[2023-03-18 07:54:29,620] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:29,620] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:29,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f059975-9e1a-4a3d-84c7-0c80c287e0de/dqc_reference
[2023-03-18 07:54:30,703] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:30,704] [INFO] Task started: Prodigal
[2023-03-18 07:54:30,704] [INFO] Running command: cat /var/lib/cwl/stg7b32e119-e885-4403-85f0-1ebfccd42016/OceanDNA-b46972.fa | prodigal -d OceanDNA-b46972/cds.fna -a OceanDNA-b46972/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:52,864] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:52,864] [INFO] Task started: HMMsearch
[2023-03-18 07:54:52,864] [INFO] Running command: hmmsearch --tblout OceanDNA-b46972/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f059975-9e1a-4a3d-84c7-0c80c287e0de/dqc_reference/reference_markers.hmm OceanDNA-b46972/protein.faa > /dev/null
[2023-03-18 07:54:53,071] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:53,072] [INFO] Found 6/6 markers.
[2023-03-18 07:54:53,094] [INFO] Query marker FASTA was written to OceanDNA-b46972/markers.fasta
[2023-03-18 07:54:53,096] [INFO] Task started: Blastn
[2023-03-18 07:54:53,096] [INFO] Running command: blastn -query OceanDNA-b46972/markers.fasta -db /var/lib/cwl/stg4f059975-9e1a-4a3d-84c7-0c80c287e0de/dqc_reference/reference_markers.fasta -out OceanDNA-b46972/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:53,603] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:53,605] [INFO] Selected 8 target genomes.
[2023-03-18 07:54:53,605] [INFO] Target genome list was writen to OceanDNA-b46972/target_genomes.txt
[2023-03-18 07:54:53,610] [INFO] Task started: fastANI
[2023-03-18 07:54:53,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b32e119-e885-4403-85f0-1ebfccd42016/OceanDNA-b46972.fa --refList OceanDNA-b46972/target_genomes.txt --output OceanDNA-b46972/fastani_result.tsv --threads 1
[2023-03-18 07:54:56,679] [INFO] Task succeeded: fastANI
[2023-03-18 07:54:56,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f059975-9e1a-4a3d-84c7-0c80c287e0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:54:56,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f059975-9e1a-4a3d-84c7-0c80c287e0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:54:56,680] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:54:56,680] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:54:56,680] [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
--------------------------------------------------------------------------------
[2023-03-18 07:54:56,681] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46972/tc_result.tsv
[2023-03-18 07:54:56,681] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:54:56,681] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:54:56,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f059975-9e1a-4a3d-84c7-0c80c287e0de/dqc_reference/checkm_data
[2023-03-18 07:54:56,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:54:56,691] [INFO] Task started: CheckM
[2023-03-18 07:54:56,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46972/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46972/checkm_input OceanDNA-b46972/checkm_result
[2023-03-18 07:55:54,810] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:54,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:55:54,814] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:54,814] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:54,814] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46972/markers.fasta)
[2023-03-18 07:55:54,814] [INFO] Task started: Blastn
[2023-03-18 07:55:54,815] [INFO] Running command: blastn -query OceanDNA-b46972/markers.fasta -db /var/lib/cwl/stg4f059975-9e1a-4a3d-84c7-0c80c287e0de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46972/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:55,488] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:55,489] [INFO] Selected 7 target genomes.
[2023-03-18 07:55:55,489] [INFO] Target genome list was writen to OceanDNA-b46972/target_genomes_gtdb.txt
[2023-03-18 07:55:55,497] [INFO] Task started: fastANI
[2023-03-18 07:55:55,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b32e119-e885-4403-85f0-1ebfccd42016/OceanDNA-b46972.fa --refList OceanDNA-b46972/target_genomes_gtdb.txt --output OceanDNA-b46972/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:56:00,037] [INFO] Task succeeded: fastANI
[2023-03-18 07:56:00,041] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:56:00,041] [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_014239335.1	s__EC70 sp014239335	98.8884	657	1007	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.68	98.68	0.76	0.76	2	conclusive
GCA_012960505.1	s__EC70 sp012960505	90.2307	929	1007	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	99.96	99.96	0.97	0.97	2	-
GCA_004211885.1	s__EC70 sp004211885	89.0739	791	1007	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591645.1	s__EC70 sp902591645	88.2015	466	1007	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	95.33	95.33	0.70	0.70	2	-
GCA_013213965.1	s__EC70 sp013213965	85.7735	621	1007	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708885.1	s__EC70 sp002708885	82.1702	663	1007	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.95	98.84	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-18 07:56:00,042] [INFO] GTDB search result was written to OceanDNA-b46972/result_gtdb.tsv
[2023-03-18 07:56:00,042] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:56:00,042] [INFO] DFAST_QC result json was written to OceanDNA-b46972/dqc_result.json
[2023-03-18 07:56:00,043] [INFO] DFAST_QC completed!
[2023-03-18 07:56:00,043] [INFO] Total running time: 0h1m30s