[2023-03-16 03:47:32,873] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,879] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,879] [INFO] DQC Reference Directory: /var/lib/cwl/stg49cfa6e5-cd4a-41ae-b1f3-9c7acf45b535/dqc_reference
[2023-03-16 03:47:34,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,531] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,531] [INFO] Running command: cat /var/lib/cwl/stg2858c24b-395a-4cf4-a64b-6bc88b16d338/OceanDNA-b46763.fa | prodigal -d OceanDNA-b46763/cds.fna -a OceanDNA-b46763/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:59,759] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:59,760] [INFO] Task started: HMMsearch
[2023-03-16 03:47:59,760] [INFO] Running command: hmmsearch --tblout OceanDNA-b46763/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49cfa6e5-cd4a-41ae-b1f3-9c7acf45b535/dqc_reference/reference_markers.hmm OceanDNA-b46763/protein.faa > /dev/null
[2023-03-16 03:48:00,016] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:48:00,016] [INFO] Found 6/6 markers.
[2023-03-16 03:48:00,050] [INFO] Query marker FASTA was written to OceanDNA-b46763/markers.fasta
[2023-03-16 03:48:00,050] [INFO] Task started: Blastn
[2023-03-16 03:48:00,050] [INFO] Running command: blastn -query OceanDNA-b46763/markers.fasta -db /var/lib/cwl/stg49cfa6e5-cd4a-41ae-b1f3-9c7acf45b535/dqc_reference/reference_markers.fasta -out OceanDNA-b46763/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:00,666] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:00,666] [INFO] Selected 22 target genomes.
[2023-03-16 03:48:00,667] [INFO] Target genome list was writen to OceanDNA-b46763/target_genomes.txt
[2023-03-16 03:48:00,681] [INFO] Task started: fastANI
[2023-03-16 03:48:00,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg2858c24b-395a-4cf4-a64b-6bc88b16d338/OceanDNA-b46763.fa --refList OceanDNA-b46763/target_genomes.txt --output OceanDNA-b46763/fastani_result.tsv --threads 1
[2023-03-16 03:48:14,675] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:14,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49cfa6e5-cd4a-41ae-b1f3-9c7acf45b535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:14,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49cfa6e5-cd4a-41ae-b1f3-9c7acf45b535/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:14,676] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:14,676] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:48:14,676] [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 03:48:14,676] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46763/tc_result.tsv
[2023-03-16 03:48:14,677] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:14,677] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:14,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49cfa6e5-cd4a-41ae-b1f3-9c7acf45b535/dqc_reference/checkm_data
[2023-03-16 03:48:14,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:14,729] [INFO] Task started: CheckM
[2023-03-16 03:48:14,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46763/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46763/checkm_input OceanDNA-b46763/checkm_result
[2023-03-16 03:49:17,800] [INFO] Task succeeded: CheckM
[2023-03-16 03:49:17,801] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:49:17,804] [INFO] ===== Completeness check finished =====
[2023-03-16 03:49:17,804] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:49:17,804] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46763/markers.fasta)
[2023-03-16 03:49:17,804] [INFO] Task started: Blastn
[2023-03-16 03:49:17,804] [INFO] Running command: blastn -query OceanDNA-b46763/markers.fasta -db /var/lib/cwl/stg49cfa6e5-cd4a-41ae-b1f3-9c7acf45b535/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46763/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:49:18,521] [INFO] Task succeeded: Blastn
[2023-03-16 03:49:18,522] [INFO] Selected 13 target genomes.
[2023-03-16 03:49:18,522] [INFO] Target genome list was writen to OceanDNA-b46763/target_genomes_gtdb.txt
[2023-03-16 03:49:18,647] [INFO] Task started: fastANI
[2023-03-16 03:49:18,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg2858c24b-395a-4cf4-a64b-6bc88b16d338/OceanDNA-b46763.fa --refList OceanDNA-b46763/target_genomes_gtdb.txt --output OceanDNA-b46763/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:27,855] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:27,860] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:49:27,860] [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_003483645.1	s__Roseibacillus_B sp003483645	98.8135	541	785	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002501065.1	s__Roseibacillus_B sp002501065	92.3555	735	785	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	-
GCA_014240355.1	s__Roseibacillus_B sp014240355	92.027	542	785	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709395.1	s__Roseibacillus_B sp002709395	78.2429	333	785	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.31	97.31	0.76	0.76	2	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	77.5281	270	785	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729275.1	s__Roseibacillus_B sp002729275	76.5693	116	785	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	98.94	98.88	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2023-03-16 03:49:27,860] [INFO] GTDB search result was written to OceanDNA-b46763/result_gtdb.tsv
[2023-03-16 03:49:27,860] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:27,861] [INFO] DFAST_QC result json was written to OceanDNA-b46763/dqc_result.json
[2023-03-16 03:49:27,861] [INFO] DFAST_QC completed!
[2023-03-16 03:49:27,861] [INFO] Total running time: 0h1m55s