[2023-03-16 06:54:58,971] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:54:58,974] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:54:58,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg949f3115-a7c6-4c4d-9fbe-e3b44875b5e9/dqc_reference
[2023-03-16 06:55:00,088] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:55:00,088] [INFO] Task started: Prodigal
[2023-03-16 06:55:00,089] [INFO] Running command: cat /var/lib/cwl/stg2e2d59e2-bd4c-46f9-891f-a13e7991b327/OceanDNA-b45626.fa | prodigal -d OceanDNA-b45626/cds.fna -a OceanDNA-b45626/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:55:15,300] [INFO] Task succeeded: Prodigal
[2023-03-16 06:55:15,300] [INFO] Task started: HMMsearch
[2023-03-16 06:55:15,300] [INFO] Running command: hmmsearch --tblout OceanDNA-b45626/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg949f3115-a7c6-4c4d-9fbe-e3b44875b5e9/dqc_reference/reference_markers.hmm OceanDNA-b45626/protein.faa > /dev/null
[2023-03-16 06:55:15,498] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:55:15,498] [INFO] Found 6/6 markers.
[2023-03-16 06:55:15,542] [INFO] Query marker FASTA was written to OceanDNA-b45626/markers.fasta
[2023-03-16 06:55:15,543] [INFO] Task started: Blastn
[2023-03-16 06:55:15,543] [INFO] Running command: blastn -query OceanDNA-b45626/markers.fasta -db /var/lib/cwl/stg949f3115-a7c6-4c4d-9fbe-e3b44875b5e9/dqc_reference/reference_markers.fasta -out OceanDNA-b45626/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:16,109] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:16,121] [INFO] Selected 22 target genomes.
[2023-03-16 06:55:16,122] [INFO] Target genome list was writen to OceanDNA-b45626/target_genomes.txt
[2023-03-16 06:55:16,135] [INFO] Task started: fastANI
[2023-03-16 06:55:16,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e2d59e2-bd4c-46f9-891f-a13e7991b327/OceanDNA-b45626.fa --refList OceanDNA-b45626/target_genomes.txt --output OceanDNA-b45626/fastani_result.tsv --threads 1
[2023-03-16 06:55:29,905] [INFO] Task succeeded: fastANI
[2023-03-16 06:55:29,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg949f3115-a7c6-4c4d-9fbe-e3b44875b5e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:55:29,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg949f3115-a7c6-4c4d-9fbe-e3b44875b5e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:55:29,906] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:55:29,906] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:55:29,906] [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
--------------------------------------------------------------------------------
[2023-03-16 06:55:29,911] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45626/tc_result.tsv
[2023-03-16 06:55:29,921] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:55:29,921] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:55:29,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg949f3115-a7c6-4c4d-9fbe-e3b44875b5e9/dqc_reference/checkm_data
[2023-03-16 06:55:29,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:55:29,930] [INFO] Task started: CheckM
[2023-03-16 06:55:29,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45626/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45626/checkm_input OceanDNA-b45626/checkm_result
[2023-03-16 06:56:12,248] [INFO] Task succeeded: CheckM
[2023-03-16 06:56:12,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 06:56:12,272] [INFO] ===== Completeness check finished =====
[2023-03-16 06:56:12,272] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:56:12,272] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45626/markers.fasta)
[2023-03-16 06:56:12,274] [INFO] Task started: Blastn
[2023-03-16 06:56:12,274] [INFO] Running command: blastn -query OceanDNA-b45626/markers.fasta -db /var/lib/cwl/stg949f3115-a7c6-4c4d-9fbe-e3b44875b5e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45626/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:56:13,177] [INFO] Task succeeded: Blastn
[2023-03-16 06:56:13,181] [INFO] Selected 20 target genomes.
[2023-03-16 06:56:13,182] [INFO] Target genome list was writen to OceanDNA-b45626/target_genomes_gtdb.txt
[2023-03-16 06:56:13,219] [INFO] Task started: fastANI
[2023-03-16 06:56:13,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e2d59e2-bd4c-46f9-891f-a13e7991b327/OceanDNA-b45626.fa --refList OceanDNA-b45626/target_genomes_gtdb.txt --output OceanDNA-b45626/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:56:23,228] [INFO] Task succeeded: fastANI
[2023-03-16 06:56:23,233] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:56:23,233] [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_018646565.1	s__MB11C04 sp018646565	97.836	340	583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905478775.1	s__MB11C04 sp002477515	93.694	485	583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.93	98.38	0.86	0.80	5	-
GCA_018675995.1	s__MB11C04 sp018675995	80.3674	124	583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645475.1	s__MB11C04 sp018645475	79.4563	167	583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580225.1	s__MB11C04 sp902580225	78.629	132	583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364975.1	s__MB11C04 sp002364975	77.2512	59	583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	99.20	99.18	0.88	0.87	3	-
GCA_002694035.1	s__MB11C04 sp002694035	76.4231	74	583	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:56:23,235] [INFO] GTDB search result was written to OceanDNA-b45626/result_gtdb.tsv
[2023-03-16 06:56:23,238] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:56:23,241] [INFO] DFAST_QC result json was written to OceanDNA-b45626/dqc_result.json
[2023-03-16 06:56:23,241] [INFO] DFAST_QC completed!
[2023-03-16 06:56:23,241] [INFO] Total running time: 0h1m24s