[2023-03-15 21:24:36,515] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,515] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg273980c0-a777-46fd-acc0-19a5cb625870/dqc_reference
[2023-03-15 21:24:37,626] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,626] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,626] [INFO] Running command: cat /var/lib/cwl/stg7d93f31e-b10d-4fea-8ce1-3a4c79680353/OceanDNA-b1864.fa | prodigal -d OceanDNA-b1864/cds.fna -a OceanDNA-b1864/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:46,296] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:46,296] [INFO] Task started: HMMsearch
[2023-03-15 21:24:46,296] [INFO] Running command: hmmsearch --tblout OceanDNA-b1864/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg273980c0-a777-46fd-acc0-19a5cb625870/dqc_reference/reference_markers.hmm OceanDNA-b1864/protein.faa > /dev/null
[2023-03-15 21:24:46,450] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:46,450] [INFO] Found 6/6 markers.
[2023-03-15 21:24:46,464] [INFO] Query marker FASTA was written to OceanDNA-b1864/markers.fasta
[2023-03-15 21:24:46,464] [INFO] Task started: Blastn
[2023-03-15 21:24:46,464] [INFO] Running command: blastn -query OceanDNA-b1864/markers.fasta -db /var/lib/cwl/stg273980c0-a777-46fd-acc0-19a5cb625870/dqc_reference/reference_markers.fasta -out OceanDNA-b1864/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:46,970] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:46,970] [INFO] Selected 10 target genomes.
[2023-03-15 21:24:46,971] [INFO] Target genome list was writen to OceanDNA-b1864/target_genomes.txt
[2023-03-15 21:24:46,977] [INFO] Task started: fastANI
[2023-03-15 21:24:46,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d93f31e-b10d-4fea-8ce1-3a4c79680353/OceanDNA-b1864.fa --refList OceanDNA-b1864/target_genomes.txt --output OceanDNA-b1864/fastani_result.tsv --threads 1
[2023-03-15 21:24:50,394] [INFO] Task succeeded: fastANI
[2023-03-15 21:24:50,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg273980c0-a777-46fd-acc0-19a5cb625870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:24:50,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg273980c0-a777-46fd-acc0-19a5cb625870/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:24:50,394] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:24:50,394] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:24:50,394] [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
--------------------------------------------------------------------------------
[2023-03-15 21:24:50,395] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1864/tc_result.tsv
[2023-03-15 21:24:50,395] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:24:50,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:24:50,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg273980c0-a777-46fd-acc0-19a5cb625870/dqc_reference/checkm_data
[2023-03-15 21:24:50,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:24:50,402] [INFO] Task started: CheckM
[2023-03-15 21:24:50,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1864/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1864/checkm_input OceanDNA-b1864/checkm_result
[2023-03-15 21:25:17,009] [INFO] Task succeeded: CheckM
[2023-03-15 21:25:17,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.15%
Contamintation: 2.78%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:25:17,011] [INFO] ===== Completeness check finished =====
[2023-03-15 21:25:17,011] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:25:17,012] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1864/markers.fasta)
[2023-03-15 21:25:17,012] [INFO] Task started: Blastn
[2023-03-15 21:25:17,012] [INFO] Running command: blastn -query OceanDNA-b1864/markers.fasta -db /var/lib/cwl/stg273980c0-a777-46fd-acc0-19a5cb625870/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1864/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:17,818] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:17,819] [INFO] Selected 17 target genomes.
[2023-03-15 21:25:17,819] [INFO] Target genome list was writen to OceanDNA-b1864/target_genomes_gtdb.txt
[2023-03-15 21:25:18,033] [INFO] Task started: fastANI
[2023-03-15 21:25:18,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d93f31e-b10d-4fea-8ce1-3a4c79680353/OceanDNA-b1864.fa --refList OceanDNA-b1864/target_genomes_gtdb.txt --output OceanDNA-b1864/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:25:24,728] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:24,731] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:25:24,731] [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_002709645.1	s__UBA8592 sp002709645	89.9058	398	517	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013912105.1	s__UBA8592 sp002171605	78.2198	145	517	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.28	98.74	0.85	0.81	5	-
GCA_002295705.1	s__UBA8592 sp002295705	76.7984	54	517	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8592;g__UBA8592	95.0	99.20	99.08	0.80	0.73	4	-
--------------------------------------------------------------------------------
[2023-03-15 21:25:24,731] [INFO] GTDB search result was written to OceanDNA-b1864/result_gtdb.tsv
[2023-03-15 21:25:24,731] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:25:24,732] [INFO] DFAST_QC result json was written to OceanDNA-b1864/dqc_result.json
[2023-03-15 21:25:24,732] [INFO] DFAST_QC completed!
[2023-03-15 21:25:24,732] [INFO] Total running time: 0h0m48s