[2023-03-18 06:30:24,794] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,794] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cb0c019-0010-4aa1-b0d2-a51dee4886aa/dqc_reference
[2023-03-18 06:30:25,881] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,881] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,881] [INFO] Running command: cat /var/lib/cwl/stg20dfbf0b-c74d-4925-910a-720128815c6b/OceanDNA-b423.fa | prodigal -d OceanDNA-b423/cds.fna -a OceanDNA-b423/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:38,834] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:38,834] [INFO] Task started: HMMsearch
[2023-03-18 06:30:38,834] [INFO] Running command: hmmsearch --tblout OceanDNA-b423/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cb0c019-0010-4aa1-b0d2-a51dee4886aa/dqc_reference/reference_markers.hmm OceanDNA-b423/protein.faa > /dev/null
[2023-03-18 06:30:38,986] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:38,986] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg20dfbf0b-c74d-4925-910a-720128815c6b/OceanDNA-b423.fa]
[2023-03-18 06:30:39,024] [INFO] Query marker FASTA was written to OceanDNA-b423/markers.fasta
[2023-03-18 06:30:39,025] [INFO] Task started: Blastn
[2023-03-18 06:30:39,025] [INFO] Running command: blastn -query OceanDNA-b423/markers.fasta -db /var/lib/cwl/stg8cb0c019-0010-4aa1-b0d2-a51dee4886aa/dqc_reference/reference_markers.fasta -out OceanDNA-b423/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:39,531] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:39,534] [INFO] Selected 22 target genomes.
[2023-03-18 06:30:39,534] [INFO] Target genome list was writen to OceanDNA-b423/target_genomes.txt
[2023-03-18 06:30:39,667] [INFO] Task started: fastANI
[2023-03-18 06:30:39,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg20dfbf0b-c74d-4925-910a-720128815c6b/OceanDNA-b423.fa --refList OceanDNA-b423/target_genomes.txt --output OceanDNA-b423/fastani_result.tsv --threads 1
[2023-03-18 06:30:53,520] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:53,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cb0c019-0010-4aa1-b0d2-a51dee4886aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:53,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cb0c019-0010-4aa1-b0d2-a51dee4886aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:53,521] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:30:53,521] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:30:53,521] [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 06:30:53,523] [INFO] DFAST Taxonomy check result was written to OceanDNA-b423/tc_result.tsv
[2023-03-18 06:30:53,523] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:53,523] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:53,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cb0c019-0010-4aa1-b0d2-a51dee4886aa/dqc_reference/checkm_data
[2023-03-18 06:30:53,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:53,533] [INFO] Task started: CheckM
[2023-03-18 06:30:53,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b423/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b423/checkm_input OceanDNA-b423/checkm_result
[2023-03-18 06:31:30,111] [INFO] Task succeeded: CheckM
[2023-03-18 06:31:30,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:31:30,167] [INFO] ===== Completeness check finished =====
[2023-03-18 06:31:30,167] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:31:30,167] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b423/markers.fasta)
[2023-03-18 06:31:30,168] [INFO] Task started: Blastn
[2023-03-18 06:31:30,168] [INFO] Running command: blastn -query OceanDNA-b423/markers.fasta -db /var/lib/cwl/stg8cb0c019-0010-4aa1-b0d2-a51dee4886aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b423/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:31:30,849] [INFO] Task succeeded: Blastn
[2023-03-18 06:31:30,852] [INFO] Selected 13 target genomes.
[2023-03-18 06:31:30,852] [INFO] Target genome list was writen to OceanDNA-b423/target_genomes_gtdb.txt
[2023-03-18 06:31:31,006] [INFO] Task started: fastANI
[2023-03-18 06:31:31,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg20dfbf0b-c74d-4925-910a-720128815c6b/OceanDNA-b423.fa --refList OceanDNA-b423/target_genomes_gtdb.txt --output OceanDNA-b423/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:35,538] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:35,545] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:31:35,545] [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_001510335.1	s__Casp-actino8 sp001510335	94.8464	387	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872155.1	s__Casp-actino8 sp903872155	83.6485	474	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.87	96.83	0.92	0.86	4	-
GCA_009700145.1	s__Casp-actino8 sp009700145	82.4808	372	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	99.51	99.42	0.81	0.73	6	-
GCA_014190215.1	s__Casp-actino8 sp014190215	77.9974	162	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694465.1	s__Casp-actino8 sp009694465	77.9577	112	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	95.85	95.85	0.64	0.64	2	-
GCA_009705435.1	s__Casp-actino8 sp009705435	77.8922	147	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.36	98.35	0.80	0.80	3	-
GCA_009704425.1	s__Casp-actino8 sp009704425	77.044	70	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379135.1	s__Casp-actino8 sp004379135	76.4014	67	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009923785.1	s__Casp-actino8 sp009923785	76.3316	50	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	98.73	98.56	0.91	0.86	10	-
GCA_016871355.1	s__Casp-actino8 sp016871355	76.2249	75	653	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:31:35,547] [INFO] GTDB search result was written to OceanDNA-b423/result_gtdb.tsv
[2023-03-18 06:31:35,547] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:35,550] [INFO] DFAST_QC result json was written to OceanDNA-b423/dqc_result.json
[2023-03-18 06:31:35,550] [INFO] DFAST_QC completed!
[2023-03-18 06:31:35,550] [INFO] Total running time: 0h1m11s