[2023-03-18 02:27:37,200] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,200] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f027f4b-b93d-4ae8-bb0b-651e182d6b47/dqc_reference
[2023-03-18 02:27:38,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,463] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,463] [INFO] Running command: cat /var/lib/cwl/stg8500a453-490f-4fcc-9baa-2210f20aaae8/OceanDNA-b4136.fa | prodigal -d OceanDNA-b4136/cds.fna -a OceanDNA-b4136/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:28:02,185] [INFO] Task succeeded: Prodigal
[2023-03-18 02:28:02,186] [INFO] Task started: HMMsearch
[2023-03-18 02:28:02,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b4136/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f027f4b-b93d-4ae8-bb0b-651e182d6b47/dqc_reference/reference_markers.hmm OceanDNA-b4136/protein.faa > /dev/null
[2023-03-18 02:28:02,466] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:28:02,467] [INFO] Found 6/6 markers.
[2023-03-18 02:28:02,489] [INFO] Query marker FASTA was written to OceanDNA-b4136/markers.fasta
[2023-03-18 02:28:02,489] [INFO] Task started: Blastn
[2023-03-18 02:28:02,489] [INFO] Running command: blastn -query OceanDNA-b4136/markers.fasta -db /var/lib/cwl/stg2f027f4b-b93d-4ae8-bb0b-651e182d6b47/dqc_reference/reference_markers.fasta -out OceanDNA-b4136/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:03,030] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:03,031] [INFO] Selected 10 target genomes.
[2023-03-18 02:28:03,031] [INFO] Target genome list was writen to OceanDNA-b4136/target_genomes.txt
[2023-03-18 02:28:03,037] [INFO] Task started: fastANI
[2023-03-18 02:28:03,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg8500a453-490f-4fcc-9baa-2210f20aaae8/OceanDNA-b4136.fa --refList OceanDNA-b4136/target_genomes.txt --output OceanDNA-b4136/fastani_result.tsv --threads 1
[2023-03-18 02:28:09,541] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:09,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f027f4b-b93d-4ae8-bb0b-651e182d6b47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:09,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f027f4b-b93d-4ae8-bb0b-651e182d6b47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:09,546] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:28:09,546] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:28:09,546] [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
Roseivirga echinicomitans	strain=KMM 6058	GCA_001592935.1	296218	296218	type	True	89.8831	857	1067	95	below_threshold
Roseivirga ehrenbergii	strain=DSM 102268	GCA_004340805.1	279360	279360	type	True	85.3912	825	1067	95	below_threshold
Roseivirga ehrenbergii	strain=KMM 6017	GCA_001593005.1	279360	279360	type	True	85.3601	821	1067	95	below_threshold
Roseivirga seohaensis subsp. aquiponti	strain=D-25	GCA_001267955.1	1566026	1914963	type	True	84.9508	793	1067	95	below_threshold
Roseivirga seohaensis	strain=SW-152	GCA_001592945.1	1914963	1914963	type	True	84.8895	801	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:09,547] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4136/tc_result.tsv
[2023-03-18 02:28:09,547] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:09,547] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:09,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f027f4b-b93d-4ae8-bb0b-651e182d6b47/dqc_reference/checkm_data
[2023-03-18 02:28:09,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:09,570] [INFO] Task started: CheckM
[2023-03-18 02:28:09,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4136/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4136/checkm_input OceanDNA-b4136/checkm_result
[2023-03-18 02:29:10,112] [INFO] Task succeeded: CheckM
[2023-03-18 02:29:10,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:29:10,115] [INFO] ===== Completeness check finished =====
[2023-03-18 02:29:10,115] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:29:10,116] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4136/markers.fasta)
[2023-03-18 02:29:10,116] [INFO] Task started: Blastn
[2023-03-18 02:29:10,116] [INFO] Running command: blastn -query OceanDNA-b4136/markers.fasta -db /var/lib/cwl/stg2f027f4b-b93d-4ae8-bb0b-651e182d6b47/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4136/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:29:10,871] [INFO] Task succeeded: Blastn
[2023-03-18 02:29:10,872] [INFO] Selected 14 target genomes.
[2023-03-18 02:29:10,872] [INFO] Target genome list was writen to OceanDNA-b4136/target_genomes_gtdb.txt
[2023-03-18 02:29:10,882] [INFO] Task started: fastANI
[2023-03-18 02:29:10,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg8500a453-490f-4fcc-9baa-2210f20aaae8/OceanDNA-b4136.fa --refList OceanDNA-b4136/target_genomes_gtdb.txt --output OceanDNA-b4136/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:29:22,633] [INFO] Task succeeded: fastANI
[2023-03-18 02:29:22,638] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:29:22,638] [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_001592935.1	s__Roseivirga echinicomitans	89.9011	856	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593005.1	s__Roseivirga ehrenbergii	85.3866	819	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001592945.1	s__Roseivirga seohaensis	84.9026	800	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	97.29	97.29	0.91	0.91	2	-
GCA_002786855.1	s__Roseivirga sp002786855	77.4306	267	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	99.94	99.94	0.97	0.97	2	-
GCF_900111145.1	s__Fabibacter pacificus	76.729	111	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001592965.1	s__Fabibacter spongicola	76.449	93	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	97.73	96.54	0.93	0.88	5	-
GCF_001747095.1	s__Fabibacter sp001747095	76.2929	78	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:29:22,638] [INFO] GTDB search result was written to OceanDNA-b4136/result_gtdb.tsv
[2023-03-18 02:29:22,638] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:29:22,639] [INFO] DFAST_QC result json was written to OceanDNA-b4136/dqc_result.json
[2023-03-18 02:29:22,639] [INFO] DFAST_QC completed!
[2023-03-18 02:29:22,639] [INFO] Total running time: 0h1m45s