[2023-03-17 09:05:02,517] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,517] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,517] [INFO] DQC Reference Directory: /var/lib/cwl/stg43b06e87-e4be-426c-b017-7518d1613878/dqc_reference
[2023-03-17 09:05:03,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,734] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,734] [INFO] Running command: cat /var/lib/cwl/stg089b6ffc-cab5-424b-b506-25b52a41bb44/OceanDNA-b39461.fa | prodigal -d OceanDNA-b39461/cds.fna -a OceanDNA-b39461/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:12,294] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:12,295] [INFO] Task started: HMMsearch
[2023-03-17 09:05:12,295] [INFO] Running command: hmmsearch --tblout OceanDNA-b39461/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43b06e87-e4be-426c-b017-7518d1613878/dqc_reference/reference_markers.hmm OceanDNA-b39461/protein.faa > /dev/null
[2023-03-17 09:05:12,465] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:12,465] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg089b6ffc-cab5-424b-b506-25b52a41bb44/OceanDNA-b39461.fa]
[2023-03-17 09:05:12,482] [INFO] Query marker FASTA was written to OceanDNA-b39461/markers.fasta
[2023-03-17 09:05:12,483] [INFO] Task started: Blastn
[2023-03-17 09:05:12,483] [INFO] Running command: blastn -query OceanDNA-b39461/markers.fasta -db /var/lib/cwl/stg43b06e87-e4be-426c-b017-7518d1613878/dqc_reference/reference_markers.fasta -out OceanDNA-b39461/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:13,115] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:13,116] [INFO] Selected 30 target genomes.
[2023-03-17 09:05:13,116] [INFO] Target genome list was writen to OceanDNA-b39461/target_genomes.txt
[2023-03-17 09:05:13,170] [INFO] Task started: fastANI
[2023-03-17 09:05:13,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg089b6ffc-cab5-424b-b506-25b52a41bb44/OceanDNA-b39461.fa --refList OceanDNA-b39461/target_genomes.txt --output OceanDNA-b39461/fastani_result.tsv --threads 1
[2023-03-17 09:05:33,122] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:33,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43b06e87-e4be-426c-b017-7518d1613878/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:33,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43b06e87-e4be-426c-b017-7518d1613878/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:33,122] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:33,122] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:05:33,122] [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 09:05:33,123] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39461/tc_result.tsv
[2023-03-17 09:05:33,123] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:33,123] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:33,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43b06e87-e4be-426c-b017-7518d1613878/dqc_reference/checkm_data
[2023-03-17 09:05:33,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:33,130] [INFO] Task started: CheckM
[2023-03-17 09:05:33,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39461/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39461/checkm_input OceanDNA-b39461/checkm_result
[2023-03-17 09:06:00,257] [INFO] Task succeeded: CheckM
[2023-03-17 09:06:00,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 09:06:00,259] [INFO] ===== Completeness check finished =====
[2023-03-17 09:06:00,259] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:06:00,260] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39461/markers.fasta)
[2023-03-17 09:06:00,260] [INFO] Task started: Blastn
[2023-03-17 09:06:00,261] [INFO] Running command: blastn -query OceanDNA-b39461/markers.fasta -db /var/lib/cwl/stg43b06e87-e4be-426c-b017-7518d1613878/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39461/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:06:01,136] [INFO] Task succeeded: Blastn
[2023-03-17 09:06:01,137] [INFO] Selected 22 target genomes.
[2023-03-17 09:06:01,137] [INFO] Target genome list was writen to OceanDNA-b39461/target_genomes_gtdb.txt
[2023-03-17 09:06:01,264] [INFO] Task started: fastANI
[2023-03-17 09:06:01,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg089b6ffc-cab5-424b-b506-25b52a41bb44/OceanDNA-b39461.fa --refList OceanDNA-b39461/target_genomes_gtdb.txt --output OceanDNA-b39461/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:06:11,827] [INFO] Task succeeded: fastANI
[2023-03-17 09:06:11,832] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:06:11,832] [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_002685715.1	s__HTCC2207 sp002685715	81.5836	172	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182265.1	s__HTCC2207 sp905182265	78.3291	62	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002334915.1	s__HTCC2207 sp002334915	77.7421	57	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_018664075.1	s__HTCC2207 sp018664075	77.3708	99	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_000153445.1	s__HTCC2207 sp000153445	77.1575	50	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_002335945.1	s__HTCC2207 sp002335945	77.101	53	344	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
--------------------------------------------------------------------------------
[2023-03-17 09:06:11,832] [INFO] GTDB search result was written to OceanDNA-b39461/result_gtdb.tsv
[2023-03-17 09:06:11,832] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:06:11,833] [INFO] DFAST_QC result json was written to OceanDNA-b39461/dqc_result.json
[2023-03-17 09:06:11,833] [INFO] DFAST_QC completed!
[2023-03-17 09:06:11,833] [INFO] Total running time: 0h1m9s