[2023-03-17 01:01:12,726] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:01:12,726] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:01:12,726] [INFO] DQC Reference Directory: /var/lib/cwl/stga2ea3a29-7db4-4d16-9556-2b1c16d63d38/dqc_reference
[2023-03-17 01:01:14,609] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:01:14,609] [INFO] Task started: Prodigal
[2023-03-17 01:01:14,609] [INFO] Running command: cat /var/lib/cwl/stgcc397a3b-fa54-4c68-8588-b88377483f19/OceanDNA-b1684.fa | prodigal -d OceanDNA-b1684/cds.fna -a OceanDNA-b1684/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:01:22,008] [INFO] Task succeeded: Prodigal
[2023-03-17 01:01:22,008] [INFO] Task started: HMMsearch
[2023-03-17 01:01:22,008] [INFO] Running command: hmmsearch --tblout OceanDNA-b1684/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2ea3a29-7db4-4d16-9556-2b1c16d63d38/dqc_reference/reference_markers.hmm OceanDNA-b1684/protein.faa > /dev/null
[2023-03-17 01:01:22,152] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:01:22,152] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgcc397a3b-fa54-4c68-8588-b88377483f19/OceanDNA-b1684.fa]
[2023-03-17 01:01:22,167] [INFO] Query marker FASTA was written to OceanDNA-b1684/markers.fasta
[2023-03-17 01:01:22,167] [INFO] Task started: Blastn
[2023-03-17 01:01:22,167] [INFO] Running command: blastn -query OceanDNA-b1684/markers.fasta -db /var/lib/cwl/stga2ea3a29-7db4-4d16-9556-2b1c16d63d38/dqc_reference/reference_markers.fasta -out OceanDNA-b1684/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:01:22,645] [INFO] Task succeeded: Blastn
[2023-03-17 01:01:22,646] [INFO] Selected 13 target genomes.
[2023-03-17 01:01:22,646] [INFO] Target genome list was writen to OceanDNA-b1684/target_genomes.txt
[2023-03-17 01:01:22,652] [INFO] Task started: fastANI
[2023-03-17 01:01:22,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc397a3b-fa54-4c68-8588-b88377483f19/OceanDNA-b1684.fa --refList OceanDNA-b1684/target_genomes.txt --output OceanDNA-b1684/fastani_result.tsv --threads 1
[2023-03-17 01:01:29,621] [INFO] Task succeeded: fastANI
[2023-03-17 01:01:29,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2ea3a29-7db4-4d16-9556-2b1c16d63d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:01:29,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2ea3a29-7db4-4d16-9556-2b1c16d63d38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:01:29,621] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:01:29,621] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 01:01:29,621] [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
--------------------------------------------------------------------------------
[2023-03-17 01:01:29,622] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1684/tc_result.tsv
[2023-03-17 01:01:29,622] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:01:29,622] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:01:29,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2ea3a29-7db4-4d16-9556-2b1c16d63d38/dqc_reference/checkm_data
[2023-03-17 01:01:29,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:01:29,632] [INFO] Task started: CheckM
[2023-03-17 01:01:29,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1684/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1684/checkm_input OceanDNA-b1684/checkm_result
[2023-03-17 01:01:53,480] [INFO] Task succeeded: CheckM
[2023-03-17 01:01:53,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 1.30%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 01:01:53,482] [INFO] ===== Completeness check finished =====
[2023-03-17 01:01:53,483] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:01:53,483] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1684/markers.fasta)
[2023-03-17 01:01:53,483] [INFO] Task started: Blastn
[2023-03-17 01:01:53,483] [INFO] Running command: blastn -query OceanDNA-b1684/markers.fasta -db /var/lib/cwl/stga2ea3a29-7db4-4d16-9556-2b1c16d63d38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1684/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:01:54,079] [INFO] Task succeeded: Blastn
[2023-03-17 01:01:54,080] [INFO] Selected 10 target genomes.
[2023-03-17 01:01:54,080] [INFO] Target genome list was writen to OceanDNA-b1684/target_genomes_gtdb.txt
[2023-03-17 01:01:54,266] [INFO] Task started: fastANI
[2023-03-17 01:01:54,266] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc397a3b-fa54-4c68-8588-b88377483f19/OceanDNA-b1684.fa --refList OceanDNA-b1684/target_genomes_gtdb.txt --output OceanDNA-b1684/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:01:58,154] [INFO] Task succeeded: fastANI
[2023-03-17 01:01:58,157] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 01:01:58,157] [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_905182565.1	s__UBA9040 sp905182565	92.4577	417	424	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA9040	95.0	99.80	99.80	0.97	0.97	2	-
GCA_002731665.1	s__UBA9040 sp002731665	87.8127	259	424	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA9040	95.0	99.68	99.68	0.65	0.65	2	-
GCA_905477545.1	s__UBA9040 sp905477545	87.4117	351	424	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA9040	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:01:58,157] [INFO] GTDB search result was written to OceanDNA-b1684/result_gtdb.tsv
[2023-03-17 01:01:58,157] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:01:58,158] [INFO] DFAST_QC result json was written to OceanDNA-b1684/dqc_result.json
[2023-03-17 01:01:58,158] [INFO] DFAST_QC completed!
[2023-03-17 01:01:58,158] [INFO] Total running time: 0h0m45s