[2023-03-16 04:52:20,128] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:52:20,128] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:52:20,129] [INFO] DQC Reference Directory: /var/lib/cwl/stgc01efb15-d5d9-4347-aa93-4a1fb3d0c030/dqc_reference
[2023-03-16 04:52:21,246] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:52:21,247] [INFO] Task started: Prodigal
[2023-03-16 04:52:21,247] [INFO] Running command: cat /var/lib/cwl/stg4431a43c-6797-4bf5-9424-836ce3b99dc1/OceanDNA-b44.fa | prodigal -d OceanDNA-b44/cds.fna -a OceanDNA-b44/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:53:01,268] [INFO] Task succeeded: Prodigal
[2023-03-16 04:53:01,268] [INFO] Task started: HMMsearch
[2023-03-16 04:53:01,268] [INFO] Running command: hmmsearch --tblout OceanDNA-b44/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc01efb15-d5d9-4347-aa93-4a1fb3d0c030/dqc_reference/reference_markers.hmm OceanDNA-b44/protein.faa > /dev/null
[2023-03-16 04:53:01,572] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:53:01,573] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4431a43c-6797-4bf5-9424-836ce3b99dc1/OceanDNA-b44.fa]
[2023-03-16 04:53:01,621] [INFO] Query marker FASTA was written to OceanDNA-b44/markers.fasta
[2023-03-16 04:53:01,621] [INFO] Task started: Blastn
[2023-03-16 04:53:01,622] [INFO] Running command: blastn -query OceanDNA-b44/markers.fasta -db /var/lib/cwl/stgc01efb15-d5d9-4347-aa93-4a1fb3d0c030/dqc_reference/reference_markers.fasta -out OceanDNA-b44/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:53:02,157] [INFO] Task succeeded: Blastn
[2023-03-16 04:53:02,157] [INFO] Selected 24 target genomes.
[2023-03-16 04:53:02,158] [INFO] Target genome list was writen to OceanDNA-b44/target_genomes.txt
[2023-03-16 04:53:02,169] [INFO] Task started: fastANI
[2023-03-16 04:53:02,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg4431a43c-6797-4bf5-9424-836ce3b99dc1/OceanDNA-b44.fa --refList OceanDNA-b44/target_genomes.txt --output OceanDNA-b44/fastani_result.tsv --threads 1
[2023-03-16 04:53:22,620] [INFO] Task succeeded: fastANI
[2023-03-16 04:53:22,620] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc01efb15-d5d9-4347-aa93-4a1fb3d0c030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:53:22,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc01efb15-d5d9-4347-aa93-4a1fb3d0c030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:53:22,625] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:53:22,625] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:53:22,625] [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
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	74.9359	55	2026	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.9232	90	2026	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8775	80	2026	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.8689	92	2026	95	below_threshold
Kitasatospora aureofaciens	strain=NRRL 2209	GCA_000978515.1	1894	1894	type	True	74.6664	73	2026	95	below_threshold
Kitasatospora aureofaciens	strain=ATCC 10762	GCA_001188955.3	1894	1894	type	True	74.6575	78	2026	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:53:22,625] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44/tc_result.tsv
[2023-03-16 04:53:22,626] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:53:22,626] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:53:22,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc01efb15-d5d9-4347-aa93-4a1fb3d0c030/dqc_reference/checkm_data
[2023-03-16 04:53:22,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:53:22,635] [INFO] Task started: CheckM
[2023-03-16 04:53:22,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44/checkm_input OceanDNA-b44/checkm_result
[2023-03-16 04:54:57,080] [INFO] Task succeeded: CheckM
[2023-03-16 04:54:57,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:54:57,085] [INFO] ===== Completeness check finished =====
[2023-03-16 04:54:57,085] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:54:57,085] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44/markers.fasta)
[2023-03-16 04:54:57,085] [INFO] Task started: Blastn
[2023-03-16 04:54:57,085] [INFO] Running command: blastn -query OceanDNA-b44/markers.fasta -db /var/lib/cwl/stgc01efb15-d5d9-4347-aa93-4a1fb3d0c030/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:57,862] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:57,863] [INFO] Selected 23 target genomes.
[2023-03-16 04:54:57,863] [INFO] Target genome list was writen to OceanDNA-b44/target_genomes_gtdb.txt
[2023-03-16 04:54:57,937] [INFO] Task started: fastANI
[2023-03-16 04:54:57,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg4431a43c-6797-4bf5-9424-836ce3b99dc1/OceanDNA-b44.fa --refList OceanDNA-b44/target_genomes_gtdb.txt --output OceanDNA-b44/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:11,976] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:11,980] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:55:11,980] [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_003697015.1	s__J023 sp003697015	76.4603	182	2026	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699405.1	s__JAAYLR01 sp016699405	75.5599	53	2026	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388555.1	s__QQVD01 sp003388555	75.4999	94	2026	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_014584695.1	s__JACTMI01 sp014584695	75.4524	52	2026	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525905.1	s__JACTMI01 sp011525905	75.3568	51	2026	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:11,980] [INFO] GTDB search result was written to OceanDNA-b44/result_gtdb.tsv
[2023-03-16 04:55:11,980] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:11,981] [INFO] DFAST_QC result json was written to OceanDNA-b44/dqc_result.json
[2023-03-16 04:55:11,981] [INFO] DFAST_QC completed!
[2023-03-16 04:55:11,981] [INFO] Total running time: 0h2m52s