143330d-34bc-4be1-8def-4a1e69e7cd0f/OceanDNA-b31529.fa | prodigal -d OceanDNA-b31529/cds.fna -a OceanDNA-b31529/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:58,007] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:58,007] [INFO] Task started: HMMsearch
[2023-03-18 20:40:58,007] [INFO] Running command: hmmsearch --tblout OceanDNA-b31529/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a6c6c75-9a60-4c6f-99e4-63ab1944cf04/dqc_reference/reference_markers.hmm OceanDNA-b31529/protein.faa > /dev/null
[2023-03-18 20:40:58,258] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:58,259] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7143330d-34bc-4be1-8def-4a1e69e7cd0f/OceanDNA-b31529.fa]
[2023-03-18 20:40:58,284] [INFO] Query marker FASTA was written to OceanDNA-b31529/markers.fasta
[2023-03-18 20:40:58,284] [INFO] Task started: Blastn
[2023-03-18 20:40:58,284] [INFO] Running command: blastn -query OceanDNA-b31529/markers.fasta -db /var/lib/cwl/stg0a6c6c75-9a60-4c6f-99e4-63ab1944cf04/dqc_reference/reference_markers.fasta -out OceanDNA-b31529/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:58,929] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:58,929] [INFO] Selected 18 target genomes.
[2023-03-18 20:40:58,930] [INFO] Target genome list was writen to OceanDNA-b31529/target_genomes.txt
[2023-03-18 20:40:58,936] [INFO] Task started: fastANI
[2023-03-18 20:40:58,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg7143330d-34bc-4be1-8def-4a1e69e7cd0f/OceanDNA-b31529.fa --refList OceanDNA-b31529/target_genomes.txt --output OceanDNA-b31529/fastani_result.tsv --threads 1
[2023-03-18 20:41:11,477] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:11,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a6c6c75-9a60-4c6f-99e4-63ab1944cf04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:11,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a6c6c75-9a60-4c6f-99e4-63ab1944cf04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:11,483] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:11,483] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:11,483] [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
Kordiimonas gwangyangensis	strain=JCM 12864	GCA_000616065.1	288022	288022	type	True	82.8952	607	870	95	below_threshold
Kordiimonas gwangyangensis	strain=DSM 19435	GCA_000375545.1	288022	288022	type	True	82.8338	618	870	95	below_threshold
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	79.2207	279	870	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	78.4066	284	870	95	below_threshold
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	78.4042	288	870	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	78.3547	256	870	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:11,483] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31529/tc_result.tsv
[2023-03-18 20:41:11,483] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:11,484] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:11,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a6c6c75-9a60-4c6f-99e4-63ab1944cf04/dqc_reference/checkm_data
[2023-03-18 20:41:11,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:11,490] [INFO] Task started: CheckM
[2023-03-18 20:41:11,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31529/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31529/checkm_input OceanDNA-b31529/checkm_result
[2023-03-18 20:41:55,959] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:55,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.32%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:55,963] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:55,963] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:55,963] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31529/markers.fasta)
[2023-03-18 20:41:55,963] [INFO] Task started: Blastn
[2023-03-18 20:41:55,963] [INFO] Running command: blastn -query OceanDNA-b31529/markers.fasta -db /var/lib/cwl/stg0a6c6c75-9a60-4c6f-99e4-63ab1944cf04/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31529/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:56,999] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:57,000] [INFO] Selected 17 target genomes.
[2023-03-18 20:41:57,000] [INFO] Target genome list was writen to OceanDNA-b31529/target_genomes_gtdb.txt
[2023-03-18 20:41:57,022] [INFO] Task started: fastANI
[2023-03-18 20:41:57,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg7143330d-34bc-4be1-8def-4a1e69e7cd0f/OceanDNA-b31529.fa --refList OceanDNA-b31529/target_genomes_gtdb.txt --output OceanDNA-b31529/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:09,249] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:09,253] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:42:09,254] [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_000375545.1	s__Kordiimonas gwangyangensis	82.8292	619	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	99.96	99.96	1.00	1.00	2	-
GCF_001550065.1	s__Kordiimonas lipolytica	79.2306	280	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226495.1	s__Kordiimonas sp006226495	78.466	320	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550055.1	s__Kordiimonas lacus	78.4042	288	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCA_013372975.1	s__Kordiimonas sp013372975	77.4295	183	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372925.1	s__Kordiimonas sp013372925	77.1961	167	870	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:09,254] [INFO] GTDB search result was written to OceanDNA-b31529/result_gtdb.tsv
[2023-03-18 20:42:09,254] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:09,255] [INFO] DFAST_QC result json was written to OceanDNA-b31529/dqc_result.json
[2023-03-18 20:42:09,255] [INFO] DFAST_QC completed!
[2023-03-18 20:42:09,255] [INFO] Total running time: 0h1m30s