[2023-03-14 14:26:08,577] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:26:08,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:26:08,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c640a7c-0d8b-4bf8-8569-1696c37e975c/dqc_reference
[2023-03-14 14:26:10,769] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:26:10,770] [INFO] Task started: Prodigal
[2023-03-14 14:26:10,770] [INFO] Running command: cat /var/lib/cwl/stg679da8cf-f1be-47e1-8f66-9cf3279cf1ec/OceanDNA-b5576.fa | prodigal -d OceanDNA-b5576/cds.fna -a OceanDNA-b5576/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:26:30,757] [INFO] Task succeeded: Prodigal
[2023-03-14 14:26:30,757] [INFO] Task started: HMMsearch
[2023-03-14 14:26:30,757] [INFO] Running command: hmmsearch --tblout OceanDNA-b5576/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c640a7c-0d8b-4bf8-8569-1696c37e975c/dqc_reference/reference_markers.hmm OceanDNA-b5576/protein.faa > /dev/null
[2023-03-14 14:26:30,953] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:26:30,954] [INFO] Found 6/6 markers.
[2023-03-14 14:26:30,969] [INFO] Query marker FASTA was written to OceanDNA-b5576/markers.fasta
[2023-03-14 14:26:30,970] [INFO] Task started: Blastn
[2023-03-14 14:26:30,970] [INFO] Running command: blastn -query OceanDNA-b5576/markers.fasta -db /var/lib/cwl/stg4c640a7c-0d8b-4bf8-8569-1696c37e975c/dqc_reference/reference_markers.fasta -out OceanDNA-b5576/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:26:31,500] [INFO] Task succeeded: Blastn
[2023-03-14 14:26:31,501] [INFO] Selected 29 target genomes.
[2023-03-14 14:26:31,502] [INFO] Target genome list was writen to OceanDNA-b5576/target_genomes.txt
[2023-03-14 14:26:31,516] [INFO] Task started: fastANI
[2023-03-14 14:26:31,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg679da8cf-f1be-47e1-8f66-9cf3279cf1ec/OceanDNA-b5576.fa --refList OceanDNA-b5576/target_genomes.txt --output OceanDNA-b5576/fastani_result.tsv --threads 1
[2023-03-14 14:26:47,237] [INFO] Task succeeded: fastANI
[2023-03-14 14:26:47,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c640a7c-0d8b-4bf8-8569-1696c37e975c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:26:47,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c640a7c-0d8b-4bf8-8569-1696c37e975c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:26:47,238] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:26:47,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:26:47,238] [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
--------------------------------------------------------------------------------
[2023-03-14 14:26:47,238] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5576/tc_result.tsv
[2023-03-14 14:26:47,238] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:26:47,238] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:26:47,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c640a7c-0d8b-4bf8-8569-1696c37e975c/dqc_reference/checkm_data
[2023-03-14 14:26:47,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:26:47,245] [INFO] Task started: CheckM
[2023-03-14 14:26:47,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5576/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5576/checkm_input OceanDNA-b5576/checkm_result
[2023-03-14 14:27:30,656] [INFO] Task succeeded: CheckM
[2023-03-14 14:27:30,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:27:30,659] [INFO] ===== Completeness check finished =====
[2023-03-14 14:27:30,659] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:27:30,659] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5576/markers.fasta)
[2023-03-14 14:27:30,660] [INFO] Task started: Blastn
[2023-03-14 14:27:30,660] [INFO] Running command: blastn -query OceanDNA-b5576/markers.fasta -db /var/lib/cwl/stg4c640a7c-0d8b-4bf8-8569-1696c37e975c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5576/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:27:31,435] [INFO] Task succeeded: Blastn
[2023-03-14 14:27:31,436] [INFO] Selected 17 target genomes.
[2023-03-14 14:27:31,436] [INFO] Target genome list was writen to OceanDNA-b5576/target_genomes_gtdb.txt
[2023-03-14 14:27:31,448] [INFO] Task started: fastANI
[2023-03-14 14:27:31,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg679da8cf-f1be-47e1-8f66-9cf3279cf1ec/OceanDNA-b5576.fa --refList OceanDNA-b5576/target_genomes_gtdb.txt --output OceanDNA-b5576/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:27:39,578] [INFO] Task succeeded: fastANI
[2023-03-14 14:27:39,584] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 14:27:39,584] [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_002167775.1	s__UBA952 sp002167775	99.2402	695	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.23	98.23	0.91	0.91	2	conclusive
GCA_002683585.1	s__UBA952 sp002683585	88.9263	341	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480215.1	s__UBA952 sp002480215	87.5767	504	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.70	99.70	0.81	0.81	2	-
GCA_905182775.1	s__UBA952 sp905182775	77.526	194	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522905.1	s__UBA952 sp011522905	77.1266	73	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665005.1	s__UBA952 sp018665005	76.7173	91	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.77	98.77	0.77	0.77	2	-
GCA_003331365.1	s__UBA952 sp003331365	76.7063	70	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480165.1	s__UBA952 sp905480165	76.629	81	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:27:39,584] [INFO] GTDB search result was written to OceanDNA-b5576/result_gtdb.tsv
[2023-03-14 14:27:39,584] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:27:39,585] [INFO] DFAST_QC result json was written to OceanDNA-b5576/dqc_result.json
[2023-03-14 14:27:39,585] [INFO] DFAST_QC completed!
[2023-03-14 14:27:39,585] [INFO] Total running time: 0h1m31s