[2023-03-16 05:09:10,899] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:09:10,900] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:09:10,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f81739f-64e8-43ea-8e69-84c8ed064eab/dqc_reference
[2023-03-16 05:09:12,096] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:09:12,096] [INFO] Task started: Prodigal
[2023-03-16 05:09:12,096] [INFO] Running command: cat /var/lib/cwl/stgeaef9527-9c28-4e66-ac18-021207e56443/OceanDNA-b31528.fa | prodigal -d OceanDNA-b31528/cds.fna -a OceanDNA-b31528/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:09:30,102] [INFO] Task succeeded: Prodigal
[2023-03-16 05:09:30,102] [INFO] Task started: HMMsearch
[2023-03-16 05:09:30,102] [INFO] Running command: hmmsearch --tblout OceanDNA-b31528/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f81739f-64e8-43ea-8e69-84c8ed064eab/dqc_reference/reference_markers.hmm OceanDNA-b31528/protein.faa > /dev/null
[2023-03-16 05:09:30,294] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:09:30,294] [INFO] Found 6/6 markers.
[2023-03-16 05:09:30,316] [INFO] Query marker FASTA was written to OceanDNA-b31528/markers.fasta
[2023-03-16 05:09:30,318] [INFO] Task started: Blastn
[2023-03-16 05:09:30,318] [INFO] Running command: blastn -query OceanDNA-b31528/markers.fasta -db /var/lib/cwl/stg7f81739f-64e8-43ea-8e69-84c8ed064eab/dqc_reference/reference_markers.fasta -out OceanDNA-b31528/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:30,890] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:30,891] [INFO] Selected 23 target genomes.
[2023-03-16 05:09:30,892] [INFO] Target genome list was writen to OceanDNA-b31528/target_genomes.txt
[2023-03-16 05:09:30,906] [INFO] Task started: fastANI
[2023-03-16 05:09:30,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaef9527-9c28-4e66-ac18-021207e56443/OceanDNA-b31528.fa --refList OceanDNA-b31528/target_genomes.txt --output OceanDNA-b31528/fastani_result.tsv --threads 1
[2023-03-16 05:09:41,932] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:41,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f81739f-64e8-43ea-8e69-84c8ed064eab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:09:41,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f81739f-64e8-43ea-8e69-84c8ed064eab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:09:41,938] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:09:41,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:09:41,938] [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 laminariae	strain=5E331	GCA_023008165.1	2917717	2917717	type	True	76.7585	105	1037	95	below_threshold
Kordiimonas pumila	strain=N18	GCA_015240255.1	2161677	2161677	type	True	76.5376	97	1037	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	76.0408	59	1037	95	below_threshold
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	76.0287	58	1037	95	below_threshold
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	75.8897	57	1037	95	below_threshold
Kordiimonas gwangyangensis	strain=DSM 19435	GCA_000375545.1	288022	288022	type	True	75.8816	64	1037	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:09:41,939] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31528/tc_result.tsv
[2023-03-16 05:09:41,939] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:09:41,939] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:09:41,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f81739f-64e8-43ea-8e69-84c8ed064eab/dqc_reference/checkm_data
[2023-03-16 05:09:41,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:09:41,944] [INFO] Task started: CheckM
[2023-03-16 05:09:41,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31528/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31528/checkm_input OceanDNA-b31528/checkm_result
[2023-03-16 05:10:28,434] [INFO] Task succeeded: CheckM
[2023-03-16 05:10:28,435] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 05:10:28,438] [INFO] ===== Completeness check finished =====
[2023-03-16 05:10:28,438] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:10:28,438] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31528/markers.fasta)
[2023-03-16 05:10:28,439] [INFO] Task started: Blastn
[2023-03-16 05:10:28,439] [INFO] Running command: blastn -query OceanDNA-b31528/markers.fasta -db /var/lib/cwl/stg7f81739f-64e8-43ea-8e69-84c8ed064eab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31528/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:10:29,369] [INFO] Task succeeded: Blastn
[2023-03-16 05:10:29,371] [INFO] Selected 33 target genomes.
[2023-03-16 05:10:29,371] [INFO] Target genome list was writen to OceanDNA-b31528/target_genomes_gtdb.txt
[2023-03-16 05:10:29,522] [INFO] Task started: fastANI
[2023-03-16 05:10:29,522] [INFO] Running command: fastANI --query /var/lib/cwl/stgeaef9527-9c28-4e66-ac18-021207e56443/OceanDNA-b31528.fa --refList OceanDNA-b31528/target_genomes_gtdb.txt --output OceanDNA-b31528/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:10:45,152] [INFO] Task succeeded: fastANI
[2023-03-16 05:10:45,158] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:10:45,158] [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
GCA_016765035.1	s__Kordiimonas sp016765035	76.9031	125	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763495.1	s__Kordiimonas sp016763495	76.8571	68	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015240255.1	s__Kordiimonas pumila	76.5376	97	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372975.1	s__Kordiimonas sp013372975	76.345	77	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401685.1	s__Kordiimonas sp002401685	76.3346	64	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764715.1	s__Kordiimonas sp016764715	76.1572	62	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640725.1	s__Kordiimonas sp017640725	76.0436	53	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	100.00	100.00	0.99	0.98	3	-
GCF_001550055.1	s__Kordiimonas lacus	76.0287	58	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCF_001550065.1	s__Kordiimonas lipolytica	75.8897	57	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656395.1	s__Kordiimonas sediminis	75.8207	55	1037	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:10:45,159] [INFO] GTDB search result was written to OceanDNA-b31528/result_gtdb.tsv
[2023-03-16 05:10:45,159] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:10:45,160] [INFO] DFAST_QC result json was written to OceanDNA-b31528/dqc_result.json
[2023-03-16 05:10:45,161] [INFO] DFAST_QC completed!
[2023-03-16 05:10:45,161] [INFO] Total running time: 0h1m34s