[2023-03-18 03:27:00,940] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,945] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,945] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b155eb1-33d0-435c-ba6f-f12a6be6fdb0/dqc_reference
[2023-03-18 03:27:02,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,637] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,637] [INFO] Running command: cat /var/lib/cwl/stgc941119f-cfd4-4cbb-a3a4-273637d48c59/OceanDNA-b22939.fa | prodigal -d OceanDNA-b22939/cds.fna -a OceanDNA-b22939/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:30,443] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:30,444] [INFO] Task started: HMMsearch
[2023-03-18 03:27:30,444] [INFO] Running command: hmmsearch --tblout OceanDNA-b22939/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b155eb1-33d0-435c-ba6f-f12a6be6fdb0/dqc_reference/reference_markers.hmm OceanDNA-b22939/protein.faa > /dev/null
[2023-03-18 03:27:30,695] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:30,696] [INFO] Found 6/6 markers.
[2023-03-18 03:27:30,728] [INFO] Query marker FASTA was written to OceanDNA-b22939/markers.fasta
[2023-03-18 03:27:30,729] [INFO] Task started: Blastn
[2023-03-18 03:27:30,729] [INFO] Running command: blastn -query OceanDNA-b22939/markers.fasta -db /var/lib/cwl/stg8b155eb1-33d0-435c-ba6f-f12a6be6fdb0/dqc_reference/reference_markers.fasta -out OceanDNA-b22939/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:31,253] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:31,254] [INFO] Selected 16 target genomes.
[2023-03-18 03:27:31,254] [INFO] Target genome list was writen to OceanDNA-b22939/target_genomes.txt
[2023-03-18 03:27:31,264] [INFO] Task started: fastANI
[2023-03-18 03:27:31,264] [INFO] Running command: fastANI --query /var/lib/cwl/stgc941119f-cfd4-4cbb-a3a4-273637d48c59/OceanDNA-b22939.fa --refList OceanDNA-b22939/target_genomes.txt --output OceanDNA-b22939/fastani_result.tsv --threads 1
[2023-03-18 03:27:44,327] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:44,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b155eb1-33d0-435c-ba6f-f12a6be6fdb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:44,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b155eb1-33d0-435c-ba6f-f12a6be6fdb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:44,331] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:44,332] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:27:44,332] [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
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.2604	55	1383	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.1451	60	1383	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:44,332] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22939/tc_result.tsv
[2023-03-18 03:27:44,332] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:44,332] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:44,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b155eb1-33d0-435c-ba6f-f12a6be6fdb0/dqc_reference/checkm_data
[2023-03-18 03:27:44,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:44,390] [INFO] Task started: CheckM
[2023-03-18 03:27:44,390] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22939/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22939/checkm_input OceanDNA-b22939/checkm_result
[2023-03-18 03:28:55,697] [INFO] Task succeeded: CheckM
[2023-03-18 03:28:55,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.37%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:28:55,701] [INFO] ===== Completeness check finished =====
[2023-03-18 03:28:55,701] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:28:55,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22939/markers.fasta)
[2023-03-18 03:28:55,701] [INFO] Task started: Blastn
[2023-03-18 03:28:55,701] [INFO] Running command: blastn -query OceanDNA-b22939/markers.fasta -db /var/lib/cwl/stg8b155eb1-33d0-435c-ba6f-f12a6be6fdb0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22939/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:56,376] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:56,377] [INFO] Selected 19 target genomes.
[2023-03-18 03:28:56,377] [INFO] Target genome list was writen to OceanDNA-b22939/target_genomes_gtdb.txt
[2023-03-18 03:28:56,397] [INFO] Task started: fastANI
[2023-03-18 03:28:56,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgc941119f-cfd4-4cbb-a3a4-273637d48c59/OceanDNA-b22939.fa --refList OceanDNA-b22939/target_genomes_gtdb.txt --output OceanDNA-b22939/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:29:14,349] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:14,353] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:29:14,354] [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_002724415.1	s__UBA8437 sp002724415	90.9642	1243	1383	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445035.1	s__UBA8437 sp003445035	79.9538	813	1383	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	79.7942	796	1383	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_002726205.1	s__GCA-2726205 sp002726205	77.7386	461	1383	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2726205	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	75.2859	53	1383	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:29:14,354] [INFO] GTDB search result was written to OceanDNA-b22939/result_gtdb.tsv
[2023-03-18 03:29:14,354] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:29:14,355] [INFO] DFAST_QC result json was written to OceanDNA-b22939/dqc_result.json
[2023-03-18 03:29:14,355] [INFO] DFAST_QC completed!
[2023-03-18 03:29:14,355] [INFO] Total running time: 0h2m13s